[med-svn] [cinema] 09/10: Update upstream source from tag 'upstream/3.0.23'
Andreas Tille
tille at debian.org
Sat Dec 2 15:28:35 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cinema.
commit 4b30e0d845b5616001ae528bbf13d74442969ca0
Merge: 60c2ddc bb40f23
Author: Andreas Tille <tille at debian.org>
Date: Sat Dec 2 16:27:06 2017 +0100
Update upstream source from tag 'upstream/3.0.23'
Update to upstream version '3.0.23'
with Debian dir a4b11f1fb75374fea6ce6cfc32bf6d4703e66349
README | 10 +
bin/cinema | 84 +
bin/cinema.cygwin | 81 +
bin/cinema.pl | 78 +
classes/uk/ac/man/bioinf/Y.class | Bin 0 -> 197 bytes
.../analysis/consensus/ConsensusCalculator.class | Bin 0 -> 384 bytes
.../analysis/consensus/ConsensusIdentifier.class | Bin 0 -> 1136 bytes
.../analysis/consensus/ConsensusSequence.class | Bin 0 -> 424 bytes
.../consensus/DefaultConsensusSequence$1.class | Bin 0 -> 1021 bytes
.../consensus/DefaultConsensusSequence.class | Bin 0 -> 4645 bytes
.../analysis/consensus/PercentageIDConsensus.class | Bin 0 -> 1891 bytes
.../consensus/ThreadedConsensusSequence$1.class | Bin 0 -> 766 bytes
.../consensus/ThreadedConsensusSequence.class | Bin 0 -> 1638 bytes
.../analysis/misc/PercentageIDCalculator.class | Bin 0 -> 2985 bytes
.../misc/PercentageIDCalculatorManager.class | Bin 0 -> 1013 bytes
.../regexp/GappedSequenceCharacterIterator.class | Bin 0 -> 1080 bytes
.../regexp/SequenceCharacterIterator.class | Bin 0 -> 964 bytes
classes/uk/ac/man/bioinf/apps/cinema/Cinema.class | Bin 0 -> 2775 bytes
.../uk/ac/man/bioinf/apps/cinema/CinemaBoot.class | Bin 0 -> 2165 bytes
.../bioinf/apps/cinema/CinemaBootIdentifier.class | Bin 0 -> 687 bytes
.../man/bioinf/apps/cinema/CinemaGuiModule.class | Bin 0 -> 2550 bytes
.../ac/man/bioinf/apps/cinema/CinemaModule.class | Bin 0 -> 3866 bytes
.../apps/cinema/CinemaModuleFactoryInstance.class | Bin 0 -> 1299 bytes
.../man/bioinf/apps/cinema/CinemaProperties.class | Bin 0 -> 459 bytes
.../ac/man/bioinf/apps/cinema/CinemaShared.class | Bin 0 -> 357 bytes
.../apps/cinema/CinemaXMLParserFactory$1.class | Bin 0 -> 967 bytes
.../apps/cinema/CinemaXMLParserFactory.class | Bin 0 -> 862 bytes
.../cinema/color/AminoAcidColorMapMetaData.class | Bin 0 -> 3083 bytes
.../apps/cinema/color/CinemaColorFactory.class | Bin 0 -> 3329 bytes
.../apps/cinema/color/CinemaColorIdentifier.class | Bin 0 -> 818 bytes
...CinemaColorSelector$ClosureAbstractAction.class | Bin 0 -> 1863 bytes
.../apps/cinema/color/CinemaColorSelector.class | Bin 0 -> 2806 bytes
.../apps/cinema/color/ColorMapMetaData.class | Bin 0 -> 605 bytes
.../cinema/color/ColormapColorMapMetaData.class | Bin 0 -> 3233 bytes
.../cinema/color/DefaultColorMapMetaData.class | Bin 0 -> 3230 bytes
.../apps/cinema/color/GrayScaleVariance.class | Bin 0 -> 2029 bytes
.../InstancePerAlignmentColorMapMetaData.class | Bin 0 -> 1407 bytes
.../cinema/color/IntenseColorMapMetaData.class | Bin 0 -> 3186 bytes
.../apps/cinema/color/NullColorMapMetaData.class | Bin 0 -> 903 bytes
.../cinema/color/PedanticColorMapMetaData.class | Bin 0 -> 3189 bytes
.../PercentageIDVarianceColorMapMetaData.class | Bin 0 -> 1905 bytes
.../apps/cinema/color/TaylorColorMapMetaData.class | Bin 0 -> 3244 bytes
...dedPercentageIDVarianceColorMapMetaData$1.class | Bin 0 -> 1093 bytes
...eadedPercentageIDVarianceColorMapMetaData.class | Bin 0 -> 3061 bytes
.../cinema/color/VariableColorMapMetaData.class | Bin 0 -> 3193 bytes
.../cinema/color/VariationsColorMapMetaData.class | Bin 0 -> 3233 bytes
.../apps/cinema/color/WhiteColorMapMetaData.class | Bin 0 -> 1195 bytes
.../apps/cinema/color/ZenecaColorMapMetaData.class | Bin 0 -> 3223 bytes
.../apps/cinema/consensus/CinemaConsensus.class | Bin 0 -> 3632 bytes
.../CinemaConsensusCalculatorMetaData.class | Bin 0 -> 452 bytes
...emaConsensusDisplay$ClosureAbstractAction.class | Bin 0 -> 1708 bytes
.../cinema/consensus/CinemaConsensusDisplay.class | Bin 0 -> 7602 bytes
.../consensus/CinemaConsensusIdentifier.class | Bin 0 -> 757 bytes
.../PercentageIDConsensusCalculatorMetaData.class | Bin 0 -> 1870 bytes
...edPercentageIDConsensusCalculatorMetaData.class | Bin 0 -> 1780 bytes
.../cinema/core/AlignmentToListCellRenderer.class | Bin 0 -> 737 bytes
.../apps/cinema/core/AlignmentToListModel.class | Bin 0 -> 1343 bytes
.../apps/cinema/core/CinemaActionProvider.class | Bin 0 -> 202 bytes
.../bioinf/apps/cinema/core/CinemaCoreGui$1.class | Bin 0 -> 830 bytes
.../bioinf/apps/cinema/core/CinemaCoreGui$2.class | Bin 0 -> 622 bytes
.../bioinf/apps/cinema/core/CinemaCoreGui.class | Bin 0 -> 5222 bytes
.../apps/cinema/core/CinemaCoreIdentifier.class | Bin 0 -> 1106 bytes
.../bioinf/apps/cinema/core/CinemaCoreView$1.class | Bin 0 -> 977 bytes
.../bioinf/apps/cinema/core/CinemaCoreView.class | Bin 0 -> 5648 bytes
.../cinema/core/CinemaFramedActionProvider.class | Bin 0 -> 271 bytes
.../ac/man/bioinf/apps/cinema/core/CinemaGo.class | Bin 0 -> 1372 bytes
.../bioinf/apps/cinema/core/CinemaMenuSystem.class | Bin 0 -> 1568 bytes
.../cinema/core/CinemaModuleCoreIdentifier.class | Bin 0 -> 801 bytes
.../apps/cinema/core/CinemaSequenceMenu.class | Bin 0 -> 1405 bytes
.../apps/cinema/core/CinemaSystemEvents.class | Bin 0 -> 1496 bytes
.../apps/cinema/core/VersionInformation.class | Bin 0 -> 1411 bytes
.../group/CinemaAnchorManager$AnchorListener.class | Bin 0 -> 2342 bytes
.../apps/cinema/group/CinemaAnchorManager.class | Bin 0 -> 3210 bytes
...inemaGroup$CinemaGroupAlignmentIdentifier.class | Bin 0 -> 789 bytes
.../man/bioinf/apps/cinema/group/CinemaGroup.class | Bin 0 -> 1774 bytes
.../CinemaGroupFrame$GroupListCellRenderer.class | Bin 0 -> 1430 bytes
.../CinemaGroupFrame$GroupMemberCellRenderer.class | Bin 0 -> 949 bytes
...istBasicUI$InformativeSwappingListHandler.class | Bin 0 -> 1748 bytes
...GroupFrame$InformativeSwappingListBasicUI.class | Bin 0 -> 1687 bytes
.../apps/cinema/group/CinemaGroupFrame.class | Bin 0 -> 10137 bytes
.../apps/cinema/group/CinemaGroupIdentifier.class | Bin 0 -> 609 bytes
.../apps/cinema/group/CinemaGroupManager.class | Bin 0 -> 5251 bytes
.../apps/cinema/group/CinemaGroupModule$1.class | Bin 0 -> 1174 bytes
.../group/CinemaGroupModule$AddToGroup.class | Bin 0 -> 1192 bytes
...nemaGroupModule$DeleteGroupActionListener.class | Bin 0 -> 1800 bytes
.../apps/cinema/group/CinemaGroupModule.class | Bin 0 -> 8477 bytes
.../apps/cinema/io/AbstractSequenceInput$1.class | Bin 0 -> 2408 bytes
.../apps/cinema/io/AbstractSequenceInput.class | Bin 0 -> 3344 bytes
...stractSequenceInputParserExceptionHandler.class | Bin 0 -> 1004 bytes
.../apps/cinema/io/AbstractSequenceOutput$1.class | Bin 0 -> 853 bytes
.../apps/cinema/io/AbstractSequenceOutput$2.class | Bin 0 -> 855 bytes
.../apps/cinema/io/AbstractSequenceOutput.class | Bin 0 -> 3485 bytes
.../AbstractSequenceParserExceptionHandler.class | Bin 0 -> 994 bytes
.../apps/cinema/io/CinemaCommandLineParser.class | Bin 0 -> 3101 bytes
.../io/CinemaCommandLineParserIdentifier.class | Bin 0 -> 648 bytes
.../bioinf/apps/cinema/io/FileSequenceInput.class | Bin 0 -> 3268 bytes
.../FileSequenceInputParserExceptionHandler.class | Bin 0 -> 479 bytes
.../bioinf/apps/cinema/io/FileSequenceOutput.class | Bin 0 -> 3025 bytes
.../io/FileSequenceParserExceptionHandler.class | Bin 0 -> 464 bytes
.../cinema/io/SequenceInputModuleIdentifier.class | Bin 0 -> 793 bytes
.../cinema/io/SequenceOutputModuleIdentifier.class | Bin 0 -> 740 bytes
.../CinemaMotifFrame$MotifFormatFileChooser.class | Bin 0 -> 2438 bytes
.../apps/cinema/motif/CinemaMotifFrame.class | Bin 0 -> 13721 bytes
.../apps/cinema/motif/CinemaMotifIdentifier.class | Bin 0 -> 633 bytes
.../apps/cinema/motif/CinemaMotifModule$1.class | Bin 0 -> 1393 bytes
.../apps/cinema/motif/CinemaMotifModule.class | Bin 0 -> 2249 bytes
.../motif/NamedAlignmentSelectionModel$1.class | Bin 0 -> 1020 bytes
.../motif/NamedAlignmentSelectionModel$2.class | Bin 0 -> 1216 bytes
...amedAlignmentSelectionModel$SelectionInfo.class | Bin 0 -> 786 bytes
.../motif/NamedAlignmentSelectionModel.class | Bin 0 -> 7808 bytes
.../apps/cinema/resources/CinemaResources.class | Bin 0 -> 2940 bytes
.../bioinf/apps/cinema/shared/CinemaDebug$1.class | Bin 0 -> 887 bytes
.../bioinf/apps/cinema/shared/CinemaDebug$2.class | Bin 0 -> 887 bytes
.../apps/cinema/shared/CinemaDebug$DebugImpl.class | Bin 0 -> 955 bytes
.../bioinf/apps/cinema/shared/CinemaDebug.class | Bin 0 -> 6760 bytes
.../cinema/shared/CinemaSharedIdentifier.class | Bin 0 -> 912 bytes
.../cinema/shared/CinemaSharedQuitExit$1.class | Bin 0 -> 1630 bytes
.../cinema/shared/CinemaSharedQuitExit$2.class | Bin 0 -> 1051 bytes
.../CinemaSharedQuitExit$QuitExitManager.class | Bin 0 -> 1722 bytes
.../apps/cinema/shared/CinemaSharedQuitExit.class | Bin 0 -> 1672 bytes
.../bioinf/apps/cinema/shared/CinemaSplash.class | Bin 0 -> 1753 bytes
.../apps/cinema/utils/CinemaAlignmentFrame.class | Bin 0 -> 6034 bytes
.../bioinf/apps/cinema/utils/CinemaDebug$1.class | Bin 0 -> 882 bytes
.../bioinf/apps/cinema/utils/CinemaDebug$2.class | Bin 0 -> 882 bytes
.../apps/cinema/utils/CinemaDebug$DebugImpl.class | Bin 0 -> 949 bytes
.../man/bioinf/apps/cinema/utils/CinemaDebug.class | Bin 0 -> 6750 bytes
.../CinemaFileOptionableExceptionHandler.class | Bin 0 -> 2153 bytes
.../apps/cinema/utils/CinemaFilePersist.class | Bin 0 -> 1713 bytes
.../bioinf/apps/cinema/utils/CinemaInvoker.class | Bin 0 -> 1594 bytes
.../apps/cinema/utils/CinemaMenuBuilder.class | Bin 0 -> 2137 bytes
.../utils/CinemaMultipleConsensusViewer.class | Bin 0 -> 5516 bytes
.../bioinf/apps/cinema/utils/CinemaPersist.class | Bin 0 -> 644 bytes
.../bioinf/apps/cinema/utils/CinemaRegexp$1.class | Bin 0 -> 1342 bytes
.../utils/CinemaRegexp$FramedAbstractAction.class | Bin 0 -> 850 bytes
.../bioinf/apps/cinema/utils/CinemaRegexp.class | Bin 0 -> 3539 bytes
...CinemaResizeElements$FramedAbstractAction.class | Bin 0 -> 1411 bytes
.../utils/CinemaResizeElements$ResizerGui.class | Bin 0 -> 5633 bytes
.../apps/cinema/utils/CinemaResizeElements.class | Bin 0 -> 1619 bytes
.../cinema/utils/CinemaSlaveViewerModule.class | Bin 0 -> 2224 bytes
.../cinema/utils/CinemaStatusInformation$1.class | Bin 0 -> 1045 bytes
.../cinema/utils/CinemaStatusInformation$2.class | Bin 0 -> 699 bytes
.../cinema/utils/CinemaStatusInformation.class | Bin 0 -> 4732 bytes
.../cinema/utils/CinemaUtilityIdentifier.class | Bin 0 -> 2015 bytes
.../utils/ConsensusPercentageIDColorMap.class | Bin 0 -> 4128 bytes
.../apps/commandline/CalculatePercentageID$1.class | Bin 0 -> 513 bytes
.../apps/commandline/CalculatePercentageID.class | Bin 0 -> 1532 bytes
.../CheckMotifLocationAgainstPrints$1.class | Bin 0 -> 456 bytes
.../CheckMotifLocationAgainstPrints.class | Bin 0 -> 7869 bytes
.../apps/commandline/GappedSequenceSearch$1.class | Bin 0 -> 434 bytes
.../apps/commandline/GappedSequenceSearch.class | Bin 0 -> 2494 bytes
.../bioinf/apps/commandline/SequenceSearch$1.class | Bin 0 -> 422 bytes
.../bioinf/apps/commandline/SequenceSearch.class | Bin 0 -> 2512 bytes
.../ac/man/bioinf/apps/invoker/AnonInvoker.class | Bin 0 -> 647 bytes
.../uk/ac/man/bioinf/apps/invoker/Invoker.class | Bin 0 -> 1213 bytes
.../InvokerInternalEventQueueException.class | Bin 0 -> 545 bytes
.../apps/invoker/InvokerInternalQueue$1.class | Bin 0 -> 530 bytes
.../bioinf/apps/invoker/InvokerInternalQueue.class | Bin 0 -> 4613 bytes
.../invoker/InvokerInternalQueueException.class | Bin 0 -> 295 bytes
.../bioinf/apps/invoker/InvokerThreadManager.class | Bin 0 -> 1107 bytes
.../apps/optionable/FileSaveableOptions.class | Bin 0 -> 1151 bytes
.../bioinf/apps/optionable/NullOptionHandler.class | Bin 0 -> 778 bytes
.../man/bioinf/apps/optionable/OptionHandler.class | Bin 0 -> 272 bytes
.../ac/man/bioinf/apps/optionable/Optionable.class | Bin 0 -> 436 bytes
.../optionable/OptionableExceptionHandler.class | Bin 0 -> 426 bytes
.../OptionableSourceNotFoundException.class | Bin 0 -> 362 bytes
.../apps/optionable/OptionableStateException.class | Bin 0 -> 281 bytes
.../bioinf/apps/optionable/SaveableOptions.class | Bin 0 -> 4507 bytes
.../man/bioinf/apps/systemevents/SystemEvent.class | Bin 0 -> 544 bytes
.../apps/systemevents/SystemEventOption.class | Bin 0 -> 593 bytes
.../apps/systemevents/SystemEventProducer.class | Bin 0 -> 280 bytes
.../SystemEventSupport$ListenerToComparable.class | Bin 0 -> 1296 bytes
.../apps/systemevents/SystemEventSupport.class | Bin 0 -> 1984 bytes
.../bioinf/apps/systemevents/SystemListener.class | Bin 0 -> 520 bytes
.../apps/systemevents/SystemVetoException.class | Bin 0 -> 544 bytes
classes/uk/ac/man/bioinf/apps/xml/ConfigNode.class | Bin 0 -> 1525 bytes
.../man/bioinf/apps/xml/DefaultXMLParser$1.class | Bin 0 -> 1054 bytes
.../ac/man/bioinf/apps/xml/DefaultXMLParser.class | Bin 0 -> 829 bytes
.../ac/man/bioinf/apps/xml/XMLBootIdentifier.class | Bin 0 -> 566 bytes
.../bioinf/apps/xml/XMLBootModule$MiniStack.class | Bin 0 -> 896 bytes
.../uk/ac/man/bioinf/apps/xml/XMLBootModule.class | Bin 0 -> 8306 bytes
.../bioinf/apps/xml/XMLBootParserListener.class | Bin 0 -> 3575 bytes
classes/uk/ac/man/bioinf/apps/xml/XMLModule.class | Bin 0 -> 1015 bytes
.../ac/man/bioinf/apps/xml/XMLParserFactory.class | Bin 0 -> 190 bytes
.../database/fetch/ExpasySequenceRetriever.class | Bin 0 -> 1834 bytes
.../fetch/FetchSequenceBySwissProtID.class | Bin 0 -> 262 bytes
.../bioinf/database/fetch/SequenceRetriever.class | Bin 0 -> 472 bytes
classes/uk/ac/man/bioinf/debug/AbstractDebug.class | Bin 0 -> 1409 bytes
classes/uk/ac/man/bioinf/debug/Debug.class | Bin 0 -> 3393 bytes
.../uk/ac/man/bioinf/debug/DebugInterface.class | Bin 0 -> 746 bytes
.../uk/ac/man/bioinf/debug/DebugMultiplexer.class | Bin 0 -> 4062 bytes
classes/uk/ac/man/bioinf/debug/DefaultDebug.class | Bin 0 -> 969 bytes
.../uk/ac/man/bioinf/debug/DefaultFileDebug.class | Bin 0 -> 1234 bytes
classes/uk/ac/man/bioinf/debug/NullDebug.class | Bin 0 -> 420 bytes
.../ac/man/bioinf/gui/color/ColorGenerator.class | Bin 0 -> 802 bytes
classes/uk/ac/man/bioinf/gui/color/ColorList.class | Bin 0 -> 1340 bytes
classes/uk/ac/man/bioinf/gui/color/ColorMap.class | Bin 0 -> 352 bytes
.../man/bioinf/gui/color/ColorMapException.class | Bin 0 -> 268 bytes
.../uk/ac/man/bioinf/gui/color/ColorStore.class | Bin 0 -> 1267 bytes
.../man/bioinf/gui/color/DoubleArrayColorMap.class | Bin 0 -> 1821 bytes
.../gui/color/IndividualElementColorMap.class | Bin 0 -> 1208 bytes
.../gui/color/PercentIDVarianceColorMap.class | Bin 0 -> 2170 bytes
.../ac/man/bioinf/gui/color/SingleColorMap.class | Bin 0 -> 825 bytes
.../man/bioinf/gui/color/ThreadableColorMap.class | Bin 0 -> 213 bytes
.../man/bioinf/gui/color/ThreadedColorMap$1.class | Bin 0 -> 1041 bytes
.../ac/man/bioinf/gui/color/ThreadedColorMap.class | Bin 0 -> 3648 bytes
.../ac/man/bioinf/gui/misc/ChunkyListModel.class | Bin 0 -> 4161 bytes
...pingListBasicUI$SwappingMouseInputHandler.class | Bin 0 -> 1702 bytes
.../man/bioinf/gui/misc/SwappingListBasicUI.class | Bin 0 -> 766 bytes
.../bioinf/gui/optionable/OptionableJFrame.class | Bin 0 -> 3331 bytes
.../gui/optionable/OptionableJSplitPane.class | Bin 0 -> 2297 bytes
.../man/bioinf/gui/util/ApplicationFrame$1.class | Bin 0 -> 1545 bytes
.../ac/man/bioinf/gui/util/ApplicationFrame.class | Bin 0 -> 8393 bytes
.../ac/man/bioinf/gui/util/PopUpHtmlDisplay.class | Bin 0 -> 1541 bytes
.../uk/ac/man/bioinf/gui/util/TripletPanel.class | Bin 0 -> 2654 bytes
.../man/bioinf/gui/util/forms/DecimalField.class | Bin 0 -> 1623 bytes
.../bioinf/gui/util/forms/FormattedDocument.class | Bin 0 -> 1695 bytes
.../util/forms/IntegerField$IntegerDocument.class | Bin 0 -> 1463 bytes
.../man/bioinf/gui/util/forms/IntegerField.class | Bin 0 -> 1764 bytes
.../man/bioinf/gui/util/forms/PasswordDialog.class | Bin 0 -> 3257 bytes
.../util/forms/ValidatedForm$ModifierCombo.class | Bin 0 -> 813 bytes
.../forms/ValidatedForm$MyDocumentListener.class | Bin 0 -> 833 bytes
.../man/bioinf/gui/util/forms/ValidatedForm.class | Bin 0 -> 7373 bytes
.../WholeNumberField$WholeNumberDocument.class | Bin 0 -> 1475 bytes
.../bioinf/gui/util/forms/WholeNumberField.class | Bin 0 -> 1605 bytes
.../gui/viewer/AlignmentSelectionModel.class | Bin 0 -> 1147 bytes
.../gui/viewer/AlignmentSelectionRenderer.class | Bin 0 -> 330 bytes
.../gui/viewer/AlignmentViewerCellRenderer.class | Bin 0 -> 393 bytes
.../BorderFastAlignmentViewerCellRenderer.class | Bin 0 -> 1086 bytes
.../bioinf/gui/viewer/ButtonViewerPopupMenu.class | Bin 0 -> 1677 bytes
.../ColorFastAlignmentViewerCellRenderer.class | Bin 0 -> 835 bytes
...CursorLessFastAlignmentViewerCellRenderer.class | Bin 0 -> 678 bytes
.../viewer/DefaultAlignmentSelectionRenderer.class | Bin 0 -> 753 bytes
.../DefaultAlignmentViewerCellRenderer.class | Bin 0 -> 1633 bytes
.../DefaultFastAlignmentViewerCellRenderer.class | Bin 0 -> 1613 bytes
.../bioinf/gui/viewer/DefaultSequenceCursor.class | Bin 0 -> 1525 bytes
.../viewer/FastAlignmentViewerCellRenderer.class | Bin 0 -> 391 bytes
classes/uk/ac/man/bioinf/gui/viewer/Install.class | Bin 0 -> 1916 bytes
.../gui/viewer/InvertedScrollPaneLayout.class | Bin 0 -> 3633 bytes
...ignmentButtonPanel$SequenceButtonListener.class | Bin 0 -> 1107 bytes
.../bioinf/gui/viewer/JAlignmentButtonPanel.class | Bin 0 -> 5226 bytes
...er$SequenceAlignmentBoundRangeModelBridge.class | Bin 0 -> 2086 bytes
.../ac/man/bioinf/gui/viewer/JAlignmentRuler.class | Bin 0 -> 3546 bytes
.../man/bioinf/gui/viewer/JAlignmentViewer.class | Bin 0 -> 14791 bytes
.../man/bioinf/gui/viewer/JChangedScrollPane.class | Bin 0 -> 1142 bytes
.../man/bioinf/gui/viewer/JLayableScrollPane.class | Bin 0 -> 1142 bytes
...ultiplexerFastAlignmentViewerCellRenderer.class | Bin 0 -> 2625 bytes
.../gui/viewer/NullAlignmentSelectionModel.class | Bin 0 -> 2165 bytes
.../gui/viewer/PrintableAlignmentPanel.class | Bin 0 -> 250 bytes
.../gui/viewer/PrintableJAlignmentViewer.class | Bin 0 -> 1169 bytes
.../man/bioinf/gui/viewer/ReadonlyException.class | Bin 0 -> 865 bytes
.../ac/man/bioinf/gui/viewer/SequenceCursor.class | Bin 0 -> 437 bytes
.../gui/viewer/SingleAlignmentSelectionModel.class | Bin 0 -> 3152 bytes
.../TextFastAlignmentViewerCellRenderer.class | Bin 0 -> 1332 bytes
.../gui/viewer/event/AlignmentSelectionEvent.class | Bin 0 -> 1283 bytes
.../viewer/event/AlignmentSelectionListener.class | Bin 0 -> 286 bytes
.../event/AlignmentSelectionListenerSupport.class | Bin 0 -> 1126 bytes
.../gui/viewer/event/ChangeListenerSupport.class | Bin 0 -> 982 bytes
.../bioinf/gui/viewer/plaf/AlignmentRulerUI.class | Bin 0 -> 251 bytes
.../bioinf/gui/viewer/plaf/AlignmentViewerUI.class | Bin 0 -> 935 bytes
.../gui/viewer/plaf/BasicAlignmentRulerUI.class | Bin 0 -> 2336 bytes
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.../BasicAlignmentViewerUI$CursorBlinkThread.class | Bin 0 -> 1042 bytes
.../plaf/BasicAlignmentViewerUI$KeyScroller.class | Bin 0 -> 1249 bytes
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.../BasicAlignmentViewerUI$SelectionClearer.class | Bin 0 -> 1002 bytes
.../BasicAlignmentViewerUI$SelectionToggler.class | Bin 0 -> 1271 bytes
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.../gui/viewer/plaf/MetalAlignmentViewerUI.class | Bin 0 -> 290 bytes
.../gui/viewer/test/BasicWindowMonitor.class | Bin 0 -> 571 bytes
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.../man/bioinf/gui/viewer/test/SliderExample.class | Bin 0 -> 1680 bytes
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.../bioinf/sequence/event/SequenceListener.class | Bin 0 -> 254 bytes
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.../sequence/event/SequenceVetoException.class | Bin 0 -> 536 bytes
.../sequence/event/VetoableSequenceEvent.class | Bin 0 -> 493 bytes
.../sequence/event/VetoableSequenceListener.class | Bin 0 -> 393 bytes
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.../sequence/geom/SequenceAlignmentPoint.class | Bin 0 -> 2107 bytes
.../sequence/geom/SequenceAlignmentRectangle.class | Bin 0 -> 3820 bytes
.../sequence/geom/SequenceAlignmentShape.class | Bin 0 -> 240 bytes
.../group/AbstractGappedSequenceGroup.class | Bin 0 -> 686 bytes
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doc/ASL | 58 +
doc/AUTHORS | 15 +
doc/CINEMA | 13 +
doc/EXTENDING_CINEMA | 17 +
doc/INSTALL | 106 +
doc/LGPL | 311 +
doc/LICENSING | 39 +
doc/cinema-changes.html | 454 ++
doc/cinema-module/cinema-module.aux | 51 +
doc/cinema-module/cinema-module.dvi | Bin 0 -> 41152 bytes
doc/cinema-module/cinema-module.log | 244 +
doc/cinema-module/cinema-module.pdf | Bin 0 -> 50450 bytes
doc/cinema-module/cinema-module.tex | 540 ++
doc/cinema-module/cinema-module.wiz | 0
doc/cinema-module/cinema-module/WARNINGS | 6 +
doc/cinema-module/cinema-module/cinema-module.css | 30 +
doc/cinema-module/cinema-module/cinema-module.html | 110 +
doc/cinema-module/cinema-module/footnode.html | 107 +
doc/cinema-module/cinema-module/index.html | 110 +
doc/cinema-module/cinema-module/internals.pl | 46 +
doc/cinema-module/cinema-module/labels.pl | 137 +
doc/cinema-module/cinema-module/node1.html | 84 +
doc/cinema-module/cinema-module/node10.html | 138 +
doc/cinema-module/cinema-module/node11.html | 225 +
doc/cinema-module/cinema-module/node12.html | 122 +
doc/cinema-module/cinema-module/node13.html | 74 +
doc/cinema-module/cinema-module/node2.html | 83 +
doc/cinema-module/cinema-module/node3.html | 157 +
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doc/cinema-module/cinema-module/node5.html | 197 +
doc/cinema-module/cinema-module/node6.html | 81 +
doc/cinema-module/cinema-module/node7.html | 86 +
doc/cinema-module/cinema-module/node8.html | 130 +
doc/cinema-module/cinema-module/node9.html | 154 +
doc/cinema-module/listings.perl | 12 +
doc/cinema-module/missfont.log | 84 +
doc/javadoc/allclasses-frame.html | 777 ++
doc/javadoc/allclasses-noframe.html | 777 ++
doc/javadoc/constant-values.html | 519 ++
doc/javadoc/deprecated-list.html | 121 +
doc/javadoc/help-doc.html | 176 +
doc/javadoc/index-all.html | 8309 ++++++++++++++++++++
doc/javadoc/index.html | 25 +
doc/javadoc/overview-frame.html | 134 +
doc/javadoc/overview-summary.html | 341 +
doc/javadoc/overview-tree.html | 517 ++
doc/javadoc/package-list | 47 +
doc/javadoc/packages.html | 26 +
doc/javadoc/serialized-form.html | 2735 +++++++
doc/javadoc/stylesheet.css | 29 +
doc/javadoc/uk/ac/man/bioinf/Y.html | 223 +
.../analysis/consensus/ConsensusCalculator.html | 252 +
.../analysis/consensus/ConsensusIdentifier.html | 286 +
.../analysis/consensus/ConsensusSequence.html | 300 +
.../consensus/DefaultConsensusSequence.html | 849 ++
.../analysis/consensus/PercentageIDConsensus.html | 336 +
.../consensus/ThreadedConsensusSequence.html | 410 +
.../bioinf/analysis/consensus/package-frame.html | 51 +
.../bioinf/analysis/consensus/package-summary.html | 182 +
.../bioinf/analysis/consensus/package-tree.html | 169 +
.../analysis/misc/PercentageIDCalculator.html | 383 +
.../misc/PercentageIDCalculatorManager.html | 271 +
.../ac/man/bioinf/analysis/misc/package-frame.html | 34 +
.../man/bioinf/analysis/misc/package-summary.html | 144 +
.../ac/man/bioinf/analysis/misc/package-tree.html | 133 +
.../regexp/GappedSequenceCharacterIterator.html | 311 +
.../analysis/regexp/SequenceCharacterIterator.html | 312 +
.../man/bioinf/analysis/regexp/package-frame.html | 34 +
.../bioinf/analysis/regexp/package-summary.html | 144 +
.../man/bioinf/analysis/regexp/package-tree.html | 132 +
.../uk/ac/man/bioinf/apps/cinema/Cinema.html | 318 +
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.../bioinf/apps/cinema/CinemaBootIdentifier.html | 292 +
.../ac/man/bioinf/apps/cinema/CinemaGuiModule.html | 518 ++
.../uk/ac/man/bioinf/apps/cinema/CinemaModule.html | 753 ++
.../apps/cinema/CinemaModuleFactoryInstance.html | 277 +
.../man/bioinf/apps/cinema/CinemaProperties.html | 262 +
.../uk/ac/man/bioinf/apps/cinema/CinemaShared.html | 304 +
.../bioinf/apps/cinema/CinemaXMLParserFactory.html | 258 +
.../cinema/color/AminoAcidColorMapMetaData.html | 375 +
.../apps/cinema/color/CinemaColorFactory.html | 466 ++
.../apps/cinema/color/CinemaColorIdentifier.html | 292 +
.../apps/cinema/color/CinemaColorSelector.html | 403 +
.../bioinf/apps/cinema/color/ColorMapMetaData.html | 293 +
.../cinema/color/ColormapColorMapMetaData.html | 374 +
.../apps/cinema/color/DefaultColorMapMetaData.html | 374 +
.../apps/cinema/color/GrayScaleVariance.html | 344 +
.../InstancePerAlignmentColorMapMetaData.html | 311 +
.../apps/cinema/color/IntenseColorMapMetaData.html | 374 +
.../apps/cinema/color/Js_TestColorMapMetaData.html | 374 +
.../apps/cinema/color/NullColorMapMetaData.html | 344 +
.../cinema/color/PedanticColorMapMetaData.html | 374 +
.../PercentageIDVarianceColorMapMetaData.html | 344 +
.../apps/cinema/color/TaylorColorMapMetaData.html | 396 +
...readedPercentageIDVarianceColorMapMetaData.html | 344 +
.../cinema/color/VariableColorMapMetaData.html | 374 +
.../cinema/color/VariationsColorMapMetaData.html | 374 +
.../apps/cinema/color/WhiteColorMapMetaData.html | 344 +
.../apps/cinema/color/ZenecaColorMapMetaData.html | 374 +
.../bioinf/apps/cinema/color/package-frame.html | 79 +
.../bioinf/apps/cinema/color/package-summary.html | 270 +
.../man/bioinf/apps/cinema/color/package-tree.html | 168 +
.../apps/cinema/consensus/CinemaConsensus.html | 431 +
.../CinemaConsensusCalculatorMetaData.html | 252 +
.../cinema/consensus/CinemaConsensusDisplay.html | 453 ++
.../consensus/CinemaConsensusIdentifier.html | 292 +
.../PercentageIDConsensusCalculatorMetaData.html | 349 +
...dedPercentageIDConsensusCalculatorMetaData.html | 313 +
.../apps/cinema/consensus/package-frame.html | 51 +
.../apps/cinema/consensus/package-summary.html | 179 +
.../bioinf/apps/cinema/consensus/package-tree.html | 155 +
.../cinema/core/AlignmentToListCellRenderer.html | 434 +
.../apps/cinema/core/AlignmentToListModel.html | 345 +
.../apps/cinema/core/CinemaActionProvider.html | 214 +
.../man/bioinf/apps/cinema/core/CinemaCoreGui.html | 714 ++
.../apps/cinema/core/CinemaCoreIdentifier.html | 328 +
.../bioinf/apps/cinema/core/CinemaCoreView.html | 733 ++
.../cinema/core/CinemaFramedActionProvider.html | 214 +
.../ac/man/bioinf/apps/cinema/core/CinemaGo.html | 338 +
.../bioinf/apps/cinema/core/CinemaMenuSystem.html | 360 +
.../cinema/core/CinemaModuleCoreIdentifier.html | 292 +
.../apps/cinema/core/CinemaSequenceMenu.html | 388 +
.../apps/cinema/core/CinemaSystemEvents.html | 413 +
.../apps/cinema/core/VersionInformation.html | 348 +
.../man/bioinf/apps/cinema/core/package-frame.html | 65 +
.../bioinf/apps/cinema/core/package-summary.html | 228 +
.../man/bioinf/apps/cinema/core/package-tree.html | 171 +
.../apps/cinema/core/test/CinemaTestLaunch.html | 294 +
.../cinema/core/test/CinemaTestModuleLaunch.html | 254 +
.../apps/cinema/core/test/package-frame.html | 34 +
.../apps/cinema/core/test/package-summary.html | 144 +
.../bioinf/apps/cinema/core/test/package-tree.html | 132 +
.../apps/cinema/group/CinemaAnchorManager.html | 372 +
.../man/bioinf/apps/cinema/group/CinemaGroup.html | 362 +
.../bioinf/apps/cinema/group/CinemaGroupFrame.html | 528 ++
.../apps/cinema/group/CinemaGroupIdentifier.html | 274 +
.../apps/cinema/group/CinemaGroupManager.html | 642 ++
.../apps/cinema/group/CinemaGroupModule.html | 553 ++
.../bioinf/apps/cinema/group/package-frame.html | 42 +
.../bioinf/apps/cinema/group/package-summary.html | 174 +
.../man/bioinf/apps/cinema/group/package-tree.html | 170 +
.../apps/cinema/io/AbstractSequenceInput.html | 540 ++
...bstractSequenceInputParserExceptionHandler.html | 330 +
.../apps/cinema/io/AbstractSequenceOutput.html | 549 ++
.../io/AbstractSequenceParserExceptionHandler.html | 330 +
.../apps/cinema/io/CinemaCommandLineParser.html | 377 +
.../io/CinemaCommandLineParserIdentifier.html | 274 +
.../bioinf/apps/cinema/io/FileSequenceInput.html | 419 +
.../FileSequenceInputParserExceptionHandler.html | 270 +
.../bioinf/apps/cinema/io/FileSequenceOutput.html | 379 +
.../io/FileSequenceParserExceptionHandler.html | 270 +
.../cinema/io/SequenceInputModuleIdentifier.html | 294 +
.../cinema/io/SequenceOutputModuleIdentifier.html | 292 +
.../man/bioinf/apps/cinema/io/package-frame.html | 54 +
.../man/bioinf/apps/cinema/io/package-summary.html | 194 +
.../ac/man/bioinf/apps/cinema/io/package-tree.html | 158 +
.../bioinf/apps/cinema/motif/CinemaMotifFrame.html | 582 ++
.../apps/cinema/motif/CinemaMotifIdentifier.html | 274 +
.../apps/cinema/motif/CinemaMotifModule.html | 373 +
.../cinema/motif/NamedAlignmentSelectionModel.html | 753 ++
.../bioinf/apps/cinema/motif/package-frame.html | 38 +
.../bioinf/apps/cinema/motif/package-summary.html | 157 +
.../man/bioinf/apps/cinema/motif/package-tree.html | 161 +
.../ac/man/bioinf/apps/cinema/package-frame.html | 48 +
.../ac/man/bioinf/apps/cinema/package-summary.html | 191 +
.../uk/ac/man/bioinf/apps/cinema/package-tree.html | 152 +
.../apps/cinema/resources/CinemaResources.html | 372 +
.../apps/cinema/resources/package-frame.html | 32 +
.../apps/cinema/resources/package-summary.html | 138 +
.../bioinf/apps/cinema/resources/package-tree.html | 132 +
.../apps/cinema/shared/CinemaDebug.DebugImpl.html | 285 +
.../man/bioinf/apps/cinema/shared/CinemaDebug.html | 394 +
.../apps/cinema/shared/CinemaSharedIdentifier.html | 310 +
.../apps/cinema/shared/CinemaSharedQuitExit.html | 289 +
.../bioinf/apps/cinema/shared/CinemaSplash.html | 341 +
.../bioinf/apps/cinema/shared/package-frame.html | 38 +
.../bioinf/apps/cinema/shared/package-summary.html | 158 +
.../bioinf/apps/cinema/shared/package-tree.html | 148 +
.../apps/cinema/utils/CinemaAlignmentFrame.html | 708 ++
.../apps/cinema/utils/CinemaDebug.DebugImpl.html | 285 +
.../man/bioinf/apps/cinema/utils/CinemaDebug.html | 394 +
.../CinemaFileOptionableExceptionHandler.html | 398 +
.../apps/cinema/utils/CinemaFilePersist.html | 373 +
.../bioinf/apps/cinema/utils/CinemaInvoker.html | 362 +
.../apps/cinema/utils/CinemaMenuBuilder.html | 358 +
.../utils/CinemaMultipleConsensusViewer.html | 489 ++
.../bioinf/apps/cinema/utils/CinemaPersist.html | 316 +
.../man/bioinf/apps/cinema/utils/CinemaRegexp.html | 318 +
.../apps/cinema/utils/CinemaResizeElements.html | 339 +
.../apps/cinema/utils/CinemaSlaveViewerModule.html | 325 +
.../apps/cinema/utils/CinemaStatusInformation.html | 355 +
.../apps/cinema/utils/CinemaUtilityIdentifier.html | 418 +
.../utils/ConsensusPercentageIDColorMap.html | 344 +
.../bioinf/apps/cinema/utils/package-frame.html | 58 +
.../bioinf/apps/cinema/utils/package-summary.html | 227 +
.../man/bioinf/apps/cinema/utils/package-tree.html | 176 +
.../apps/commandline/CalculatePercentageID.html | 254 +
.../CheckMotifLocationAgainstPrints.html | 343 +
.../apps/commandline/GappedSequenceSearch.html | 256 +
.../bioinf/apps/commandline/SequenceSearch.html | 256 +
.../man/bioinf/apps/commandline/package-frame.html | 38 +
.../bioinf/apps/commandline/package-summary.html | 158 +
.../man/bioinf/apps/commandline/package-tree.html | 132 +
.../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html | 346 +
.../uk/ac/man/bioinf/apps/invoker/Invoker.html | 439 ++
.../InvokerInternalEventQueueException.html | 271 +
.../bioinf/apps/invoker/InvokerInternalQueue.html | 578 ++
.../invoker/InvokerInternalQueueException.html | 238 +
.../bioinf/apps/invoker/InvokerThreadManager.html | 304 +
.../ac/man/bioinf/apps/invoker/package-frame.html | 51 +
.../man/bioinf/apps/invoker/package-summary.html | 182 +
.../ac/man/bioinf/apps/invoker/package-tree.html | 143 +
.../apps/optionable/FileSaveableOptions.html | 321 +
.../bioinf/apps/optionable/NullOptionHandler.html | 315 +
.../man/bioinf/apps/optionable/OptionHandler.html | 269 +
.../ac/man/bioinf/apps/optionable/Optionable.html | 324 +
.../optionable/OptionableExceptionHandler.html | 333 +
.../OptionableSourceNotFoundException.html | 252 +
.../apps/optionable/OptionableStateException.html | 239 +
.../bioinf/apps/optionable/SaveableOptions.html | 497 ++
.../man/bioinf/apps/optionable/package-frame.html | 64 +
.../bioinf/apps/optionable/package-summary.html | 207 +
.../man/bioinf/apps/optionable/package-tree.html | 148 +
.../man/bioinf/apps/systemevents/SystemEvent.html | 287 +
.../apps/systemevents/SystemEventOption.html | 262 +
.../apps/systemevents/SystemEventProducer.html | 234 +
.../apps/systemevents/SystemEventSupport.html | 334 +
.../bioinf/apps/systemevents/SystemListener.html | 348 +
.../apps/systemevents/SystemVetoException.html | 270 +
.../bioinf/apps/systemevents/package-frame.html | 60 +
.../bioinf/apps/systemevents/package-summary.html | 191 +
.../man/bioinf/apps/systemevents/package-tree.html | 148 +
.../uk/ac/man/bioinf/apps/xml/ConfigNode.html | 373 +
.../ac/man/bioinf/apps/xml/DefaultXMLParser.html | 258 +
.../ac/man/bioinf/apps/xml/XMLBootIdentifier.html | 274 +
.../bioinf/apps/xml/XMLBootModule.MiniStack.html | 280 +
.../uk/ac/man/bioinf/apps/xml/XMLBootModule.html | 874 ++
.../man/bioinf/apps/xml/XMLBootParserListener.html | 574 ++
.../uk/ac/man/bioinf/apps/xml/XMLModule.html | 290 +
.../ac/man/bioinf/apps/xml/XMLParserFactory.html | 214 +
.../uk/ac/man/bioinf/apps/xml/package-frame.html | 53 +
.../uk/ac/man/bioinf/apps/xml/package-summary.html | 189 +
.../uk/ac/man/bioinf/apps/xml/package-tree.html | 146 +
.../man/bioinf/apps/xml/test/XMLLoadingTest.html | 330 +
.../ac/man/bioinf/apps/xml/test/XMLStartTest.html | 254 +
.../ac/man/bioinf/apps/xml/test/package-frame.html | 34 +
.../man/bioinf/apps/xml/test/package-summary.html | 144 +
.../ac/man/bioinf/apps/xml/test/package-tree.html | 135 +
.../database/fetch/ExpasySequenceRetriever.html | 358 +
.../database/fetch/FetchSequenceBySwissProtID.html | 220 +
.../bioinf/database/fetch/SequenceRetriever.html | 281 +
.../man/bioinf/database/fetch/package-frame.html | 45 +
.../man/bioinf/database/fetch/package-summary.html | 160 +
.../ac/man/bioinf/database/fetch/package-tree.html | 138 +
.../uk/ac/man/bioinf/debug/AbstractDebug.html | 487 ++
doc/javadoc/uk/ac/man/bioinf/debug/Debug.html | 560 ++
.../uk/ac/man/bioinf/debug/DebugInterface.html | 413 +
.../uk/ac/man/bioinf/debug/DebugMultiplexer.html | 524 ++
.../uk/ac/man/bioinf/debug/DefaultDebug.html | 296 +
.../uk/ac/man/bioinf/debug/DefaultFileDebug.html | 296 +
doc/javadoc/uk/ac/man/bioinf/debug/NullDebug.html | 297 +
.../uk/ac/man/bioinf/debug/package-frame.html | 53 +
.../uk/ac/man/bioinf/debug/package-summary.html | 188 +
.../uk/ac/man/bioinf/debug/package-tree.html | 141 +
.../uk/ac/man/bioinf/gui/color/ColorGenerator.html | 306 +
.../uk/ac/man/bioinf/gui/color/ColorList.html | 413 +
.../uk/ac/man/bioinf/gui/color/ColorMap.html | 250 +
.../ac/man/bioinf/gui/color/ColorMapException.html | 238 +
.../uk/ac/man/bioinf/gui/color/ColorStore.html | 194 +
.../man/bioinf/gui/color/DoubleArrayColorMap.html | 303 +
.../gui/color/IndividualElementColorMap.html | 300 +
.../gui/color/PercentIDVarianceColorMap.html | 364 +
.../uk/ac/man/bioinf/gui/color/SingleColorMap.html | 313 +
.../man/bioinf/gui/color/ThreadableColorMap.html | 234 +
.../ac/man/bioinf/gui/color/ThreadedColorMap.html | 495 ++
.../uk/ac/man/bioinf/gui/color/package-frame.html | 70 +
.../ac/man/bioinf/gui/color/package-summary.html | 228 +
.../uk/ac/man/bioinf/gui/color/package-tree.html | 151 +
.../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html | 1054 +++
...ppingListBasicUI.SwappingMouseInputHandler.html | 302 +
.../man/bioinf/gui/misc/SwappingListBasicUI.html | 368 +
.../uk/ac/man/bioinf/gui/misc/package-frame.html | 34 +
.../uk/ac/man/bioinf/gui/misc/package-summary.html | 143 +
.../uk/ac/man/bioinf/gui/misc/package-tree.html | 144 +
.../bioinf/gui/optionable/OptionableJFrame.html | 788 ++
.../gui/optionable/OptionableJSplitPane.html | 634 ++
.../man/bioinf/gui/optionable/package-frame.html | 34 +
.../man/bioinf/gui/optionable/package-summary.html | 145 +
.../ac/man/bioinf/gui/optionable/package-tree.html | 154 +
.../ac/man/bioinf/gui/util/ApplicationFrame.html | 852 ++
.../ac/man/bioinf/gui/util/PopUpHtmlDisplay.html | 239 +
.../uk/ac/man/bioinf/gui/util/TripletPanel.html | 489 ++
.../ac/man/bioinf/gui/util/forms/DecimalField.html | 481 ++
.../bioinf/gui/util/forms/FormattedDocument.html | 370 +
.../util/forms/IntegerField.IntegerDocument.html | 330 +
.../ac/man/bioinf/gui/util/forms/IntegerField.html | 499 ++
.../man/bioinf/gui/util/forms/PasswordDialog.html | 533 ++
.../man/bioinf/gui/util/forms/ValidatedForm.html | 776 ++
.../WholeNumberField.WholeNumberDocument.html | 330 +
.../bioinf/gui/util/forms/WholeNumberField.html | 467 ++
.../man/bioinf/gui/util/forms/package-frame.html | 42 +
.../man/bioinf/gui/util/forms/package-summary.html | 154 +
.../ac/man/bioinf/gui/util/forms/package-tree.html | 154 +
.../uk/ac/man/bioinf/gui/util/package-frame.html | 36 +
.../uk/ac/man/bioinf/gui/util/package-summary.html | 142 +
.../uk/ac/man/bioinf/gui/util/package-tree.html | 152 +
.../bioinf/gui/viewer/AlignmentSelectionModel.html | 469 ++
.../gui/viewer/AlignmentSelectionRenderer.html | 226 +
.../gui/viewer/AlignmentViewerCellRenderer.html | 237 +
.../BorderFastAlignmentViewerCellRenderer.html | 293 +
.../bioinf/gui/viewer/ButtonViewerPopupMenu.html | 404 +
.../ColorFastAlignmentViewerCellRenderer.html | 293 +
.../CursorLessFastAlignmentViewerCellRenderer.html | 298 +
.../viewer/DefaultAlignmentSelectionRenderer.html | 270 +
.../viewer/DefaultAlignmentViewerCellRenderer.html | 415 +
.../DefaultFastAlignmentViewerCellRenderer.html | 318 +
.../bioinf/gui/viewer/DefaultSequenceCursor.html | 388 +
.../viewer/FastAlignmentViewerCellRenderer.html | 255 +
.../uk/ac/man/bioinf/gui/viewer/Install.html | 289 +
.../gui/viewer/InvertedScrollPaneLayout.html | 310 +
.../bioinf/gui/viewer/JAlignmentButtonPanel.html | 692 ++
.../ac/man/bioinf/gui/viewer/JAlignmentRuler.html | 671 ++
.../ac/man/bioinf/gui/viewer/JAlignmentViewer.html | 2037 +++++
.../man/bioinf/gui/viewer/JChangedScrollPane.html | 386 +
.../man/bioinf/gui/viewer/JLayableScrollPane.html | 391 +
...MultiplexerFastAlignmentViewerCellRenderer.html | 344 +
.../gui/viewer/NullAlignmentSelectionModel.html | 569 ++
.../bioinf/gui/viewer/PrintableAlignmentPanel.html | 344 +
.../gui/viewer/PrintableJAlignmentViewer.html | 516 ++
.../man/bioinf/gui/viewer/ReadonlyException.html | 319 +
.../ac/man/bioinf/gui/viewer/SequenceCursor.html | 323 +
.../gui/viewer/SingleAlignmentSelectionModel.html | 549 ++
.../TextFastAlignmentViewerCellRenderer.html | 293 +
.../gui/viewer/event/AlignmentSelectionEvent.html | 327 +
.../viewer/event/AlignmentSelectionListener.html | 220 +
.../event/AlignmentSelectionListenerSupport.html | 290 +
.../gui/viewer/event/ChangeListenerSupport.html | 290 +
.../man/bioinf/gui/viewer/event/package-frame.html | 47 +
.../bioinf/gui/viewer/event/package-summary.html | 168 +
.../man/bioinf/gui/viewer/event/package-tree.html | 142 +
.../uk/ac/man/bioinf/gui/viewer/package-frame.html | 102 +
.../ac/man/bioinf/gui/viewer/package-summary.html | 341 +
.../uk/ac/man/bioinf/gui/viewer/package-tree.html | 189 +
.../bioinf/gui/viewer/plaf/AlignmentRulerUI.html | 231 +
.../bioinf/gui/viewer/plaf/AlignmentViewerUI.html | 346 +
.../gui/viewer/plaf/BasicAlignmentRulerUI.html | 508 ++
.../plaf/BasicAlignmentViewerUI.KeyScroller.html | 335 +
.../plaf/BasicAlignmentViewerUI.PointListener.html | 248 +
.../BasicAlignmentViewerUI.SelectionClearer.html | 248 +
.../BasicAlignmentViewerUI.SelectionToggler.html | 248 +
.../gui/viewer/plaf/BasicAlignmentViewerUI.html | 1014 +++
.../gui/viewer/plaf/MetalAlignmentViewerUI.html | 272 +
.../man/bioinf/gui/viewer/plaf/package-frame.html | 40 +
.../bioinf/gui/viewer/plaf/package-summary.html | 165 +
.../man/bioinf/gui/viewer/plaf/package-tree.html | 147 +
.../gui/viewer/test/AlignmentViewerTest.html | 426 +
.../bioinf/gui/viewer/test/BasicWindowMonitor.html | 256 +
.../bioinf/gui/viewer/test/ButtonPanelTest.html | 282 +
.../viewer/test/CellRendererPaneReplacement.html | 373 +
.../gui/viewer/test/SingleSelectionModelTest.html | 252 +
.../man/bioinf/gui/viewer/test/SliderExample.html | 365 +
.../man/bioinf/gui/viewer/test/package-frame.html | 42 +
.../bioinf/gui/viewer/test/package-summary.html | 166 +
.../man/bioinf/gui/viewer/test/package-tree.html | 159 +
.../uk/ac/man/bioinf/io/AlignmentInputParser.html | 281 +
.../uk/ac/man/bioinf/io/AlignmentOutputParser.html | 257 +
.../bioinf/io/DefaultParserExceptionHandler.html | 261 +
.../io/InvalidSequenceTypeParserException.html | 329 +
.../uk/ac/man/bioinf/io/NarrowedInputStream.html | 302 +
.../man/bioinf/io/NullParserExceptionHandler.html | 290 +
.../uk/ac/man/bioinf/io/ParserException.html | 390 +
.../ac/man/bioinf/io/ParserExceptionHandler.html | 216 +
.../uk/ac/man/bioinf/io/SequenceInputParser.html | 238 +
.../ac/man/bioinf/io/SequenceWriterException.html | 250 +
.../ac/man/bioinf/io/UnknownElementException.html | 319 +
doc/javadoc/uk/ac/man/bioinf/io/package-frame.html | 70 +
.../uk/ac/man/bioinf/io/package-summary.html | 207 +
doc/javadoc/uk/ac/man/bioinf/io/package-tree.html | 150 +
.../AbstractProteinAlignmentInputParser.html | 274 +
.../AbstractProteinSequenceInputParser.html | 323 +
.../man/bioinf/io/parsers/FastaSequenceParser.html | 314 +
.../ac/man/bioinf/io/parsers/MotProteinParser.html | 303 +
.../io/parsers/PIRProteinAlignmentParser.html | 372 +
.../uk/ac/man/bioinf/io/parsers/package-frame.html | 40 +
.../ac/man/bioinf/io/parsers/package-summary.html | 159 +
.../uk/ac/man/bioinf/io/parsers/package-tree.html | 140 +
.../man/bioinf/io/test/AlignmentParserIOTest.html | 252 +
.../bioinf/io/test/AlignmentParserInputTest.html | 252 +
.../uk/ac/man/bioinf/io/test/package-frame.html | 34 +
.../uk/ac/man/bioinf/io/test/package-summary.html | 144 +
.../uk/ac/man/bioinf/io/test/package-tree.html | 132 +
.../module/AbstractEnumeratedModuleIdentifier.html | 424 +
.../ac/man/bioinf/module/DefaultModuleContext.html | 298 +
.../module/DefaultModuleFactoryInstance.html | 631 ++
.../man/bioinf/module/GenericModuleIdentifier.html | 318 +
doc/javadoc/uk/ac/man/bioinf/module/Module.html | 713 ++
.../uk/ac/man/bioinf/module/ModuleContext.html | 437 +
.../uk/ac/man/bioinf/module/ModuleException.html | 350 +
.../ac/man/bioinf/module/ModuleExceptionType.html | 342 +
.../man/bioinf/module/ModuleFactoryInstance.html | 471 ++
.../uk/ac/man/bioinf/module/ModuleIdentifier.html | 262 +
.../ac/man/bioinf/module/ModuleIdentifierList.html | 454 ++
.../uk/ac/man/bioinf/module/ModuleList.html | 453 ++
.../man/bioinf/module/ModuleStorageStructure.html | 478 ++
.../ac/man/bioinf/module/NoSuchRequiredModule.html | 270 +
.../uk/ac/man/bioinf/module/NullModuleFactory.html | 578 ++
.../uk/ac/man/bioinf/module/package-frame.html | 78 +
.../uk/ac/man/bioinf/module/package-summary.html | 245 +
.../uk/ac/man/bioinf/module/package-tree.html | 152 +
doc/javadoc/uk/ac/man/bioinf/package-frame.html | 32 +
doc/javadoc/uk/ac/man/bioinf/package-summary.html | 137 +
doc/javadoc/uk/ac/man/bioinf/package-tree.html | 132 +
.../bioinf/sequence/AbstractEditableSequence.html | 550 ++
.../bioinf/sequence/AbstractMutableSequence.html | 436 +
.../ac/man/bioinf/sequence/AbstractSequence.html | 484 ++
.../sequence/ComplexEditableGappedSequence.html | 236 +
.../bioinf/sequence/DefaultEditableSequence.html | 506 ++
.../uk/ac/man/bioinf/sequence/DefaultSequence.html | 385 +
.../ac/man/bioinf/sequence/EditableSequence.html | 420 +
doc/javadoc/uk/ac/man/bioinf/sequence/Element.html | 225 +
.../uk/ac/man/bioinf/sequence/EmptySequence.html | 437 +
.../sequence/InvalidSequenceTypeException.html | 240 +
.../uk/ac/man/bioinf/sequence/MutableSequence.html | 219 +
.../sequence/NoSuchSequenceElementException.html | 286 +
doc/javadoc/uk/ac/man/bioinf/sequence/Residue.html | 198 +
.../uk/ac/man/bioinf/sequence/Sequence.html | 391 +
.../ac/man/bioinf/sequence/SequenceException.html | 238 +
.../uk/ac/man/bioinf/sequence/SequenceFactory.html | 364 +
.../uk/ac/man/bioinf/sequence/SequenceType.html | 413 +
.../uk/ac/man/bioinf/sequence/Sequences.html | 667 ++
.../sequence/alignment/AbstractGappedSequence.html | 563 ++
.../alignment/AbstractSequenceAlignment.html | 807 ++
.../bioinf/sequence/alignment/AlignmentColumn.html | 363 +
.../sequence/alignment/DefaultGappedSequence.html | 777 ++
.../alignment/DefaultSequenceAlignment.html | 673 ++
.../sequence/alignment/EmptyGappedSequence.html | 871 ++
.../sequence/alignment/EmptySequenceAlignment.html | 855 ++
.../uk/ac/man/bioinf/sequence/alignment/Gap.html | 307 +
.../bioinf/sequence/alignment/GappedSequence.html | 556 ++
.../alignment/NoGapAtThisPositionException.html | 328 +
.../alignment/NoSuchSequenceException.html | 287 +
.../sequence/alignment/SequenceAlignment.html | 554 ++
.../alignment/SingleSequenceAlignment.html | 300 +
.../sequence/alignment/event/AlignmentEvent.html | 363 +
.../alignment/event/AlignmentEventProvider.html | 284 +
.../alignment/event/AlignmentEventType.html | 353 +
.../alignment/event/AlignmentListener.html | 225 +
.../alignment/event/AlignmentListenerSupport.html | 368 +
.../alignment/event/AlignmentVetoException.html | 276 +
.../alignment/event/VetoableAlignmentEvent.html | 286 +
.../alignment/event/VetoableAlignmentListener.html | 240 +
.../sequence/alignment/event/package-frame.html | 64 +
.../sequence/alignment/event/package-summary.html | 205 +
.../sequence/alignment/event/package-tree.html | 151 +
.../bioinf/sequence/alignment/package-frame.html | 74 +
.../bioinf/sequence/alignment/package-summary.html | 237 +
.../bioinf/sequence/alignment/package-tree.html | 185 +
.../sequence/complex/AbstractComplexSequence.html | 566 ++
.../complex/AbstractComplexSequenceType.html | 408 +
.../bioinf/sequence/complex/ComplexElement.html | 273 +
.../sequence/complex/ComplexElementFactory.html | 376 +
.../complex/ComplexElementFactoryInterface.html | 274 +
.../bioinf/sequence/complex/ComplexSequence.html | 355 +
.../sequence/complex/ComplexSequenceType.html | 317 +
.../sequence/complex/DefaultComplexElement.html | 346 +
.../sequence/complex/DefaultComplexSequence.html | 450 ++
.../complex/DefaultComplexSequenceType.html | 604 ++
.../complex/DefaultGappedComplexSequence.html | 910 +++
.../sequence/complex/GappedComplexSequence.html | 231 +
.../complex/HardModificationSetFactory.html | 326 +
.../IllegalDuplicateModificationException.html | 238 +
.../man/bioinf/sequence/complex/Methylation.html | 240 +
.../man/bioinf/sequence/complex/Modification.html | 233 +
.../sequence/complex/ModificationFactory.html | 273 +
.../complex/ModificationSetFactoryInterface.html | 273 +
.../complex/NoSuchModificationException.html | 238 +
.../sequence/complex/SingletonModification.html | 258 +
.../complex/WeakModificationSetFactory.html | 326 +
.../man/bioinf/sequence/complex/package-frame.html | 90 +
.../bioinf/sequence/complex/package-summary.html | 314 +
.../man/bioinf/sequence/complex/package-tree.html | 192 +
.../man/bioinf/sequence/event/SequenceEvent.html | 387 +
.../sequence/event/SequenceEventProvider.html | 284 +
.../bioinf/sequence/event/SequenceEventType.html | 354 +
.../bioinf/sequence/event/SequenceListener.html | 224 +
.../sequence/event/SequenceListenerSupport.html | 391 +
.../sequence/event/SequenceVetoException.html | 276 +
.../sequence/event/VetoableSequenceEvent.html | 285 +
.../sequence/event/VetoableSequenceListener.html | 246 +
.../man/bioinf/sequence/event/package-frame.html | 64 +
.../man/bioinf/sequence/event/package-summary.html | 205 +
.../ac/man/bioinf/sequence/event/package-tree.html | 153 +
.../sequence/geom/SequenceAlignmentDimension.html | 427 +
.../sequence/geom/SequenceAlignmentPoint.html | 571 ++
.../sequence/geom/SequenceAlignmentRectangle.html | 830 ++
.../sequence/geom/SequenceAlignmentShape.html | 220 +
.../ac/man/bioinf/sequence/geom/package-frame.html | 47 +
.../man/bioinf/sequence/geom/package-summary.html | 165 +
.../ac/man/bioinf/sequence/geom/package-tree.html | 139 +
.../group/AbstractGappedSequenceGroup.html | 278 +
.../sequence/group/DefaultGappedSequenceGroup.html | 444 ++
.../bioinf/sequence/group/GappedSequenceGroup.html | 237 +
.../sequence/group/GroupSequenceAlignment.html | 1071 +++
.../man/bioinf/sequence/group/SequenceGroup.html | 355 +
.../man/bioinf/sequence/group/package-frame.html | 49 +
.../man/bioinf/sequence/group/package-summary.html | 175 +
.../ac/man/bioinf/sequence/group/package-tree.html | 143 +
.../sequence/identifier/AbstractIdentifier.html | 300 +
.../sequence/identifier/DatabaseIdentifier.html | 313 +
.../man/bioinf/sequence/identifier/FileSource.html | 284 +
.../bioinf/sequence/identifier/Identifiable.html | 217 +
.../man/bioinf/sequence/identifier/Identifier.html | 262 +
.../identifier/MalformedAccessionException.html | 242 +
.../bioinf/sequence/identifier/NoIdentifier.html | 328 +
.../man/bioinf/sequence/identifier/NoSource.html | 262 +
.../bioinf/sequence/identifier/ReaderSource.html | 238 +
.../bioinf/sequence/identifier/SequenceSource.html | 221 +
.../sequence/identifier/SimpleIdentifier.html | 286 +
.../bioinf/sequence/identifier/SimpleSource.html | 266 +
.../ac/man/bioinf/sequence/identifier/Source.html | 221 +
.../sequence/identifier/StreamSequenceSource.html | 294 +
.../sequence/identifier/SwissProtIdentifier.html | 283 +
.../sequence/identifier/URLSequenceSource.html | 293 +
.../bioinf/sequence/identifier/package-frame.html | 80 +
.../sequence/identifier/package-summary.html | 260 +
.../bioinf/sequence/identifier/package-tree.html | 160 +
.../uk/ac/man/bioinf/sequence/package-frame.html | 84 +
.../uk/ac/man/bioinf/sequence/package-summary.html | 288 +
.../uk/ac/man/bioinf/sequence/package-tree.html | 187 +
.../test/ComplexElementAndModificationTest.html | 252 +
.../bioinf/sequence/test/ComplexSequenceTest.html | 273 +
.../bioinf/sequence/test/EditableSequenceTest.html | 271 +
.../bioinf/sequence/test/GappableSequenceTest.html | 271 +
.../bioinf/sequence/test/GappedSequenceTest.html | 254 +
.../sequence/test/SequenceAlignmentTest.html | 338 +
.../bioinf/sequence/test/SequenceColumnTest.html | 254 +
.../bioinf/sequence/test/SequenceFactoryTest.html | 252 +
.../ac/man/bioinf/sequence/test/SequencesTest.html | 252 +
.../ac/man/bioinf/sequence/test/package-frame.html | 48 +
.../man/bioinf/sequence/test/package-summary.html | 193 +
.../ac/man/bioinf/sequence/test/package-tree.html | 133 +
.../man/bioinf/sequence/types/AbstractElement.html | 323 +
.../types/AbstractEnumeratedSequenceType.html | 335 +
.../sequence/types/AbstractSequenceType.html | 490 ++
.../uk/ac/man/bioinf/sequence/types/AminoAcid.html | 760 ++
.../man/bioinf/sequence/types/DNANucleotide.html | 394 +
.../ac/man/bioinf/sequence/types/DNAResidue.html | 195 +
.../man/bioinf/sequence/types/DNASequenceType.html | 292 +
.../bioinf/sequence/types/EmptySequenceType.html | 512 ++
.../bioinf/sequence/types/NucleotideResidue.html | 198 +
.../man/bioinf/sequence/types/ProteinResidue.html | 195 +
.../bioinf/sequence/types/ProteinSequenceType.html | 290 +
.../man/bioinf/sequence/types/RNANucleotide.html | 396 +
.../ac/man/bioinf/sequence/types/RNAResidue.html | 195 +
.../man/bioinf/sequence/types/RNASequenceType.html | 317 +
.../man/bioinf/sequence/types/package-frame.html | 67 +
.../man/bioinf/sequence/types/package-summary.html | 234 +
.../ac/man/bioinf/sequence/types/package-tree.html | 156 +
.../util/AbstractEnumeration.ElementIterator.html | 292 +
.../uk/ac/man/bioinf/util/AbstractEnumeration.html | 415 +
.../uk/ac/man/bioinf/util/ArrayManipulation.html | 297 +
doc/javadoc/uk/ac/man/bioinf/util/Changeable.html | 233 +
.../uk/ac/man/bioinf/util/ChangeableEvent.html | 250 +
.../uk/ac/man/bioinf/util/ChangeableListener.html | 211 +
.../man/bioinf/util/ChangeableListenerSupport.html | 293 +
.../uk/ac/man/bioinf/util/CollectionPrinter.html | 271 +
doc/javadoc/uk/ac/man/bioinf/util/Direction.html | 315 +
.../uk/ac/man/bioinf/util/ExceptionHandler.html | 212 +
.../uk/ac/man/bioinf/util/IntArrayList.html | 651 ++
.../ac/man/bioinf/util/PackageResourceAdapter.html | 315 +
.../uk/ac/man/bioinf/util/ResourceAdapter.html | 487 ++
.../util/SequenceAlignmentToChangeableAdaptor.html | 350 +
.../uk/ac/man/bioinf/util/package-frame.html | 67 +
.../uk/ac/man/bioinf/util/package-summary.html | 229 +
.../uk/ac/man/bioinf/util/package-tree.html | 148 +
doc/sequence/alignment.sgml | 136 +
doc/sequence/conclusions.sgml | 19 +
doc/sequence/elementandtype.sgml | 174 +
doc/sequence/implementation.sgml | 172 +
doc/sequence/intro.sgml | 32 +
doc/sequence/requirements.sgml | 197 +
doc/sequence/seqimpl.sgml | 315 +
doc/sequence/sequence.sgml | 74 +
lib/app_support.jar | Bin 0 -> 17154 bytes
lib/cinema.jar | Bin 0 -> 190247 bytes
lib/emboss.jar | Bin 0 -> 22 bytes
lib/ext/gnu-getopt.jar | Bin 0 -> 12530 bytes
lib/ext/jakarta-regexp.jar | Bin 0 -> 29871 bytes
lib/ext/xerces.jar | Bin 0 -> 1867525 bytes
lib/graph.jar | Bin 0 -> 22 bytes
lib/gui.jar | Bin 0 -> 92040 bytes
lib/mxc.jar | Bin 0 -> 25118 bytes
lib/sequence.jar | Bin 0 -> 124579 bytes
lib/src.jar | Bin 0 -> 753592 bytes
lib/util.jar | Bin 0 -> 21613 bytes
src/uk/ac/man/bioinf/Y.java | 47 +
.../analysis/consensus/ConsensusCalculator.java | 78 +
.../analysis/consensus/ConsensusIdentifier.java | 81 +
.../analysis/consensus/ConsensusSequence.java | 70 +
.../consensus/DefaultConsensusSequence.java | 244 +
.../analysis/consensus/PercentageIDConsensus.java | 129 +
.../consensus/ThreadedConsensusSequence.java | 129 +
.../analysis/misc/PercentageIDCalculator.java | 206 +
.../misc/PercentageIDCalculatorManager.java | 84 +
.../regexp/GappedSequenceCharacterIterator.java | 87 +
.../analysis/regexp/SequenceCharacterIterator.java | 90 +
src/uk/ac/man/bioinf/apps/cinema/Cinema.java | 180 +
src/uk/ac/man/bioinf/apps/cinema/CinemaBoot.java | 130 +
.../bioinf/apps/cinema/CinemaBootIdentifier.java | 76 +
.../ac/man/bioinf/apps/cinema/CinemaGuiModule.java | 167 +
src/uk/ac/man/bioinf/apps/cinema/CinemaModule.java | 224 +
.../apps/cinema/CinemaModuleFactoryInstance.java | 93 +
.../man/bioinf/apps/cinema/CinemaProperties.java | 70 +
src/uk/ac/man/bioinf/apps/cinema/CinemaShared.java | 48 +
.../bioinf/apps/cinema/CinemaXMLParserFactory.java | 96 +
src/uk/ac/man/bioinf/apps/cinema/changes.html | 454 ++
.../cinema/color/AminoAcidColorMapMetaData.java | 156 +
.../apps/cinema/color/CinemaColorFactory.java | 170 +
.../apps/cinema/color/CinemaColorIdentifier.java | 77 +
.../apps/cinema/color/CinemaColorSelector.java | 158 +
.../bioinf/apps/cinema/color/ColorMapMetaData.java | 93 +
.../cinema/color/ColormapColorMapMetaData.java | 145 +
.../apps/cinema/color/DefaultColorMapMetaData.java | 145 +
.../apps/cinema/color/GrayScaleVariance.java | 77 +
.../InstancePerAlignmentColorMapMetaData.java | 92 +
.../apps/cinema/color/IntenseColorMapMetaData.java | 145 +
.../apps/cinema/color/Js_TestColorMapMetaData.java | 145 +
.../apps/cinema/color/NullColorMapMetaData.java | 84 +
.../cinema/color/PedanticColorMapMetaData.java | 145 +
.../PercentageIDVarianceColorMapMetaData.java | 102 +
.../apps/cinema/color/TaylorColorMapMetaData.java | 147 +
...readedPercentageIDVarianceColorMapMetaData.java | 119 +
.../cinema/color/VariableColorMapMetaData.java | 145 +
.../cinema/color/VariationsColorMapMetaData.java | 145 +
.../apps/cinema/color/WhiteColorMapMetaData.java | 86 +
.../apps/cinema/color/ZenecaColorMapMetaData.java | 145 +
.../apps/cinema/consensus/CinemaConsensus.java | 191 +
.../CinemaConsensusCalculatorMetaData.java | 67 +
.../cinema/consensus/CinemaConsensusDisplay.java | 287 +
.../consensus/CinemaConsensusIdentifier.java | 75 +
.../PercentageIDConsensusCalculatorMetaData.java | 105 +
...dedPercentageIDConsensusCalculatorMetaData.java | 98 +
.../cinema/core/AlignmentToListCellRenderer.java | 82 +
.../apps/cinema/core/AlignmentToListModel.java | 92 +
.../apps/cinema/core/CinemaActionProvider.java | 58 +
.../man/bioinf/apps/cinema/core/CinemaCoreGui.java | 297 +
.../apps/cinema/core/CinemaCoreIdentifier.java | 92 +
.../bioinf/apps/cinema/core/CinemaCoreView.java | 301 +
.../cinema/core/CinemaFramedActionProvider.java | 60 +
.../ac/man/bioinf/apps/cinema/core/CinemaGo.java | 119 +
.../bioinf/apps/cinema/core/CinemaMenuSystem.java | 104 +
.../cinema/core/CinemaModuleCoreIdentifier.java | 74 +
.../apps/cinema/core/CinemaSequenceMenu.java | 110 +
.../apps/cinema/core/CinemaSystemEvents.java | 133 +
.../apps/cinema/core/VersionInformation.java | 166 +
.../apps/cinema/core/test/CinemaTestLaunch.java | 328 +
.../cinema/core/test/CinemaTestModuleLaunch.java | 82 +
.../apps/cinema/group/CinemaAnchorManager.java | 210 +
.../man/bioinf/apps/cinema/group/CinemaGroup.java | 137 +
.../bioinf/apps/cinema/group/CinemaGroupFrame.java | 487 ++
.../apps/cinema/group/CinemaGroupIdentifier.java | 73 +
.../apps/cinema/group/CinemaGroupManager.java | 278 +
.../apps/cinema/group/CinemaGroupModule.java | 387 +
.../apps/cinema/io/AbstractSequenceInput.java | 284 +
...bstractSequenceInputParserExceptionHandler.java | 103 +
.../apps/cinema/io/AbstractSequenceOutput.java | 188 +
.../io/AbstractSequenceParserExceptionHandler.java | 106 +
.../apps/cinema/io/CinemaCommandLineParser.java | 204 +
.../io/CinemaCommandLineParserIdentifier.java | 73 +
.../bioinf/apps/cinema/io/FileSequenceInput.java | 238 +
.../FileSequenceInputParserExceptionHandler.java | 76 +
.../bioinf/apps/cinema/io/FileSequenceOutput.java | 167 +
.../io/FileSequenceParserExceptionHandler.java | 79 +
.../cinema/io/SequenceInputModuleIdentifier.java | 84 +
.../cinema/io/SequenceOutputModuleIdentifier.java | 78 +
.../bioinf/apps/cinema/motif/CinemaMotifFrame.java | 748 ++
.../apps/cinema/motif/CinemaMotifIdentifier.java | 68 +
.../apps/cinema/motif/CinemaMotifModule.java | 113 +
.../cinema/motif/NamedAlignmentSelectionModel.java | 426 +
.../apps/cinema/resources/CinemaResources.java | 211 +
.../man/bioinf/apps/cinema/resources/MakeCinemaJar | 5 +
.../bioinf/apps/cinema/resources/build-install.xml | 133 +
.../apps/cinema/resources/cinema-calculate.xml | 69 +
.../apps/cinema/resources/cinema-identifiers.xml | 81 +
.../man/bioinf/apps/cinema/resources/cinema-io.xml | 82 +
.../bioinf/apps/cinema/resources/cinema-main.xml | 96 +
.../apps/cinema/resources/cinema-manipulate.xml | 38 +
.../bioinf/apps/cinema/resources/cinema-menu.xml | 117 +
.../bioinf/apps/cinema/resources/cinema-shared.xml | 66 +
.../bioinf/apps/cinema/resources/cinema-view.xml | 99 +
.../ac/man/bioinf/apps/cinema/resources/cinema.jpg | Bin 0 -> 10954 bytes
.../ac/man/bioinf/apps/cinema/resources/cinema.xml | 252 +
.../bioinf/apps/cinema/resources/color-convert.el | 282 +
.../man/bioinf/apps/cinema/resources/manifest.mf | 1 +
.../ac/man/bioinf/apps/cinema/resources/module.dtd | 127 +
.../ac/man/bioinf/apps/cinema/resources/shared.xml | 77 +
.../man/bioinf/apps/cinema/shared/CinemaDebug.java | 328 +
.../apps/cinema/shared/CinemaSharedIdentifier.java | 74 +
.../apps/cinema/shared/CinemaSharedQuitExit.java | 150 +
.../bioinf/apps/cinema/shared/CinemaSplash.java | 138 +
.../apps/cinema/utils/CinemaAlignmentFrame.java | 329 +
.../man/bioinf/apps/cinema/utils/CinemaDebug.java | 324 +
.../CinemaFileOptionableExceptionHandler.java | 139 +
.../apps/cinema/utils/CinemaFilePersist.java | 105 +
.../bioinf/apps/cinema/utils/CinemaInvoker.java | 107 +
.../apps/cinema/utils/CinemaMenuBuilder.java | 181 +
.../utils/CinemaMultipleConsensusViewer.java | 205 +
.../bioinf/apps/cinema/utils/CinemaPersist.java | 75 +
.../man/bioinf/apps/cinema/utils/CinemaRegexp.java | 166 +
.../apps/cinema/utils/CinemaResizeElements.java | 385 +
.../apps/cinema/utils/CinemaSlaveViewerModule.java | 126 +
.../apps/cinema/utils/CinemaStatusInformation.java | 181 +
.../apps/cinema/utils/CinemaUtilityIdentifier.java | 135 +
.../utils/ConsensusPercentageIDColorMap.java | 179 +
.../apps/commandline/CalculatePercentageID.java | 75 +
.../CheckMotifLocationAgainstPrints.java | 282 +
.../apps/commandline/GappedSequenceSearch.java | 100 +
.../bioinf/apps/commandline/SequenceSearch.java | 102 +
src/uk/ac/man/bioinf/apps/invoker/AnonInvoker.java | 105 +
src/uk/ac/man/bioinf/apps/invoker/Invoker.java | 174 +
.../InvokerInternalEventQueueException.java | 70 +
.../bioinf/apps/invoker/InvokerInternalQueue.java | 315 +
.../invoker/InvokerInternalQueueException.java | 61 +
.../bioinf/apps/invoker/InvokerThreadManager.java | 78 +
.../apps/optionable/FileSaveableOptions.java | 155 +
.../bioinf/apps/optionable/NullOptionHandler.java | 81 +
.../man/bioinf/apps/optionable/OptionHandler.java | 110 +
.../ac/man/bioinf/apps/optionable/Optionable.java | 101 +
.../optionable/OptionableExceptionHandler.class | Bin 0 -> 360 bytes
.../optionable/OptionableExceptionHandler.java | 87 +
.../OptionableSourceNotFoundException.class | Bin 0 -> 329 bytes
.../OptionableSourceNotFoundException.java | 48 +
.../apps/optionable/OptionableStateException.java | 66 +
.../bioinf/apps/optionable/SaveableOptions.java | 275 +
.../man/bioinf/apps/systemevents/SystemEvent.java | 88 +
.../apps/systemevents/SystemEventOption.java | 89 +
.../apps/systemevents/SystemEventProducer.java | 65 +
.../apps/systemevents/SystemEventSupport.java | 172 +
.../bioinf/apps/systemevents/SystemListener.java | 132 +
.../apps/systemevents/SystemVetoException.java | 76 +
src/uk/ac/man/bioinf/apps/xml/ConfigNode.java | 131 +
.../ac/man/bioinf/apps/xml/DefaultXMLParser.java | 119 +
.../ac/man/bioinf/apps/xml/XMLBootIdentifier.java | 69 +
src/uk/ac/man/bioinf/apps/xml/XMLBootModule.java | 530 ++
.../man/bioinf/apps/xml/XMLBootParserListener.java | 276 +
src/uk/ac/man/bioinf/apps/xml/XMLModule.java | 94 +
.../ac/man/bioinf/apps/xml/XMLParserFactory.java | 63 +
.../man/bioinf/apps/xml/test/XMLLoadingTest.java | 116 +
.../ac/man/bioinf/apps/xml/test/XMLStartTest.java | 67 +
src/uk/ac/man/bioinf/bin/cinema | 84 +
src/uk/ac/man/bioinf/bin/cinema.cygwin | 81 +
src/uk/ac/man/bioinf/bin/cinema.pl | 78 +
src/uk/ac/man/bioinf/build.xml | 333 +
src/uk/ac/man/bioinf/build/cinema-build.xml | 180 +
src/uk/ac/man/bioinf/build/manifest | 2 +
src/uk/ac/man/bioinf/build/package-list | 59 +
src/uk/ac/man/bioinf/build/project-ext.dtd | 34 +
src/uk/ac/man/bioinf/build/project.dtd | 273 +
.../database/fetch/ExpasySequenceRetriever.java | 115 +
.../database/fetch/FetchSequenceBySwissProtID.java | 63 +
.../bioinf/database/fetch/SequenceRetriever.java | 68 +
src/uk/ac/man/bioinf/debug/AbstractDebug.java | 92 +
src/uk/ac/man/bioinf/debug/Debug.java | 210 +
src/uk/ac/man/bioinf/debug/DebugInterface.java | 79 +
src/uk/ac/man/bioinf/debug/DebugMultiplexer.java | 341 +
src/uk/ac/man/bioinf/debug/DefaultDebug.java | 77 +
src/uk/ac/man/bioinf/debug/DefaultFileDebug.java | 85 +
src/uk/ac/man/bioinf/debug/NullDebug.java | 67 +
src/uk/ac/man/bioinf/gui/color/ColorGenerator.java | 93 +
src/uk/ac/man/bioinf/gui/color/ColorList.java | 126 +
src/uk/ac/man/bioinf/gui/color/ColorMap.java | 87 +
.../ac/man/bioinf/gui/color/ColorMapException.java | 60 +
src/uk/ac/man/bioinf/gui/color/ColorStore.java | 146 +
.../man/bioinf/gui/color/DoubleArrayColorMap.java | 106 +
.../gui/color/IndividualElementColorMap.java | 143 +
.../gui/color/PercentIDVarianceColorMap.java | 145 +
src/uk/ac/man/bioinf/gui/color/SingleColorMap.java | 94 +
.../man/bioinf/gui/color/ThreadableColorMap.java | 64 +
.../ac/man/bioinf/gui/color/ThreadedColorMap.java | 175 +
src/uk/ac/man/bioinf/gui/misc/ChunkyListModel.java | 362 +
.../man/bioinf/gui/misc/SwappingListBasicUI.java | 145 +
.../bioinf/gui/optionable/OptionableJFrame.java | 288 +
.../gui/optionable/OptionableJSplitPane.java | 160 +
.../ac/man/bioinf/gui/util/ApplicationFrame.java | 377 +
.../ac/man/bioinf/gui/util/PopUpHtmlDisplay.java | 61 +
src/uk/ac/man/bioinf/gui/util/SwingWorker.java | 147 +
src/uk/ac/man/bioinf/gui/util/TripletPanel.java | 121 +
.../ac/man/bioinf/gui/util/forms/DecimalField.java | 73 +
.../bioinf/gui/util/forms/FormattedDocument.java | 70 +
.../ac/man/bioinf/gui/util/forms/IntegerField.java | 97 +
.../man/bioinf/gui/util/forms/PasswordDialog.java | 139 +
.../man/bioinf/gui/util/forms/ValidatedForm.java | 414 +
.../bioinf/gui/util/forms/WholeNumberField.java | 82 +
.../bioinf/gui/viewer/AlignmentSelectionModel.java | 151 +
.../gui/viewer/AlignmentSelectionRenderer.java | 63 +
.../gui/viewer/AlignmentViewerCellRenderer.java | 97 +
.../BorderFastAlignmentViewerCellRenderer.java | 103 +
.../bioinf/gui/viewer/ButtonViewerPopupMenu.java | 99 +
.../ColorFastAlignmentViewerCellRenderer.java | 94 +
.../CursorLessFastAlignmentViewerCellRenderer.java | 87 +
.../viewer/DefaultAlignmentSelectionRenderer.java | 71 +
.../viewer/DefaultAlignmentViewerCellRenderer.java | 135 +
.../DefaultFastAlignmentViewerCellRenderer.java | 131 +
.../bioinf/gui/viewer/DefaultSequenceCursor.java | 115 +
.../viewer/FastAlignmentViewerCellRenderer.java | 104 +
src/uk/ac/man/bioinf/gui/viewer/Install.java | 119 +
.../gui/viewer/InvertedScrollPaneLayout.java | 327 +
.../bioinf/gui/viewer/JAlignmentButtonPanel.java | 269 +
.../ac/man/bioinf/gui/viewer/JAlignmentRuler.java | 248 +
.../ac/man/bioinf/gui/viewer/JAlignmentViewer.java | 900 +++
.../man/bioinf/gui/viewer/JChangedScrollPane.java | 83 +
.../man/bioinf/gui/viewer/JLayableScrollPane.java | 89 +
...MultiplexerFastAlignmentViewerCellRenderer.java | 180 +
.../gui/viewer/NullAlignmentSelectionModel.java | 137 +
.../bioinf/gui/viewer/PrintableAlignmentPanel.java | 65 +
.../gui/viewer/PrintableJAlignmentViewer.java | 130 +
.../man/bioinf/gui/viewer/ReadonlyException.java | 96 +
.../ac/man/bioinf/gui/viewer/SequenceCursor.java | 97 +
.../gui/viewer/SingleAlignmentSelectionModel.java | 191 +
.../TextFastAlignmentViewerCellRenderer.java | 103 +
.../gui/viewer/event/AlignmentSelectionEvent.java | 90 +
.../viewer/event/AlignmentSelectionListener.java | 63 +
.../event/AlignmentSelectionListenerSupport.java | 83 +
.../gui/viewer/event/ChangeListenerSupport.java | 86 +
.../bioinf/gui/viewer/plaf/AlignmentRulerUI.java | 62 +
.../bioinf/gui/viewer/plaf/AlignmentViewerUI.java | 90 +
.../gui/viewer/plaf/BasicAlignmentRulerUI.java | 181 +
.../gui/viewer/plaf/BasicAlignmentViewerUI.java | 1061 +++
.../gui/viewer/plaf/MetalAlignmentViewerUI.java | 61 +
.../gui/viewer/test/AlignmentViewerTest.java | 355 +
.../bioinf/gui/viewer/test/BasicWindowMonitor.java | 30 +
.../bioinf/gui/viewer/test/ButtonPanelTest.java | 87 +
.../viewer/test/CellRendererPaneReplacement.java | 115 +
src/uk/ac/man/bioinf/gui/viewer/test/Makefile | 73 +
.../gui/viewer/test/SingleSelectionModelTest.java | 71 +
.../man/bioinf/gui/viewer/test/SliderExample.java | 56 +
src/uk/ac/man/bioinf/io/AlignmentInputParser.java | 109 +
src/uk/ac/man/bioinf/io/AlignmentOutputParser.java | 89 +
.../bioinf/io/DefaultParserExceptionHandler.java | 73 +
.../io/InvalidSequenceTypeParserException.java | 96 +
src/uk/ac/man/bioinf/io/NarrowedInputStream.java | 222 +
.../man/bioinf/io/NullParserExceptionHandler.java | 83 +
src/uk/ac/man/bioinf/io/ParserException.java | 137 +
.../ac/man/bioinf/io/ParserExceptionHandler.java | 71 +
src/uk/ac/man/bioinf/io/SequenceInputParser.java | 66 +
.../ac/man/bioinf/io/SequenceWriterException.java | 62 +
.../ac/man/bioinf/io/UnknownElementException.java | 94 +
.../AbstractProteinAlignmentInputParser.java | 148 +
.../AbstractProteinSequenceInputParser.java | 115 +
.../man/bioinf/io/parsers/FastaSequenceParser.java | 118 +
.../ac/man/bioinf/io/parsers/MotProteinParser.java | 122 +
.../io/parsers/PIRProteinAlignmentParser.java | 299 +
.../man/bioinf/io/test/AlignmentParserIOTest.java | 115 +
.../bioinf/io/test/AlignmentParserInputTest.java | 101 +
.../module/AbstractEnumeratedModuleIdentifier.java | 158 +
.../ac/man/bioinf/module/DefaultModuleContext.java | 74 +
.../module/DefaultModuleFactoryInstance.java | 317 +
.../man/bioinf/module/GenericModuleIdentifier.java | 96 +
src/uk/ac/man/bioinf/module/Module.java | 298 +
src/uk/ac/man/bioinf/module/ModuleContext.java | 156 +
src/uk/ac/man/bioinf/module/ModuleException.java | 104 +
.../ac/man/bioinf/module/ModuleExceptionType.java | 97 +
.../man/bioinf/module/ModuleFactoryInstance.java | 182 +
src/uk/ac/man/bioinf/module/ModuleIdentifier.java | 82 +
.../ac/man/bioinf/module/ModuleIdentifierList.java | 180 +
src/uk/ac/man/bioinf/module/ModuleList.java | 177 +
.../man/bioinf/module/ModuleStorageStructure.java | 197 +
.../ac/man/bioinf/module/NoSuchRequiredModule.java | 69 +
src/uk/ac/man/bioinf/module/NullModuleFactory.java | 150 +
.../bioinf/sequence/AbstractEditableSequence.java | 173 +
.../bioinf/sequence/AbstractMutableSequence.java | 114 +
.../ac/man/bioinf/sequence/AbstractSequence.java | 170 +
.../sequence/ComplexEditableGappedSequence.java | 63 +
.../bioinf/sequence/DefaultEditableSequence.java | 149 +
src/uk/ac/man/bioinf/sequence/DefaultSequence.java | 134 +
.../ac/man/bioinf/sequence/EditableSequence.java | 125 +
src/uk/ac/man/bioinf/sequence/Element.java | 71 +
src/uk/ac/man/bioinf/sequence/EmptySequence.java | 114 +
.../sequence/InvalidSequenceTypeException.java | 64 +
src/uk/ac/man/bioinf/sequence/MutableSequence.java | 69 +
.../sequence/NoSuchSequenceElementException.java | 76 +
src/uk/ac/man/bioinf/sequence/Residue.java | 58 +
src/uk/ac/man/bioinf/sequence/Sequence.java | 127 +
.../ac/man/bioinf/sequence/SequenceException.java | 63 +
src/uk/ac/man/bioinf/sequence/SequenceFactory.java | 169 +
src/uk/ac/man/bioinf/sequence/SequenceType.java | 153 +
src/uk/ac/man/bioinf/sequence/Sequences.java | 339 +
.../sequence/alignment/AbstractGappedSequence.java | 201 +
.../alignment/AbstractSequenceAlignment.java | 471 ++
.../bioinf/sequence/alignment/AlignmentColumn.java | 142 +
.../sequence/alignment/DefaultGappedSequence.java | 394 +
.../alignment/DefaultSequenceAlignment.java | 516 ++
.../sequence/alignment/EmptyGappedSequence.java | 202 +
.../sequence/alignment/EmptySequenceAlignment.java | 234 +
src/uk/ac/man/bioinf/sequence/alignment/Gap.java | 85 +
.../bioinf/sequence/alignment/GappedSequence.java | 148 +
.../alignment/NoGapAtThisPositionException.java | 99 +
.../alignment/NoSuchSequenceException.java | 77 +
.../sequence/alignment/SequenceAlignment.java | 227 +
.../alignment/SingleSequenceAlignment.java | 96 +
.../sequence/alignment/event/AlignmentEvent.java | 130 +
.../alignment/event/AlignmentEventProvider.java | 88 +
.../alignment/event/AlignmentEventType.java | 116 +
.../alignment/event/AlignmentListener.java | 69 +
.../alignment/event/AlignmentListenerSupport.java | 158 +
.../alignment/event/AlignmentVetoException.java | 83 +
.../alignment/event/VetoableAlignmentEvent.java | 72 +
.../alignment/event/VetoableAlignmentListener.java | 76 +
.../sequence/complex/AbstractComplexSequence.java | 178 +
.../complex/AbstractComplexSequenceType.java | 114 +
.../sequence/complex/AbstractModification.java | 79 +
.../bioinf/sequence/complex/ComplexElement.java | 63 +
.../sequence/complex/ComplexElementFactory.java | 125 +
.../complex/ComplexElementFactoryInterface.java | 68 +
.../bioinf/sequence/complex/ComplexSequence.java | 87 +
.../sequence/complex/ComplexSequenceType.java | 97 +
.../sequence/complex/DefaultComplexElement.java | 168 +
.../sequence/complex/DefaultComplexSequence.java | 141 +
.../complex/DefaultComplexSequenceType.java | 143 +
.../complex/DefaultGappedComplexSequence.java | 267 +
.../sequence/complex/GappedComplexSequence.java | 59 +
.../sequence/complex/GenericModification.java | 82 +
.../complex/HardComplexElementFactory.java | 144 +
.../complex/HardModificationSetFactory.java | 131 +
.../IllegalDuplicateModificationException.java | 62 +
.../man/bioinf/sequence/complex/Methylation.java | 68 +
.../man/bioinf/sequence/complex/Modification.java | 63 +
.../sequence/complex/ModificationFactory.java | 105 +
.../bioinf/sequence/complex/ModificationSet.java | 143 +
.../sequence/complex/ModificationSetFactory.java | 89 +
.../complex/ModificationSetFactoryInterface.java | 68 +
.../complex/NoSuchModificationException.java | 61 +
.../sequence/complex/SingletonModification.java | 69 +
.../complex/WeakComplexElementFactory.java | 188 +
.../complex/WeakModificationSetFactory.java | 136 +
src/uk/ac/man/bioinf/sequence/complex/package.html | 13 +
.../man/bioinf/sequence/event/SequenceEvent.java | 132 +
.../sequence/event/SequenceEventProvider.java | 90 +
.../bioinf/sequence/event/SequenceEventType.java | 82 +
.../bioinf/sequence/event/SequenceListener.java | 66 +
.../sequence/event/SequenceListenerSupport.java | 183 +
.../sequence/event/SequenceVetoException.java | 85 +
.../sequence/event/VetoableSequenceEvent.java | 72 +
.../sequence/event/VetoableSequenceListener.java | 73 +
.../sequence/geom/SequenceAlignmentDimension.java | 169 +
.../sequence/geom/SequenceAlignmentPoint.java | 250 +
.../sequence/geom/SequenceAlignmentRectangle.java | 379 +
.../sequence/geom/SequenceAlignmentShape.java | 64 +
.../group/AbstractGappedSequenceGroup.java | 78 +
.../sequence/group/DefaultGappedSequenceGroup.java | 137 +
.../bioinf/sequence/group/GappedSequenceGroup.java | 67 +
.../sequence/group/GroupSequenceAlignment.java | 406 +
.../man/bioinf/sequence/group/SequenceGroup.java | 115 +
.../sequence/identifier/AbstractIdentifier.java | 80 +
.../sequence/identifier/DatabaseIdentifier.java | 82 +
.../man/bioinf/sequence/identifier/FileSource.java | 75 +
.../bioinf/sequence/identifier/Identifiable.java | 63 +
.../man/bioinf/sequence/identifier/Identifier.java | 81 +
.../identifier/MalformedAccessionException.java | 64 +
.../bioinf/sequence/identifier/NoIdentifier.java | 92 +
.../man/bioinf/sequence/identifier/NoSource.java | 67 +
.../bioinf/sequence/identifier/ReaderSource.java | 69 +
.../bioinf/sequence/identifier/SequenceSource.java | 68 +
.../sequence/identifier/SimpleIdentifier.java | 81 +
.../bioinf/sequence/identifier/SimpleSource.java | 70 +
.../ac/man/bioinf/sequence/identifier/Source.java | 73 +
.../sequence/identifier/StreamSequenceSource.java | 76 +
.../sequence/identifier/SwissProtIdentifier.java | 81 +
.../sequence/identifier/URLSequenceSource.java | 78 +
src/uk/ac/man/bioinf/sequence/package.html | 12 +
.../test/ComplexElementAndModificationTest.java | 256 +
.../bioinf/sequence/test/ComplexSequenceTest.java | 187 +
.../bioinf/sequence/test/EditableSequenceTest.java | 241 +
.../bioinf/sequence/test/GappableSequenceTest.java | 215 +
.../bioinf/sequence/test/GappedSequenceTest.java | 134 +
.../sequence/test/SequenceAlignmentTest.java | 246 +
.../bioinf/sequence/test/SequenceColumnTest.java | 79 +
.../bioinf/sequence/test/SequenceFactoryTest.java | 85 +
.../ac/man/bioinf/sequence/test/SequencesTest.java | 104 +
.../man/bioinf/sequence/types/AbstractElement.java | 102 +
.../types/AbstractEnumeratedSequenceType.java | 85 +
.../sequence/types/AbstractSequenceType.java | 168 +
src/uk/ac/man/bioinf/sequence/types/AminoAcid.java | 168 +
.../man/bioinf/sequence/types/DNANucleotide.java | 95 +
.../ac/man/bioinf/sequence/types/DNAResidue.java | 65 +
.../man/bioinf/sequence/types/DNASequenceType.java | 73 +
.../bioinf/sequence/types/EmptySequenceType.java | 115 +
.../bioinf/sequence/types/NucleotideResidue.java | 66 +
.../man/bioinf/sequence/types/ProteinResidue.java | 73 +
.../bioinf/sequence/types/ProteinSequenceType.java | 78 +
.../man/bioinf/sequence/types/RNANucleotide.java | 105 +
.../ac/man/bioinf/sequence/types/RNAResidue.java | 62 +
.../man/bioinf/sequence/types/RNASequenceType.java | 71 +
src/uk/ac/man/bioinf/util/AbstractEnumeration.java | 286 +
src/uk/ac/man/bioinf/util/ArrayManipulation.java | 106 +
src/uk/ac/man/bioinf/util/Changeable.java | 60 +
src/uk/ac/man/bioinf/util/ChangeableEvent.java | 62 +
src/uk/ac/man/bioinf/util/ChangeableListener.java | 59 +
.../man/bioinf/util/ChangeableListenerSupport.java | 84 +
src/uk/ac/man/bioinf/util/CollectionPrinter.java | 86 +
src/uk/ac/man/bioinf/util/Direction.java | 68 +
src/uk/ac/man/bioinf/util/ExceptionHandler.java | 65 +
src/uk/ac/man/bioinf/util/IntArrayList.java | 347 +
.../ac/man/bioinf/util/PackageResourceAdapter.java | 55 +
src/uk/ac/man/bioinf/util/ResourceAdapter.java | 113 +
.../util/SequenceAlignmentToChangeableAdaptor.java | 93 +
1446 files changed, 238371 insertions(+)
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