[jalview] branch master updated (446e236 -> b42f7b5)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 8 08:36:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository jalview.
from 446e236 Introduced EDAM annotation for Jalview
new fbf9e2a replace new-upstream script with Files-Excluded
new ae517a4 Imported Upstream version 2.9+dfsg
new b42f7b5 v2.9, refresh patches, add testng
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
JalviewApplet.jpx | 150 +-
JalviewX.jpx | 94 +-
README | 2 +-
build.xml | 1329 ++--
debian/changelog | 7 +-
debian/control | 4 +-
debian/copyright | 10 +-
debian/new-upstream | 45 -
debian/patches/drop-lib | 100 +
debian/patches/encoding-fix | 11 +
debian/patches/mutilate-build-system.diff | 58 +-
debian/patches/newer-jmol-api.diff | 304 +-
debian/patches/newer-mime4j-api.diff | 8 +-
debian/patches/series | 4 +-
debian/patches/testng | 11 +
debian/watch | 4 +-
doc/AddingGroovySupport.html | 7 +-
doc/AnnotationPostAnalysis.txt | 59 +
doc/JalviewRNASupport.html | 84 +
doc/UnitTesting.html | 111 +
doc/biojsmsa-templates.html | 101 +
doc/building.html | 12 +-
doc/developing.html | 83 +-
doc/i18n.html | 96 +
doc/index.html | 307 +-
doc/newdmobj.html | 73 +-
help/help.hs | 104 +-
help/help.jhm | 56 +-
help/helpTOC.html | 45 +-
help/helpTOC.xml | 274 +-
help/html/Jalview_Logo.png | Bin 0 -> 15420 bytes
help/html/calculations/consensus.html | 73 +-
help/html/calculations/conservation.html | 91 +-
help/html/calculations/pairwise.html | 55 +-
help/html/calculations/pca.html | 187 +-
help/html/calculations/pcaviewer.gif | Bin 0 -> 27629 bytes
help/html/calculations/quality.html | 69 +-
help/html/calculations/recoverInputdata.html | 35 +-
help/html/calculations/redundancy.html | 37 +-
help/html/calculations/referenceseq.html | 50 +
help/html/calculations/scorematrices.html | 1662 +++++
help/html/calculations/sorting.html | 131 +-
help/html/calculations/structureconsensus.html | 54 +
help/html/calculations/tree.html | 177 +-
help/html/calculations/treeviewer.html | 210 +-
help/html/colourSchemes/abovePID.html | 33 +-
.../html/colourSchemes/annotationColourSetting.gif | Bin 0 -> 13891 bytes
.../html/colourSchemes/annotationColourSetting.jpg | Bin 43293 -> 0 bytes
help/html/colourSchemes/annotationColouring.html | 124 +-
help/html/colourSchemes/annotationColours.gif | Bin 0 -> 23564 bytes
help/html/colourSchemes/annotationColours.jpg | Bin 107885 -> 0 bytes
help/html/colourSchemes/blosum.html | 30 +-
help/html/colourSchemes/buried.html | 97 +-
help/html/colourSchemes/clustal.html | 139 +-
help/html/colourSchemes/colbytcoffee.png | Bin 0 -> 137157 bytes
help/html/colourSchemes/conservation.html | 70 +-
help/html/colourSchemes/helix.html | 97 +-
help/html/colourSchemes/hydrophobic.html | 104 +-
help/html/colourSchemes/index.html | 647 +-
help/html/colourSchemes/nucleotide.html | 43 +-
help/html/colourSchemes/pid.html | 60 +-
help/html/colourSchemes/purinepyrimidine.html | 48 +
help/html/colourSchemes/rnahelicesColouring.html | 68 +
help/html/colourSchemes/rnahelicescoloring.png | Bin 0 -> 34699 bytes
help/html/colourSchemes/strand.html | 97 +-
help/html/colourSchemes/taylor.html | 95 +-
help/html/colourSchemes/textcolour.html | 47 +-
help/html/colourSchemes/turn.html | 97 +-
help/html/colourSchemes/user.html | 66 +-
help/html/colourSchemes/userDefined_java6.gif | Bin 0 -> 42343 bytes
help/html/colourSchemes/userDefined_java7.gif | Bin 0 -> 38939 bytes
help/html/colourSchemes/zappo.html | 90 +-
help/html/editing/index.html | 152 +-
.../features/AnnotationColumnSelectionWithSM.gif | Bin 0 -> 42694 bytes
.../AnnotationColumnSelectionWithoutSM.gif | Bin 0 -> 37778 bytes
help/html/features/annotation.html | 65 +-
help/html/features/annotationsFormat.html | 559 +-
help/html/features/bioJsonFormat.html | 83 +
help/html/features/biojsmsa.html | 58 +
help/html/features/chimera.html | 254 +
help/html/features/clarguments.html | 404 +-
help/html/features/codingfeatures.html | 72 +-
help/html/features/columnFilterByAnnotation.html | 83 +
help/html/features/commandline.html | 91 +-
help/html/features/creatinFeatures.html | 84 +-
help/html/features/cursorMode.html | 123 +-
help/html/features/dasfeatures.html | 98 +-
help/html/features/dassettings.html | 91 +-
help/html/features/editingFeatures.html | 65 +-
help/html/features/featuresFormat.html | 311 +-
help/html/features/featureschemes.html | 139 +-
help/html/features/featuresettings.html | 168 +-
help/html/features/groovy.html | 193 +-
help/html/features/hiddenRegions.html | 176 +-
help/html/features/jalarchive.html | 43 +-
help/html/features/jmol.html | 494 +-
help/html/features/multipleViews.html | 136 +-
help/html/features/newkeystrokes.html | 76 +-
help/html/features/overview.html | 38 +-
help/html/features/pdbseqfetcher.png | Bin 0 -> 97462 bytes
help/html/features/pdbsequencefetcher.html | 103 +
help/html/features/pdbviewer.html | 296 +-
help/html/features/preferences.html | 468 +-
help/html/features/schooser_enter-id.png | Bin 0 -> 29766 bytes
help/html/features/schooser_main.png | Bin 0 -> 58895 bytes
help/html/features/search.html | 201 +-
help/html/features/selectfetchdb.gif | Bin 0 -> 41486 bytes
help/html/features/seqfeatures.html | 157 +-
help/html/features/seqfetch.html | 135 +-
help/html/features/seqfetcher.gif | Bin 8702 -> 11434 bytes
help/html/features/seqmappings.html | 85 +-
help/html/features/splitView.html | 163 +
help/html/features/structurechooser.html | 127 +
help/html/features/varna.html | 93 +
help/html/features/viewingpdbs.html | 226 +-
help/html/features/wrap.html | 637 +-
help/html/features/xsspannotation.html | 96 +
help/html/index.html | 108 +-
help/html/io/export.html | 112 +-
help/html/io/exportseqreport.html | 59 +
help/html/io/fileformats.html | 130 +-
help/html/io/index.html | 144 +-
help/html/io/modellerpir.html | 76 +-
help/html/io/seqreport.gif | Bin 0 -> 25151 bytes
help/html/io/tcoffeescores.html | 84 +
help/html/jalviewjnlp.html | 78 -
help/html/keys.html | 568 +-
help/html/memory.html | 212 +-
help/html/menus/alignmentMenu.html | 1199 +--
help/html/menus/alwannotation.html | 91 +
help/html/menus/alwannotationpanel.html | 117 +
help/html/menus/alwannotations.html | 87 -
help/html/menus/alwcalculate.html | 184 +-
help/html/menus/alwcolour.html | 89 +-
help/html/menus/alwedit.html | 180 +-
help/html/menus/alwfile.html | 214 +-
help/html/menus/alwformat.html | 116 +-
help/html/menus/alwselect.html | 88 +-
help/html/menus/alwview.html | 129 +-
help/html/menus/desktopMenu.html | 234 +-
help/html/menus/index.html | 52 +-
help/html/menus/popupMenu.html | 320 +-
help/html/menus/wsmenu.html | 163 +-
help/html/misc/aaproperties.html | 54 +-
help/html/misc/aminoAcids.html | 529 +-
help/html/misc/geneticCode.html | 153 +-
help/html/na/index.html | 124 +
help/html/privacy.html | 127 +-
help/html/releases.html | 3120 +++++---
help/html/vamsas/index.html | 256 +-
help/html/webServices/AACon.html | 74 +
help/html/webServices/JABAWS.html | 106 +-
help/html/webServices/RNAalifold.html | 89 +
help/html/webServices/RNAalifoldAnnotationRows.png | Bin 0 -> 31732 bytes
help/html/webServices/dbreffetcher.html | 174 +-
help/html/webServices/index.html | 157 +-
help/html/webServices/jnet.html | 217 +-
help/html/webServices/msaclient.html | 129 +-
help/html/webServices/newsreader.html | 64 +-
help/html/webServices/proteinDisorder.html | 253 +
help/html/webServices/shmr.html | 103 +-
help/html/webServices/urllinks.html | 157 +-
help/html/webServices/webServicesParams.html | 150 +-
help/html/webServices/webServicesPrefs.html | 146 +-
help/html/webServices/wsprefs.gif | Bin 18473 -> 23662 bytes
help/html/whatsNew.html | 152 +-
jalview-jalopy.xml | 7 +-
nbbuild.xml | 38 +-
nbproject/genfiles.properties | 12 +-
nbproject/project.properties | 24 +-
nbproject/project.xml | 37 +-
resources/authors.props | 4 +
resources/embl_mapping.xml | 310 +-
resources/images/JalviewLogo_Huge.png | Bin 0 -> 53903 bytes
resources/images/JalviewLogo_big.png | Bin 0 -> 4539 bytes
resources/images/Jalview_Logo.png | Bin 0 -> 15420 bytes
resources/images/Jalview_Logo_small.png | Bin 0 -> 1687 bytes
resources/images/dna.png | Bin 0 -> 895 bytes
resources/images/error.png | Bin 0 -> 633 bytes
resources/images/good.png | Bin 0 -> 965 bytes
resources/images/loading.gif | Bin 0 -> 1849 bytes
resources/images/logo.gif | Bin 615 -> 14501 bytes
resources/images/logo_big.gif | Bin 6804 -> 16656 bytes
resources/images/{logo_big.gif => logo_big_v2.gif} | Bin
resources/images/{logo.gif => logo_v2.gif} | Bin
resources/images/protein.png | Bin 0 -> 524 bytes
resources/images/sugar.png | Bin 0 -> 542 bytes
resources/images/warning.gif | Bin 0 -> 239 bytes
resources/lang/Messages.properties | 1282 ++++
resources/lang/Messages_es.properties | 1136 +++
resources/uniprot_mapping.xml | 7 +-
schemas/JalviewUserColours.xsd | 30 +-
schemas/JalviewWsParamSet.xsd | 7 +-
schemas/castor-mapping.xsd | 629 +-
schemas/jalview.nodesc.properties | 43 +-
schemas/jalview.properties | 43 +-
schemas/jalview.xsd | 730 +-
schemas/jalviewJvV1.xsd | 325 +-
schemas/vamsas.xsd | 18 +-
schemas/vamsasJvV1.xsd | 183 +-
src/MCview/AppletPDBCanvas.java | 244 +-
src/MCview/AppletPDBViewer.java | 87 +-
src/MCview/Atom.java | 55 +-
src/MCview/Bond.java | 33 +-
src/MCview/MCMatrix.java | 13 +-
src/MCview/PDBCanvas.java | 252 +-
src/MCview/PDBChain.java | 405 +-
src/MCview/PDBViewer.java | 163 +-
src/MCview/PDBfile.java | 423 +-
src/MCview/Residue.java | 29 +-
src/MCview/Zsort.java | 36 +-
src/com/github/reinert/jjschema/Attributes.java | 68 +
src/com/stevesoft/pat/Any.java | 2 +-
src/com/stevesoft/pat/BackG.java | 2 +-
src/com/stevesoft/pat/BackMatch.java | 2 +-
src/com/stevesoft/pat/Backup.java | 2 +-
src/com/stevesoft/pat/Bits.java | 4 +-
src/com/stevesoft/pat/Boundary.java | 2 +-
src/com/stevesoft/pat/Bracket.java | 3 +-
src/com/stevesoft/pat/Ctrl.java | 97 +-
src/com/stevesoft/pat/Custom.java | 6 +-
src/com/stevesoft/pat/CustomEndpoint.java | 2 +-
src/com/stevesoft/pat/DotMulti.java | 2 +-
src/com/stevesoft/pat/End.java | 2 +-
src/com/stevesoft/pat/FastBracket.java | 3 +-
src/com/stevesoft/pat/FastMulti.java | 2 +-
src/com/stevesoft/pat/FileRegex.java | 81 +-
src/com/stevesoft/pat/Group.java | 2 +-
src/com/stevesoft/pat/Multi.java | 8 +-
src/com/stevesoft/pat/Multi_stage2.java | 2 +-
src/com/stevesoft/pat/NoPattern.java | 2 +-
src/com/stevesoft/pat/NullPattern.java | 2 +-
src/com/stevesoft/pat/Or.java | 3 +-
src/com/stevesoft/pat/OrMark.java | 2 +-
src/com/stevesoft/pat/Pattern.java | 10 +-
src/com/stevesoft/pat/Pthings.java | 2 +-
src/com/stevesoft/pat/PushRule.java | 5 +-
src/com/stevesoft/pat/Range.java | 2 +-
src/com/stevesoft/pat/RegOpt.java | 4 +-
src/com/stevesoft/pat/RegRes.java | 4 +-
src/com/stevesoft/pat/Regex.java | 73 +-
src/com/stevesoft/pat/RegexReader.java | 5 +-
src/com/stevesoft/pat/RegexTokenizer.java | 3 +-
src/com/stevesoft/pat/RegexWriter.java | 56 +-
src/com/stevesoft/pat/ReplaceRule.java | 2 +-
src/com/stevesoft/pat/Replacer.java | 8 +-
src/com/stevesoft/pat/Skip.java | 4 +-
src/com/stevesoft/pat/SkipBMH.java | 10 +-
src/com/stevesoft/pat/Skipped.java | 6 +-
src/com/stevesoft/pat/Start.java | 2 +-
src/com/stevesoft/pat/StringLike.java | 8 +-
src/com/stevesoft/pat/Transformer.java | 8 +-
src/com/stevesoft/pat/lookAhead.java | 2 +-
src/com/stevesoft/pat/oneChar.java | 2 +-
.../stevesoft/pat/wrap/CharArrayBufferWrap.java | 3 +-
src/com/stevesoft/pat/wrap/CharArrayWrap.java | 3 +-
.../stevesoft/pat/wrap/RandomAccessFileWrap.java | 18 +-
src/com/stevesoft/pat/wrap/StringBufferWrap.java | 3 +-
src/com/stevesoft/pat/wrap/StringWrap.java | 3 +-
src/com/stevesoft/pat/wrap/WriterWrap.java | 6 +-
src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java | 951 +++
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java | 372 +
.../edu/ucsf/rbvi/strucviz2/ChimeraManager.java | 899 +++
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java | 557 ++
.../edu/ucsf/rbvi/strucviz2/ChimeraResidue.java | 456 ++
.../rbvi/strucviz2/ChimeraStructuralObject.java | 112 +
.../edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java | 216 +
.../edu/ucsf/rbvi/strucviz2/StructureManager.java | 960 +++
.../edu/ucsf/rbvi/strucviz2/StructureSettings.java | 30 +
.../ucsf/rbvi/strucviz2/port/ListenerThreads.java | 302 +
src/ext/vamsas/IRegistry.java | 13 +-
src/ext/vamsas/IRegistryService.java | 13 +-
src/ext/vamsas/IRegistryServiceLocator.java | 27 +-
src/ext/vamsas/Jpred.java | 13 +-
src/ext/vamsas/JpredService.java | 13 +-
src/ext/vamsas/JpredServiceLocator.java | 27 +-
src/ext/vamsas/JpredSoapBindingStub.java | 27 +-
src/ext/vamsas/MuscleWS.java | 13 +-
src/ext/vamsas/MuscleWSService.java | 13 +-
src/ext/vamsas/MuscleWSServiceLocator.java | 27 +-
src/ext/vamsas/MuscleWSSoapBindingStub.java | 28 +-
src/ext/vamsas/RegistryServiceSoapBindingStub.java | 16 +-
src/ext/vamsas/SeqSearchI.java | 77 +-
src/ext/vamsas/SeqSearchServiceLocator.java | 373 +-
src/ext/vamsas/SeqSearchServiceService.java | 61 +-
.../vamsas/SeqSearchServiceSoapBindingStub.java | 977 +--
src/ext/vamsas/ServiceHandle.java | 19 +-
src/ext/vamsas/ServiceHandles.java | 19 +-
src/jalview/analysis/AAFrequency.java | 594 +-
src/jalview/analysis/AlignSeq.java | 445 +-
src/jalview/analysis/AlignmentAnnotationUtils.java | 243 +
src/jalview/analysis/AlignmentSorter.java | 193 +-
src/jalview/analysis/AlignmentUtils.java | 1424 ++++
src/jalview/analysis/AnnotationSorter.java | 416 ++
src/jalview/analysis/CodingUtils.java | 139 +
src/jalview/analysis/CodonComparator.java | 111 +
src/jalview/analysis/Conservation.java | 142 +-
src/jalview/analysis/CrossRef.java | 1188 ++-
src/jalview/analysis/Dna.java | 1525 ++--
src/jalview/analysis/Finder.java | 55 +-
src/jalview/analysis/Grouping.java | 142 +-
src/jalview/analysis/NJTree.java | 191 +-
src/jalview/analysis/PCA.java | 140 +-
src/jalview/analysis/ParseProperties.java | 56 +-
src/jalview/analysis/Rna.java | 284 +
src/jalview/analysis/SecStrConsensus.java | 254 +
src/jalview/analysis/SeqsetUtils.java | 29 +-
src/jalview/analysis/SequenceIdMatcher.java | 144 +-
src/jalview/analysis/StructureFrequency.java | 541 ++
src/jalview/analysis/WUSSParseException.java | 43 +
.../analysis/scoremodels/FeatureScoreModel.java | 158 +
.../analysis/scoremodels/PIDScoreModel.java | 75 +
.../scoremodels/PairwiseSeqScoreModel.java | 80 +
src/jalview/analysis/scoremodels/SWScoreModel.java | 94 +
src/jalview/api/AlignCalcManagerI.java | 161 +
src/jalview/api/AlignCalcWorkerI.java | 33 +
src/jalview/api/AlignExportSettingI.java | 73 +
src/jalview/api/AlignViewControllerGuiI.java | 65 +
src/jalview/api/AlignViewControllerI.java | 98 +
src/jalview/api/AlignViewportI.java | 378 +
src/jalview/api/AlignmentViewPanel.java | 57 +-
src/jalview/api/BuildDetailsI.java | 30 +
src/jalview/api/ComplexAlignFile.java | 69 +
src/jalview/api/FeatureRenderer.java | 153 +-
src/jalview/api/FeatureSettingsControllerI.java | 28 +
src/jalview/api/FeatureSettingsModelI.java | 26 +
src/jalview/api/FeaturesDisplayedI.java | 49 +
src/jalview/api/OOMHandlerI.java | 28 +
src/jalview/api/RotatableCanvasI.java | 39 +
src/jalview/api/SequenceRenderer.java | 15 +-
src/jalview/api/SequenceStructureBinding.java | 34 +-
src/jalview/api/SplitContainerI.java | 58 +
.../api/StructureSelectionManagerProvider.java | 29 +-
src/jalview/api/ViewStyleI.java | 260 +
src/jalview/api/analysis/ScoreModelI.java | 36 +
src/jalview/api/analysis/ViewBasedAnalysisI.java | 37 +
.../api/structures/JalviewStructureDisplayI.java | 65 +
src/jalview/appletgui/APopupMenu.java | 694 +-
src/jalview/appletgui/AlignFrame.java | 7822 +++++++++++---------
src/jalview/appletgui/AlignViewport.java | 1643 +---
src/jalview/appletgui/AlignmentPanel.java | 708 +-
src/jalview/appletgui/AnnotationColourChooser.java | 190 +-
src/jalview/appletgui/AnnotationColumnChooser.java | 945 +++
src/jalview/appletgui/AnnotationLabels.java | 271 +-
src/jalview/appletgui/AnnotationPanel.java | 939 +--
src/jalview/appletgui/AnnotationRowFilter.java | 212 +
src/jalview/appletgui/AppletJmol.java | 238 +-
src/jalview/appletgui/AppletJmolBinding.java | 105 +-
src/jalview/appletgui/CutAndPasteTransfer.java | 362 +-
src/jalview/appletgui/EditNameDialog.java | 20 +-
src/jalview/appletgui/EmbmenuFrame.java | 586 +-
src/jalview/appletgui/ExtJmol.java | 102 +-
src/jalview/appletgui/FeatureColourChooser.java | 94 +-
src/jalview/appletgui/FeatureRenderer.java | 904 +--
src/jalview/appletgui/FeatureSettings.java | 277 +-
src/jalview/appletgui/Finder.java | 98 +-
src/jalview/appletgui/FontChooser.java | 369 +-
src/jalview/appletgui/IdCanvas.java | 123 +-
src/jalview/appletgui/IdPanel.java | 80 +-
src/jalview/appletgui/IdwidthAdjuster.java | 51 +-
src/jalview/appletgui/JVDialog.java | 23 +-
src/jalview/appletgui/OverviewPanel.java | 113 +-
src/jalview/appletgui/PCAPanel.java | 202 +-
src/jalview/appletgui/PaintRefresher.java | 41 +-
src/jalview/appletgui/PairwiseAlignPanel.java | 53 +-
src/jalview/appletgui/RedundancyPanel.java | 139 +-
src/jalview/appletgui/RotatableCanvas.java | 58 +-
src/jalview/appletgui/ScalePanel.java | 116 +-
src/jalview/appletgui/SeqCanvas.java | 291 +-
src/jalview/appletgui/SeqPanel.java | 596 +-
src/jalview/appletgui/SequenceRenderer.java | 127 +-
src/jalview/appletgui/SliderPanel.java | 113 +-
src/jalview/appletgui/SplitFrame.java | 240 +
src/jalview/appletgui/TitledPanel.java | 95 +
src/jalview/appletgui/Tooltip.java | 478 +-
src/jalview/appletgui/TreeCanvas.java | 139 +-
src/jalview/appletgui/TreePanel.java | 113 +-
src/jalview/appletgui/UserDefinedColours.java | 130 +-
src/jalview/bin/BuildDetails.java | 75 +
src/jalview/bin/Cache.java | 342 +-
src/jalview/bin/Jalview.java | 618 +-
src/jalview/bin/JalviewLite.java | 5687 +++++++-------
src/jalview/bin/JalviewLiteURLRetrieve.java | 20 +-
src/jalview/binding/Alignment.java | 322 +-
src/jalview/binding/Annotation.java | 854 +--
src/jalview/binding/AnnotationElement.java | 563 +-
src/jalview/binding/Colour.java | 956 ++-
src/jalview/binding/Feature.java | 561 +-
src/jalview/binding/FeatureSettings.java | 481 +-
src/jalview/binding/Features.java | 195 +-
src/jalview/binding/JGroup.java | 1474 ++--
src/jalview/binding/JSeq.java | 1243 ++--
src/jalview/binding/JalviewModel.java | 426 +-
src/jalview/binding/JalviewModelSequence.java | 1852 ++---
src/jalview/binding/JalviewUserColours.java | 635 +-
src/jalview/binding/Pdbentry.java | 631 +-
src/jalview/binding/PdbentryItem.java | 361 +-
src/jalview/binding/Pdbids.java | 195 +-
src/jalview/binding/Property.java | 322 +-
src/jalview/binding/Sequence.java | 195 +-
src/jalview/binding/SequenceSet.java | 1027 +--
src/jalview/binding/SequenceType.java | 373 +-
src/jalview/binding/Setting.java | 479 +-
src/jalview/binding/Tree.java | 1638 ++--
src/jalview/binding/UserColourScheme.java | 196 +-
src/jalview/binding/UserColours.java | 323 +-
src/jalview/binding/VAMSAS.java | 1158 +--
src/jalview/binding/VamsasModel.java | 194 +-
src/jalview/binding/Viewport.java | 2810 +++----
src/jalview/commands/ChangeCaseCommand.java | 30 +-
src/jalview/commands/CommandI.java | 13 +-
src/jalview/commands/EditCommand.java | 697 +-
src/jalview/commands/OrderCommand.java | 55 +-
src/jalview/commands/RemoveGapColCommand.java | 26 +-
src/jalview/commands/RemoveGapsCommand.java | 28 +-
src/jalview/commands/SlideSequencesCommand.java | 44 +-
src/jalview/commands/TrimRegionCommand.java | 36 +-
src/jalview/controller/AlignViewController.java | 423 ++
.../controller/FeatureSettingsController.java | 35 +
.../controller/FeatureSettingsControllerGuiI.java | 26 +
src/jalview/datamodel/ASequence.java | 33 +
src/jalview/datamodel/ASequenceI.java | 32 +
src/jalview/datamodel/AlignedCodon.java | 108 +
src/jalview/datamodel/AlignedCodonFrame.java | 780 +-
src/jalview/datamodel/Alignment.java | 824 ++-
src/jalview/datamodel/AlignmentAnnotation.java | 682 +-
src/jalview/datamodel/AlignmentExportData.java | 83 +
src/jalview/datamodel/AlignmentI.java | 244 +-
src/jalview/datamodel/AlignmentOrder.java | 56 +-
src/jalview/datamodel/AlignmentView.java | 2389 +++---
src/jalview/datamodel/AnnotatedCollectionI.java | 46 +
src/jalview/datamodel/Annotation.java | 109 +-
src/jalview/datamodel/BinaryNode.java | 13 +-
src/jalview/datamodel/BinarySequence.java | 109 +-
src/jalview/datamodel/CigarArray.java | 780 +-
src/jalview/datamodel/CigarBase.java | 1306 ++--
src/jalview/datamodel/CigarCigar.java | 125 +-
src/jalview/datamodel/CigarSimple.java | 67 +-
src/jalview/datamodel/ColumnSelection.java | 2637 +++----
src/jalview/datamodel/DBRefEntry.java | 34 +-
src/jalview/datamodel/DBRefSource.java | 273 +-
src/jalview/datamodel/FeatureProperties.java | 121 +-
src/jalview/datamodel/GraphLine.java | 29 +-
src/jalview/datamodel/HiddenSequences.java | 89 +-
.../datamodel/IncompleteCodonException.java | 33 +
src/jalview/datamodel/Mapping.java | 329 +-
src/jalview/datamodel/NodeTransformI.java | 13 +-
src/jalview/datamodel/PDBEntry.java | 95 +-
src/jalview/datamodel/Provenance.java | 15 +-
src/jalview/datamodel/ProvenanceEntry.java | 13 +-
src/jalview/datamodel/RnaViewerModel.java | 64 +
src/jalview/datamodel/SearchResults.java | 298 +-
.../datamodel/SecondaryStructureAnnotation.java | 52 +
src/jalview/datamodel/SeqCigar.java | 222 +-
src/jalview/datamodel/Sequence.java | 409 +-
src/jalview/datamodel/SequenceCollectionI.java | 67 +
src/jalview/datamodel/SequenceDummy.java | 53 +
src/jalview/datamodel/SequenceFeature.java | 43 +-
src/jalview/datamodel/SequenceGroup.java | 468 +-
src/jalview/datamodel/SequenceI.java | 150 +-
src/jalview/datamodel/SequenceNode.java | 15 +-
src/jalview/datamodel/SequencePoint.java | 13 +-
src/jalview/datamodel/StructureViewerModel.java | 225 +
src/jalview/datamodel/UniprotEntry.java | 44 +-
src/jalview/datamodel/UniprotFile.java | 25 +-
src/jalview/datamodel/UniprotProteinName.java | 84 +-
src/jalview/datamodel/UniprotSequence.java | 39 +-
src/jalview/datamodel/xdb/embl/BasePosition.java | 19 +-
src/jalview/datamodel/xdb/embl/EmblEntry.java | 216 +-
src/jalview/datamodel/xdb/embl/EmblError.java | 18 +-
src/jalview/datamodel/xdb/embl/EmblFeature.java | 39 +-
.../datamodel/xdb/embl/EmblFeatureLocElement.java | 19 +-
.../datamodel/xdb/embl/EmblFeatureLocations.java | 41 +-
src/jalview/datamodel/xdb/embl/EmblFile.java | 67 +-
src/jalview/datamodel/xdb/embl/EmblSequence.java | 18 +-
src/jalview/datamodel/xdb/embl/Qualifier.java | 21 +-
src/jalview/exceptions/JalviewException.java | 45 +
.../exceptions/NoFileSelectedException.java | 30 +
src/jalview/ext/jmol/JalviewJmolBinding.java | 3001 ++++----
src/jalview/ext/jmol/JmolCommands.java | 332 +-
src/jalview/ext/jmol/PDBFileWithJmol.java | 465 ++
src/jalview/ext/paradise/Annotate3D.java | 248 +
src/jalview/ext/rbvi/chimera/ChimeraCommands.java | 293 +
src/jalview/ext/rbvi/chimera/ChimeraListener.java | 149 +
.../ext/rbvi/chimera/JalviewChimeraBinding.java | 1118 +++
src/jalview/ext/varna/JalviewVarnaBinding.java | 35 +
src/jalview/ext/varna/RnaModel.java | 52 +
src/jalview/ext/varna/VarnaCommands.java | 170 +
src/jalview/gui/AlignExportSettings.java | 118 +
src/jalview/gui/AlignFrame.java | 2999 +++++---
src/jalview/gui/AlignViewport.java | 2457 ++----
src/jalview/gui/AlignmentPanel.java | 1021 ++-
src/jalview/gui/AnnotationChooser.java | 657 ++
src/jalview/gui/AnnotationColourChooser.java | 511 +-
src/jalview/gui/AnnotationColumnChooser.java | 920 +++
src/jalview/gui/AnnotationExporter.java | 611 +-
src/jalview/gui/AnnotationLabels.java | 554 +-
src/jalview/gui/AnnotationPanel.java | 1209 +--
src/jalview/gui/AnnotationRowFilter.java | 401 +
src/jalview/gui/AppJmol.java | 849 +--
src/jalview/gui/AppJmolBinding.java | 142 +-
src/jalview/gui/AppVarna.java | 752 ++
src/jalview/gui/AppVarnaBinding.java | 577 ++
src/jalview/gui/AssociatePdbFileWithSeq.java | 106 +-
src/jalview/gui/BlogReader.java | 87 +-
src/jalview/gui/ChimeraViewFrame.java | 1211 +++
src/jalview/gui/ConservationThread.java | 103 -
src/jalview/gui/Console.java | 42 +-
src/jalview/gui/CutAndPasteHtmlTransfer.java | 244 +
src/jalview/gui/CutAndPasteTransfer.java | 175 +-
src/jalview/gui/DasSourceBrowser.java | 1806 +++--
src/jalview/gui/Desktop.java | 1339 +++-
src/jalview/gui/EPSOptions.java | 47 +-
src/jalview/gui/EditNameDialog.java | 30 +-
src/jalview/gui/FeatureColourChooser.java | 104 +-
src/jalview/gui/FeatureRenderer.java | 1169 +--
src/jalview/gui/FeatureSettings.java | 584 +-
src/jalview/gui/Finder.java | 201 +-
src/jalview/gui/FontChooser.java | 166 +-
src/jalview/gui/HTMLOptions.java | 162 +
src/jalview/gui/Help.java | 110 +
src/jalview/gui/IProgressIndicator.java | 107 +-
src/jalview/gui/IProgressIndicatorHandler.java | 73 +-
src/jalview/gui/IdCanvas.java | 163 +-
src/jalview/gui/IdPanel.java | 251 +-
src/jalview/gui/IdwidthAdjuster.java | 50 +-
src/jalview/gui/JDatabaseTree.java | 573 ++
src/jalview/gui/Jalview2XML.java | 4147 +++++++----
src/jalview/gui/Jalview2XML_V1.java | 980 +--
src/jalview/gui/JalviewAppender.java | 13 +-
src/jalview/gui/JalviewChangeSupport.java | 32 +-
src/jalview/gui/JalviewChimeraBindingModel.java | 138 +
src/jalview/gui/JalviewDialog.java | 99 +-
src/jalview/gui/JvSwingUtils.java | 184 +-
src/jalview/gui/MenuChooser.java | 99 +
src/jalview/gui/OOMWarning.java | 177 +-
src/jalview/gui/OptsAndParamsPage.java | 188 +-
src/jalview/gui/OptsParametersContainerI.java | 26 +-
src/jalview/gui/OverviewPanel.java | 115 +-
src/jalview/gui/PCAPanel.java | 453 +-
src/jalview/gui/PDBSearchPanel.java | 317 +
src/jalview/gui/PaintRefresher.java | 134 +-
src/jalview/gui/PairwiseAlignPanel.java | 50 +-
src/jalview/gui/PopupMenu.java | 1185 ++-
src/jalview/gui/Preferences.java | 583 +-
src/jalview/gui/ProgressBar.java | 255 +
src/jalview/gui/PromptUserConfig.java | 24 +-
src/jalview/gui/RedundancyPanel.java | 157 +-
src/jalview/gui/RestInputParamEditDialog.java | 155 +-
src/jalview/gui/RestServiceEditorPane.java | 318 +-
src/jalview/gui/RotatableCanvas.java | 81 +-
src/jalview/gui/SVGOptions.java | 162 +
src/jalview/gui/ScalePanel.java | 156 +-
src/jalview/gui/ScriptWindow.java | 732 --
src/jalview/gui/SeqCanvas.java | 270 +-
src/jalview/gui/SeqPanel.java | 971 +--
src/jalview/gui/SequenceFetcher.java | 865 ++-
src/jalview/gui/SequenceRenderer.java | 184 +-
src/jalview/gui/SliderPanel.java | 95 +-
src/jalview/gui/SplashScreen.java | 304 +-
src/jalview/gui/SplitFrame.java | 661 ++
src/jalview/gui/StructureChooser.java | 972 +++
src/jalview/gui/StructureViewer.java | 216 +
src/jalview/gui/StructureViewerBase.java | 495 ++
src/jalview/gui/TextColourChooser.java | 100 +-
src/jalview/gui/TreeCanvas.java | 168 +-
src/jalview/gui/TreePanel.java | 190 +-
src/jalview/gui/UserDefinedColours.java | 322 +-
src/jalview/gui/UserQuestionnaireCheck.java | 34 +-
src/jalview/gui/VamsasApplication.java | 63 +-
src/jalview/gui/ViewSelectionMenu.java | 165 +-
src/jalview/gui/WebserviceInfo.java | 170 +-
src/jalview/gui/WsJobParameters.java | 379 +-
src/jalview/gui/WsParamSetManager.java | 43 +-
src/jalview/gui/WsPreferences.java | 303 +-
src/jalview/httpserver/AbstractRequestHandler.java | 205 +
src/jalview/httpserver/HttpServer.java | 300 +
src/jalview/io/AMSAFile.java | 16 +-
src/jalview/io/AlignFile.java | 171 +-
src/jalview/io/AlignmentProperties.java | 35 +-
src/jalview/io/AnnotationFile.java | 3289 ++++----
src/jalview/io/AppletFormatAdapter.java | 420 +-
src/jalview/io/BLCFile.java | 28 +-
src/jalview/io/BioJsHTMLOutput.java | 384 +
src/jalview/io/ClansFile.java | 57 +-
src/jalview/io/ClustalFile.java | 74 +-
src/jalview/io/DBRefFile.java | 91 +-
src/jalview/io/FastaFile.java | 70 +-
src/jalview/io/FeaturesFile.java | 2534 ++++---
src/jalview/io/FileLoader.java | 177 +-
src/jalview/io/FileParse.java | 224 +-
src/jalview/io/FormatAdapter.java | 158 +-
src/jalview/io/Gff3File.java | 174 +
src/jalview/io/HTMLOutput.java | 40 +-
src/jalview/io/HtmlFile.java | 174 +
src/jalview/io/HtmlSvgOutput.java | 682 ++
src/jalview/io/IdentifyFile.java | 192 +-
src/jalview/io/InputStreamParser.java | 57 +
src/jalview/io/JPredFile.java | 39 +-
src/jalview/io/JSONFile.java | 787 ++
src/jalview/io/JalviewFileChooser.java | 119 +-
src/jalview/io/JalviewFileFilter.java | 19 +-
src/jalview/io/JalviewFileView.java | 33 +-
src/jalview/io/JnetAnnotationMaker.java | 210 +-
src/jalview/io/MSFfile.java | 37 +-
src/jalview/io/MatrixFile.java | 69 +-
src/jalview/io/ModellerDescription.java | 94 +-
src/jalview/io/NewickFile.java | 48 +-
src/jalview/io/PIRFile.java | 20 +-
src/jalview/io/PfamFile.java | 28 +-
src/jalview/io/PhylipFile.java | 329 +
src/jalview/io/PileUpfile.java | 31 +-
src/jalview/io/RnamlFile.java | 242 +
src/jalview/io/SequenceAnnotationReport.java | 386 +
src/jalview/io/SimpleBlastFile.java | 28 +-
src/jalview/io/StockholmFile.java | 1780 +++--
src/jalview/io/TCoffeeScoreFile.java | 651 ++
src/jalview/io/VamsasAppDatastore.java | 192 +-
src/jalview/io/WSWUBlastClient.java | 65 +-
src/jalview/io/packed/DataProvider.java | 47 +-
src/jalview/io/packed/JalviewDataset.java | 277 +-
src/jalview/io/packed/ParsePackedSet.java | 63 +-
src/jalview/io/packed/SimpleDataProvider.java | 41 +-
src/jalview/io/vamsas/Datasetsequence.java | 553 +-
src/jalview/io/vamsas/DatastoreItem.java | 68 +-
src/jalview/io/vamsas/DatastoreRegistry.java | 19 +-
src/jalview/io/vamsas/Dbref.java | 17 +-
src/jalview/io/vamsas/LocalDocSyncObject.java | 13 +-
src/jalview/io/vamsas/Rangetype.java | 46 +-
src/jalview/io/vamsas/Sequencefeature.java | 718 +-
src/jalview/io/vamsas/Sequencemapping.java | 50 +-
src/jalview/io/vamsas/Tree.java | 68 +-
src/jalview/javascript/JSFunctionExec.java | 540 +-
src/jalview/javascript/JalviewLiteJsApi.java | 166 +-
src/jalview/javascript/JsCallBack.java | 26 +-
src/jalview/javascript/JsSelectionSender.java | 42 +-
src/jalview/javascript/MouseOverListener.java | 39 +-
.../javascript/MouseOverStructureListener.java | 632 +-
src/jalview/jbgui/GAlignExportSettings.java | 192 +
src/jalview/jbgui/GAlignFrame.java | 2089 ++++--
src/jalview/jbgui/GAlignmentPanel.java | 26 +-
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java | 262 +
src/jalview/jbgui/GCutAndPasteTransfer.java | 50 +-
src/jalview/jbgui/GDasSourceBrowser.java | 472 +-
src/jalview/jbgui/GDesktop.java | 125 +-
src/jalview/jbgui/GFinder.java | 103 +-
src/jalview/jbgui/GFontChooser.java | 202 +-
src/jalview/jbgui/GPCAPanel.java | 185 +-
src/jalview/jbgui/GPDBSearchPanel.java | 396 +
src/jalview/jbgui/GPairwiseAlignPanel.java | 28 +-
src/jalview/jbgui/GPreferences.java | 1567 ++--
src/jalview/jbgui/GRestInputParamEditDialog.java | 118 +-
src/jalview/jbgui/GRestServiceEditorPane.java | 273 +-
src/jalview/jbgui/GRnaStructureViewer.java | 43 +
src/jalview/jbgui/GSequenceLink.java | 49 +-
src/jalview/jbgui/GSliderPanel.java | 43 +-
src/jalview/jbgui/GSplitFrame.java | 163 +
src/jalview/jbgui/GStructureChooser.java | 581 ++
src/jalview/jbgui/GStructureViewer.java | 290 +-
src/jalview/jbgui/GTreePanel.java | 72 +-
src/jalview/jbgui/GUserDefinedColours.java | 72 +-
src/jalview/jbgui/GWebserviceInfo.java | 45 +-
src/jalview/jbgui/GWsPreferences.java | 121 +-
src/jalview/jbgui/PDBDocFieldPreferences.java | 267 +
.../json/binding/biojs/BioJSReleasePojo.java | 66 +
.../json/binding/biojs/BioJSRepositoryPojo.java | 111 +
.../biojson/v1/AlignmentAnnotationPojo.java | 74 +
.../json/binding/biojson/v1/AlignmentPojo.java | 158 +
.../json/binding/biojson/v1/AnnotationPojo.java | 86 +
.../biojson/v1/JalviewBioJsColorSchemeMapper.java | 94 +
.../binding/biojson/v1/SequenceFeaturesPojo.java | 183 +
.../json/binding/biojson/v1/SequenceGrpPojo.java | 181 +
.../json/binding/biojson/v1/SequencePojo.java | 143 +
src/jalview/math/AlignmentDimension.java | 55 +
src/jalview/math/Matrix.java | 44 +-
src/jalview/math/RotatableMatrix.java | 13 +-
src/jalview/renderer/AnnotationRenderer.java | 1608 ++++
src/jalview/renderer/AwtRenderPanelI.java | 62 +
.../renderer/seqfeatures/FeatureRenderer.java | 423 ++
src/jalview/rest/RestHandler.java | 115 +
src/jalview/schemabinding/version2/.castor.cdr | 15 +-
src/jalview/schemabinding/version2/AlcodMap.java | 349 +-
src/jalview/schemabinding/version2/Alcodon.java | 501 +-
.../schemabinding/version2/AlcodonFrame.java | 845 +--
src/jalview/schemabinding/version2/Annotation.java | 2456 +++---
.../version2/AnnotationColourScheme.java | 497 ++
.../schemabinding/version2/AnnotationColours.java | 465 +-
.../schemabinding/version2/AnnotationElement.java | 669 +-
.../schemabinding/version2/CalcIdParam.java | 300 +
src/jalview/schemabinding/version2/Colour.java | 957 ++-
src/jalview/schemabinding/version2/DBRef.java | 425 +-
src/jalview/schemabinding/version2/Feature.java | 1042 +--
.../schemabinding/version2/FeatureSettings.java | 841 +--
src/jalview/schemabinding/version2/Features.java | 195 +-
src/jalview/schemabinding/version2/Group.java | 386 +-
.../schemabinding/version2/HiddenColumns.java | 416 +-
src/jalview/schemabinding/version2/JGroup.java | 2385 +++---
src/jalview/schemabinding/version2/JSeq.java | 1783 +++--
.../schemabinding/version2/JalviewModel.java | 429 +-
.../version2/JalviewModelSequence.java | 1886 ++---
.../schemabinding/version2/JalviewUserColours.java | 638 +-
.../schemabinding/version2/MapListFrom.java | 416 +-
src/jalview/schemabinding/version2/MapListTo.java | 416 +-
.../schemabinding/version2/MapListType.java | 1152 ++-
src/jalview/schemabinding/version2/Mapping.java | 307 +-
.../schemabinding/version2/MappingChoice.java | 325 +-
src/jalview/schemabinding/version2/OtherData.java | 324 +-
src/jalview/schemabinding/version2/Pdbentry.java | 688 +-
.../schemabinding/version2/PdbentryItem.java | 369 +-
src/jalview/schemabinding/version2/Pdbids.java | 498 +-
src/jalview/schemabinding/version2/Property.java | 324 +-
src/jalview/schemabinding/version2/RnaViewer.java | 668 ++
.../schemabinding/version2/SecondaryStructure.java | 290 +
src/jalview/schemabinding/version2/Sequence.java | 596 +-
.../schemabinding/version2/SequenceSet.java | 1654 +++--
.../version2/SequenceSetProperties.java | 326 +-
.../schemabinding/version2/SequenceType.java | 426 +-
src/jalview/schemabinding/version2/Setting.java | 1330 ++--
.../schemabinding/version2/StructureState.java | 1357 ++--
.../schemabinding/version2/ThresholdLine.java | 469 +-
src/jalview/schemabinding/version2/Tree.java | 1705 ++---
.../schemabinding/version2/UserColourScheme.java | 199 +-
.../schemabinding/version2/UserColours.java | 325 +-
src/jalview/schemabinding/version2/VAMSAS.java | 830 ++-
.../schemabinding/version2/VamsasModel.java | 195 +-
src/jalview/schemabinding/version2/Viewport.java | 5128 +++++++------
.../version2/WebServiceParameterSet.java | 836 +--
.../version2/descriptors/AlcodMapDescriptor.java | 448 +-
.../version2/descriptors/AlcodonDescriptor.java | 540 +-
.../descriptors/AlcodonFrameDescriptor.java | 460 +-
.../AnnotationColourSchemeDescriptor.java | 573 ++
.../descriptors/AnnotationColoursDescriptor.java | 530 +-
.../version2/descriptors/AnnotationDescriptor.java | 2161 +++---
.../descriptors/AnnotationElementDescriptor.java | 806 +-
.../descriptors/CalcIdParamDescriptor.java | 313 +
.../version2/descriptors/ColourDescriptor.java | 1059 +--
.../version2/descriptors/DBRefDescriptor.java | 584 +-
.../version2/descriptors/FeatureDescriptor.java | 980 +--
.../descriptors/FeatureSettingsDescriptor.java | 460 +-
.../version2/descriptors/FeaturesDescriptor.java | 277 +-
.../version2/descriptors/GroupDescriptor.java | 443 +-
.../descriptors/HiddenColumnsDescriptor.java | 440 +-
.../version2/descriptors/JGroupDescriptor.java | 2162 +++---
.../version2/descriptors/JSeqDescriptor.java | 1093 +--
.../descriptors/JalviewModelDescriptor.java | 600 +-
.../JalviewModelSequenceDescriptor.java | 815 +-
.../descriptors/JalviewUserColoursDescriptor.java | 523 +-
.../descriptors/MapListFromDescriptor.java | 442 +-
.../version2/descriptors/MapListToDescriptor.java | 442 +-
.../descriptors/MapListTypeDescriptor.java | 652 +-
.../descriptors/MappingChoiceDescriptor.java | 440 +-
.../version2/descriptors/MappingDescriptor.java | 371 +-
.../version2/descriptors/OtherDataDescriptor.java | 448 +-
.../version2/descriptors/PdbentryDescriptor.java | 605 +-
.../descriptors/PdbentryItemDescriptor.java | 387 +-
.../version2/descriptors/PdbidsDescriptor.java | 390 +-
.../version2/descriptors/PropertyDescriptor.java | 448 +-
.../version2/descriptors/RnaViewerDescriptor.java | 634 ++
.../descriptors/SecondaryStructureDescriptor.java | 345 +
.../version2/descriptors/SequenceDescriptor.java | 431 +-
.../descriptors/SequenceSetDescriptor.java | 815 +-
.../SequenceSetPropertiesDescriptor.java | 440 +-
.../descriptors/SequenceTypeDescriptor.java | 594 +-
.../version2/descriptors/SettingDescriptor.java | 1296 ++--
.../descriptors/StructureStateDescriptor.java | 1218 +--
.../descriptors/ThresholdLineDescriptor.java | 536 +-
.../version2/descriptors/TreeDescriptor.java | 1719 +++--
.../descriptors/UserColourSchemeDescriptor.java | 278 +-
.../descriptors/UserColoursDescriptor.java | 445 +-
.../version2/descriptors/VAMSASDescriptor.java | 471 +-
.../descriptors/VamsasModelDescriptor.java | 277 +-
.../version2/descriptors/ViewportDescriptor.java | 4612 +++++++-----
.../WebServiceParameterSetDescriptor.java | 693 +-
src/jalview/schemes/AnnotationColourGradient.java | 318 +-
src/jalview/schemes/Blosum62ColourScheme.java | 34 +-
src/jalview/schemes/BuriedColourScheme.java | 19 +-
src/jalview/schemes/ClustalxColourScheme.java | 227 +-
src/jalview/schemes/ColourSchemeI.java | 100 +-
src/jalview/schemes/ColourSchemeProperty.java | 180 +-
src/jalview/schemes/Consensus.java | 13 +-
src/jalview/schemes/CovariationColourScheme.java | 124 +
src/jalview/schemes/FollowerColourScheme.java | 70 +
src/jalview/schemes/GraduatedColor.java | 19 +-
src/jalview/schemes/HelixColourScheme.java | 19 +-
src/jalview/schemes/HydrophobicColourScheme.java | 19 +-
src/jalview/schemes/NucleotideColourScheme.java | 24 +-
src/jalview/schemes/PIDColourScheme.java | 23 +-
.../schemes/PurinePyrimidineColourScheme.java | 90 +
src/jalview/schemes/RNAHelicesColour.java | 201 +
src/jalview/schemes/RNAHelicesColourChooser.java | 132 +
.../schemes/RNAInteractionColourScheme.java | 85 +
src/jalview/schemes/ResidueColourScheme.java | 87 +-
src/jalview/schemes/ResidueProperties.java | 904 ++-
src/jalview/schemes/ScoreColourScheme.java | 25 +-
src/jalview/schemes/ScoreMatrix.java | 259 +-
src/jalview/schemes/StrandColourScheme.java | 19 +-
src/jalview/schemes/TCoffeeColourScheme.java | 140 +
src/jalview/schemes/TaylorColourScheme.java | 15 +-
src/jalview/schemes/TurnColourScheme.java | 19 +-
src/jalview/schemes/UserColourScheme.java | 44 +-
src/jalview/schemes/ZappoColourScheme.java | 15 +-
.../structure/AlignmentViewPanelListener.java | 26 +-
src/jalview/structure/AtomSpec.java | 85 +
src/jalview/structure/CommandListener.java | 55 +
.../structure/SecondaryStructureListener.java | 39 +
src/jalview/structure/SelectionListener.java | 13 +-
src/jalview/structure/SelectionSource.java | 13 +-
src/jalview/structure/SequenceListener.java | 20 +-
src/jalview/structure/StructureListener.java | 71 +-
src/jalview/structure/StructureMapping.java | 64 +-
.../structure/StructureMappingcommandSet.java | 49 +-
.../structure/StructureSelectionManager.java | 1001 ++-
src/jalview/structure/VamsasListener.java | 75 +-
src/jalview/structure/VamsasSource.java | 30 +-
.../structures/models/AAStructureBindingModel.java | 656 ++
.../models/SequenceStructureBindingModel.java | 72 +
src/jalview/util/AWTConsole.java | 35 +-
src/jalview/util/BrowserLauncher.java | 194 +-
src/jalview/util/ColorUtils.java | 106 +
src/jalview/util/Comparison.java | 179 +-
src/jalview/util/DBRefUtils.java | 192 +-
src/jalview/util/Format.java | 26 +-
src/jalview/util/GroupUrlLink.java | 59 +-
src/jalview/util/ImageMaker.java | 208 +-
src/jalview/util/MapList.java | 694 +-
src/jalview/util/MappingUtils.java | 678 ++
src/jalview/util/MessageManager.java | 127 +
src/jalview/util/ParseHtmlBodyAndLinks.java | 155 +-
src/jalview/util/Platform.java | 131 +-
src/jalview/util/QuickSort.java | 351 +-
src/jalview/util/ReverseListIterator.java | 63 +
src/jalview/util/ShiftList.java | 297 +-
src/jalview/util/StringUtils.java | 251 +
src/jalview/util/TableSorter.java | 1213 +--
src/jalview/util/UrlLink.java | 794 +-
src/jalview/util/jarInputStreamProvider.java | 93 +-
src/jalview/viewmodel/AlignmentViewport.java | 2560 +++++++
src/jalview/viewmodel/PCAModel.java | 246 +
.../AnnotationFilterParameter.java | 122 +
.../seqfeatures/FeatureRendererModel.java | 956 +++
.../seqfeatures/FeatureRendererSettings.java | 97 +
.../seqfeatures/FeatureSettingsModel.java | 28 +
.../viewmodel/seqfeatures/FeaturesDisplayed.java | 114 +
src/jalview/viewmodel/styles/ViewStyle.java | 1097 +++
src/jalview/workers/AlignCalcManager.java | 385 +
src/jalview/workers/AlignCalcWorker.java | 98 +
src/jalview/workers/ComplementConsensusThread.java | 107 +
src/jalview/workers/ConsensusThread.java | 218 +
src/jalview/workers/ConservationThread.java | 143 +
src/jalview/workers/StrucConsensusThread.java | 169 +
src/jalview/ws/AWSThread.java | 110 +-
src/jalview/ws/AWsJob.java | 13 +-
src/jalview/ws/DBRefFetcher.java | 1478 ++--
src/jalview/ws/DasSequenceFeatureFetcher.java | 1824 ++---
src/jalview/ws/EnfinEnvision2OneWay.java | 709 --
src/jalview/ws/HttpClientUtils.java | 169 +
src/jalview/ws/JobStateSummary.java | 36 +-
src/jalview/ws/SequenceFetcher.java | 859 ++-
src/jalview/ws/WSClient.java | 15 +-
src/jalview/ws/WSClientI.java | 13 +-
src/jalview/ws/WSMenuEntryProviderI.java | 17 +-
src/jalview/ws/dbsources/DasSequenceSource.java | 176 -
.../ws/dbsources/EbiFileRetrievedProxy.java | 130 +-
src/jalview/ws/dbsources/EmblCdsSouce.java | 183 +-
src/jalview/ws/dbsources/EmblSource.java | 253 +-
src/jalview/ws/dbsources/EmblXmlSource.java | 320 +-
src/jalview/ws/dbsources/GeneDbSource.java | 259 +-
src/jalview/ws/dbsources/PDBRestClient.java | 422 ++
src/jalview/ws/dbsources/Pdb.java | 464 +-
src/jalview/ws/dbsources/Pfam.java | 313 +-
src/jalview/ws/dbsources/PfamFull.java | 139 +-
src/jalview/ws/dbsources/PfamSeed.java | 138 +-
src/jalview/ws/dbsources/Rfam.java | 118 +
src/jalview/ws/dbsources/RfamFull.java | 81 +
src/jalview/ws/dbsources/RfamSeed.java | 80 +
src/jalview/ws/dbsources/Uniprot.java | 211 +-
src/jalview/ws/dbsources/UnprotName.java | 85 +-
src/jalview/ws/dbsources/Xfam.java | 73 +
.../dbsources/das/DasSequenceSourceListener.java | 165 -
.../ws/dbsources/das/api/DasSourceRegistryI.java | 57 +
.../ws/dbsources/das/api/jalviewSourceI.java | 87 +
.../dbsources/das/datamodel/DasSequenceSource.java | 355 +
.../dbsources/das/datamodel/DasSourceRegistry.java | 486 ++
.../ws/dbsources/das/datamodel/JalviewSource.java | 383 +
src/jalview/ws/ebi/EBIFetchClient.java | 487 +-
src/jalview/ws/io/mime/HttpContentHandler.java | 25 +-
.../ws/io/mime/JalviewMimeContentHandler.java | 77 +-
src/jalview/ws/io/mime/MimeTypes.java | 67 +-
src/jalview/ws/jws1/Annotate3D.java | 282 +
src/jalview/ws/jws1/Discoverer.java | 58 +-
src/jalview/ws/jws1/JPredClient.java | 69 +-
src/jalview/ws/jws1/JPredThread.java | 203 +-
src/jalview/ws/jws1/JWS1Thread.java | 21 +-
src/jalview/ws/jws1/MsaWSClient.java | 53 +-
src/jalview/ws/jws1/MsaWSThread.java | 71 +-
src/jalview/ws/jws1/SeqSearchWSClient.java | 55 +-
src/jalview/ws/jws1/SeqSearchWSThread.java | 72 +-
src/jalview/ws/jws1/WS1Client.java | 20 +-
src/jalview/ws/jws1/WSJob.java | 13 +-
src/jalview/ws/jws2/AAConClient.java | 128 +
src/jalview/ws/jws2/AADisorderClient.java | 379 +
src/jalview/ws/jws2/AWS2Thread.java | 13 +-
src/jalview/ws/jws2/AbstractJabaCalcWorker.java | 621 ++
src/jalview/ws/jws2/JPred301Client.java | 300 +
src/jalview/ws/jws2/JWs2Job.java | 17 +-
src/jalview/ws/jws2/JabaParamStore.java | 121 +-
src/jalview/ws/jws2/JabaPreset.java | 30 +-
src/jalview/ws/jws2/JabaWsServerQuery.java | 236 +-
src/jalview/ws/jws2/JabawsCalcWorker.java | 237 +
.../ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java | 226 +
src/jalview/ws/jws2/Jws2Client.java | 380 +-
src/jalview/ws/jws2/Jws2Discoverer.java | 758 +-
src/jalview/ws/jws2/MsaWSClient.java | 266 +-
src/jalview/ws/jws2/MsaWSThread.java | 383 +-
src/jalview/ws/jws2/ParameterUtils.java | 34 +-
src/jalview/ws/jws2/RNAalifoldClient.java | 405 +
.../ws/jws2/SequenceAnnotationWSClient.java | 258 +
src/jalview/ws/jws2/dm/AAConSettings.java | 153 +
src/jalview/ws/jws2/dm/JabaOption.java | 30 +-
src/jalview/ws/jws2/dm/JabaParameter.java | 15 +-
src/jalview/ws/jws2/dm/JabaValueConstrain.java | 31 +-
src/jalview/ws/jws2/dm/JabaWsParamSet.java | 35 +-
src/jalview/ws/jws2/jabaws2/Jws2Instance.java | 252 +
.../ws/jws2/jabaws2/Jws2InstanceFactory.java | 97 +
src/jalview/ws/params/ArgumentI.java | 14 +-
src/jalview/ws/params/AutoCalcSetting.java | 90 +
.../ws/params/InvalidArgumentException.java | 22 +-
src/jalview/ws/params/OptionI.java | 13 +-
src/jalview/ws/params/ParamDatastoreI.java | 13 +-
src/jalview/ws/params/ParamManager.java | 15 +-
src/jalview/ws/params/ParameterI.java | 17 +-
src/jalview/ws/params/ValueConstrainI.java | 23 +-
src/jalview/ws/params/WsParamSetI.java | 13 +-
src/jalview/ws/params/simple/BooleanOption.java | 38 +-
src/jalview/ws/params/simple/IntegerParameter.java | 75 +-
src/jalview/ws/params/simple/Option.java | 62 +-
src/jalview/ws/params/simple/Parameter.java | 33 +-
.../ws/params/simple/StringChoiceParameter.java | 23 +-
src/jalview/ws/rest/AlignmentProcessor.java | 32 +-
src/jalview/ws/rest/HttpResultSet.java | 36 +-
src/jalview/ws/rest/InputType.java | 312 +-
src/jalview/ws/rest/NoValidInputDataException.java | 31 +-
src/jalview/ws/rest/RestClient.java | 279 +-
src/jalview/ws/rest/RestJob.java | 129 +-
src/jalview/ws/rest/RestJobThread.java | 45 +-
src/jalview/ws/rest/RestServiceDescription.java | 375 +-
src/jalview/ws/rest/params/Alignment.java | 57 +-
src/jalview/ws/rest/params/AnnotationFile.java | 91 +-
src/jalview/ws/rest/params/JobConstant.java | 56 +-
.../ws/rest/params/SeqGroupIndexVector.java | 142 +-
src/jalview/ws/rest/params/SeqIdVector.java | 39 +-
src/jalview/ws/rest/params/SeqVector.java | 74 +-
src/jalview/ws/rest/params/Tree.java | 57 +-
src/jalview/ws/seqfetcher/ASequenceFetcher.java | 784 +-
src/jalview/ws/seqfetcher/DbSourceProxy.java | 278 +-
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 279 +-
src/jalview/ws/uimodel/AlignAnalysisUIText.java | 134 +
src/jalview/ws/uimodel/PDBRestRequest.java | 142 +
src/jalview/ws/uimodel/PDBRestResponse.java | 223 +
.../biojava/dasobert/das/DAS_FeatureRetrieve.java | 287 -
.../biojava/dasobert/das/DAS_Feature_Handler.java | 314 -
.../biojava/dasobert/das/DAS_Sequence_Handler.java | 161 -
src/org/biojava/dasobert/das/FeatureThread.java | 198 -
src/org/biojava/dasobert/das/SequenceThread.java | 299 -
src/org/biojava/dasobert/das2/Das2Capability.java | 51 -
.../biojava/dasobert/das2/Das2CapabilityImpl.java | 131 -
src/org/biojava/dasobert/das2/Das2Source.java | 42 -
src/org/biojava/dasobert/das2/Das2SourceImpl.java | 157 -
.../biojava/dasobert/das2/DasSourceConverter.java | 92 -
.../dasobert/das2/io/DAS2SourceHandler.java | 216 -
.../biojava/dasobert/das2/io/DasSourceReader.java | 33 -
.../dasobert/das2/io/DasSourceReaderImpl.java | 183 -
.../biojava/dasobert/dasregistry/Das1Source.java | 305 -
.../dasobert/dasregistry/Das2Validator.java | 44 -
.../dasregistry/DasCoordSysComparator.java | 128 -
.../dasobert/dasregistry/DasCoordinateSystem.java | 233 -
.../biojava/dasobert/dasregistry/DasSource.java | 130 -
.../dasobert/dasregistry/DasSourceComparator.java | 190 -
.../dasobert/eventmodel/AbstractDasEvent.java | 43 -
.../biojava/dasobert/eventmodel/FeatureEvent.java | 96 -
.../dasobert/eventmodel/FeatureListener.java | 48 -
.../dasobert/eventmodel/ObjectListener.java | 51 -
.../biojava/dasobert/eventmodel/SequenceEvent.java | 62 -
.../dasobert/eventmodel/SequenceListener.java | 64 -
.../dasobert/feature/AbstractFeatureTrack.java | 278 -
.../biojava/dasobert/feature/AbstractSegment.java | 256 -
.../dasobert/feature/FeatureComparator.java | 87 -
.../dasobert/feature/FeatureMapComparator.java | 68 -
src/org/biojava/dasobert/feature/FeatureTrack.java | 127 -
.../dasobert/feature/FeatureTrackConverter.java | 526 --
.../biojava/dasobert/feature/FeatureTrackImpl.java | 68 -
.../biojava/dasobert/feature/HistogramFeature.java | 95 -
.../biojava/dasobert/feature/HistogramSegment.java | 67 -
src/org/biojava/dasobert/feature/Segment.java | 84 -
.../dasobert/feature/SegmentComparator.java | 45 -
src/org/biojava/dasobert/feature/SegmentImpl.java | 83 -
src/org/jibble/epsgraphics/EpsDocument.java | 47 +-
src/org/jibble/epsgraphics/EpsException.java | 34 +-
src/org/jibble/epsgraphics/EpsGraphics2D.java | 112 +-
src/uk/ac/ebi/picr/model/CrossReference.java | 675 +-
.../ac/ebi/picr/model/CrossReference_Helper.java | 253 +-
src/uk/ac/ebi/picr/model/UPEntry.java | 591 +-
src/uk/ac/ebi/picr/model/UPEntry_Helper.java | 215 +-
src/uk/ac/ebi/www/Data.java | 21 +-
src/uk/ac/ebi/www/InputParams.java | 21 +-
src/uk/ac/ebi/www/WSFile.java | 21 +-
src/uk/ac/ebi/www/WSWUBlast.java | 13 +-
src/uk/ac/ebi/www/WSWUBlastService.java | 13 +-
src/uk/ac/ebi/www/WSWUBlastServiceLocator.java | 23 +-
src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java | 39 +-
.../AccessionMapperBindingStub.java | 795 +-
.../AccessionMapperInterface.java | 71 +-
.../AccessionMapperService.java | 61 +-
.../AccessionMapperServiceLocator.java | 385 +-
src/vamsas/IMsaWS.java | 18 +-
src/vamsas/objects/simple/Alignment.java | 25 +-
src/vamsas/objects/simple/Alignment_Helper.java | 13 +-
src/vamsas/objects/simple/JpredResult.java | 21 +-
src/vamsas/objects/simple/JpredResult_Helper.java | 13 +-
src/vamsas/objects/simple/MsaResult.java | 40 +-
src/vamsas/objects/simple/MsaResult_Helper.java | 30 +-
src/vamsas/objects/simple/Msfalignment.java | 21 +-
src/vamsas/objects/simple/Msfalignment_Helper.java | 13 +-
src/vamsas/objects/simple/Object.java | 26 +-
src/vamsas/objects/simple/Object_Helper.java | 13 +-
src/vamsas/objects/simple/Result.java | 25 +-
src/vamsas/objects/simple/Result_Helper.java | 13 +-
src/vamsas/objects/simple/Secstructpred.java | 19 +-
.../objects/simple/Secstructpred_Helper.java | 13 +-
src/vamsas/objects/simple/SeqSearchResult.java | 381 +-
.../objects/simple/SeqSearchResult_Helper.java | 175 +-
src/vamsas/objects/simple/Sequence.java | 25 +-
src/vamsas/objects/simple/SequenceSet.java | 25 +-
src/vamsas/objects/simple/SequenceSet_Helper.java | 13 +-
src/vamsas/objects/simple/Sequence_Helper.java | 13 +-
src/vamsas/objects/simple/WsJobId.java | 25 +-
src/vamsas/objects/simple/WsJobId_Helper.java | 13 +-
1037 files changed, 193576 insertions(+), 116823 deletions(-)
delete mode 100755 debian/new-upstream
create mode 100644 debian/patches/drop-lib
create mode 100644 debian/patches/encoding-fix
create mode 100644 debian/patches/testng
create mode 100644 doc/AnnotationPostAnalysis.txt
create mode 100644 doc/JalviewRNASupport.html
create mode 100644 doc/UnitTesting.html
create mode 100644 doc/biojsmsa-templates.html
create mode 100644 doc/i18n.html
create mode 100644 help/html/Jalview_Logo.png
create mode 100644 help/html/calculations/pcaviewer.gif
create mode 100644 help/html/calculations/referenceseq.html
create mode 100644 help/html/calculations/scorematrices.html
create mode 100644 help/html/calculations/structureconsensus.html
create mode 100644 help/html/colourSchemes/annotationColourSetting.gif
delete mode 100644 help/html/colourSchemes/annotationColourSetting.jpg
create mode 100644 help/html/colourSchemes/annotationColours.gif
delete mode 100644 help/html/colourSchemes/annotationColours.jpg
create mode 100644 help/html/colourSchemes/colbytcoffee.png
create mode 100644 help/html/colourSchemes/purinepyrimidine.html
create mode 100644 help/html/colourSchemes/rnahelicesColouring.html
create mode 100644 help/html/colourSchemes/rnahelicescoloring.png
create mode 100644 help/html/colourSchemes/userDefined_java6.gif
create mode 100644 help/html/colourSchemes/userDefined_java7.gif
create mode 100644 help/html/features/AnnotationColumnSelectionWithSM.gif
create mode 100644 help/html/features/AnnotationColumnSelectionWithoutSM.gif
create mode 100644 help/html/features/bioJsonFormat.html
create mode 100644 help/html/features/biojsmsa.html
create mode 100644 help/html/features/chimera.html
create mode 100644 help/html/features/columnFilterByAnnotation.html
create mode 100644 help/html/features/pdbseqfetcher.png
create mode 100644 help/html/features/pdbsequencefetcher.html
create mode 100644 help/html/features/schooser_enter-id.png
create mode 100644 help/html/features/schooser_main.png
create mode 100644 help/html/features/selectfetchdb.gif
create mode 100644 help/html/features/splitView.html
create mode 100644 help/html/features/structurechooser.html
create mode 100644 help/html/features/varna.html
create mode 100644 help/html/features/xsspannotation.html
create mode 100644 help/html/io/exportseqreport.html
create mode 100644 help/html/io/seqreport.gif
create mode 100644 help/html/io/tcoffeescores.html
delete mode 100644 help/html/jalviewjnlp.html
create mode 100644 help/html/menus/alwannotation.html
create mode 100644 help/html/menus/alwannotationpanel.html
delete mode 100644 help/html/menus/alwannotations.html
create mode 100644 help/html/na/index.html
create mode 100644 help/html/webServices/AACon.html
create mode 100644 help/html/webServices/RNAalifold.html
create mode 100644 help/html/webServices/RNAalifoldAnnotationRows.png
create mode 100644 help/html/webServices/proteinDisorder.html
create mode 100644 resources/authors.props
create mode 100644 resources/images/JalviewLogo_Huge.png
create mode 100644 resources/images/JalviewLogo_big.png
create mode 100644 resources/images/Jalview_Logo.png
create mode 100644 resources/images/Jalview_Logo_small.png
create mode 100644 resources/images/dna.png
create mode 100644 resources/images/error.png
create mode 100644 resources/images/good.png
create mode 100644 resources/images/loading.gif
copy resources/images/{logo_big.gif => logo_big_v2.gif} (100%)
copy resources/images/{logo.gif => logo_v2.gif} (100%)
create mode 100644 resources/images/protein.png
create mode 100644 resources/images/sugar.png
create mode 100644 resources/images/warning.gif
create mode 100644 resources/lang/Messages.properties
create mode 100644 resources/lang/Messages_es.properties
create mode 100644 src/com/github/reinert/jjschema/Attributes.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java
create mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java
create mode 100644 src/jalview/analysis/AlignmentAnnotationUtils.java
create mode 100644 src/jalview/analysis/AlignmentUtils.java
create mode 100644 src/jalview/analysis/AnnotationSorter.java
create mode 100644 src/jalview/analysis/CodingUtils.java
create mode 100644 src/jalview/analysis/CodonComparator.java
create mode 100644 src/jalview/analysis/Rna.java
create mode 100644 src/jalview/analysis/SecStrConsensus.java
create mode 100644 src/jalview/analysis/StructureFrequency.java
create mode 100644 src/jalview/analysis/WUSSParseException.java
create mode 100644 src/jalview/analysis/scoremodels/FeatureScoreModel.java
create mode 100644 src/jalview/analysis/scoremodels/PIDScoreModel.java
create mode 100644 src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
create mode 100644 src/jalview/analysis/scoremodels/SWScoreModel.java
create mode 100644 src/jalview/api/AlignCalcManagerI.java
create mode 100644 src/jalview/api/AlignCalcWorkerI.java
create mode 100644 src/jalview/api/AlignExportSettingI.java
create mode 100644 src/jalview/api/AlignViewControllerGuiI.java
create mode 100644 src/jalview/api/AlignViewControllerI.java
create mode 100644 src/jalview/api/AlignViewportI.java
create mode 100644 src/jalview/api/BuildDetailsI.java
create mode 100644 src/jalview/api/ComplexAlignFile.java
create mode 100644 src/jalview/api/FeatureSettingsControllerI.java
create mode 100644 src/jalview/api/FeatureSettingsModelI.java
create mode 100644 src/jalview/api/FeaturesDisplayedI.java
create mode 100644 src/jalview/api/OOMHandlerI.java
create mode 100644 src/jalview/api/RotatableCanvasI.java
create mode 100644 src/jalview/api/SplitContainerI.java
create mode 100644 src/jalview/api/ViewStyleI.java
create mode 100644 src/jalview/api/analysis/ScoreModelI.java
create mode 100644 src/jalview/api/analysis/ViewBasedAnalysisI.java
create mode 100644 src/jalview/api/structures/JalviewStructureDisplayI.java
create mode 100644 src/jalview/appletgui/AnnotationColumnChooser.java
create mode 100644 src/jalview/appletgui/AnnotationRowFilter.java
create mode 100644 src/jalview/appletgui/SplitFrame.java
create mode 100644 src/jalview/appletgui/TitledPanel.java
create mode 100644 src/jalview/bin/BuildDetails.java
create mode 100644 src/jalview/controller/AlignViewController.java
create mode 100644 src/jalview/controller/FeatureSettingsController.java
create mode 100644 src/jalview/controller/FeatureSettingsControllerGuiI.java
create mode 100644 src/jalview/datamodel/ASequence.java
create mode 100644 src/jalview/datamodel/ASequenceI.java
create mode 100644 src/jalview/datamodel/AlignedCodon.java
create mode 100644 src/jalview/datamodel/AlignmentExportData.java
create mode 100644 src/jalview/datamodel/AnnotatedCollectionI.java
create mode 100644 src/jalview/datamodel/IncompleteCodonException.java
create mode 100644 src/jalview/datamodel/RnaViewerModel.java
create mode 100644 src/jalview/datamodel/SecondaryStructureAnnotation.java
create mode 100644 src/jalview/datamodel/SequenceCollectionI.java
create mode 100644 src/jalview/datamodel/SequenceDummy.java
create mode 100644 src/jalview/datamodel/StructureViewerModel.java
create mode 100644 src/jalview/exceptions/JalviewException.java
create mode 100644 src/jalview/exceptions/NoFileSelectedException.java
create mode 100644 src/jalview/ext/jmol/PDBFileWithJmol.java
create mode 100644 src/jalview/ext/paradise/Annotate3D.java
create mode 100644 src/jalview/ext/rbvi/chimera/ChimeraCommands.java
create mode 100644 src/jalview/ext/rbvi/chimera/ChimeraListener.java
create mode 100644 src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
create mode 100644 src/jalview/ext/varna/JalviewVarnaBinding.java
create mode 100644 src/jalview/ext/varna/RnaModel.java
create mode 100644 src/jalview/ext/varna/VarnaCommands.java
create mode 100644 src/jalview/gui/AlignExportSettings.java
create mode 100644 src/jalview/gui/AnnotationChooser.java
create mode 100644 src/jalview/gui/AnnotationColumnChooser.java
create mode 100644 src/jalview/gui/AnnotationRowFilter.java
create mode 100644 src/jalview/gui/AppVarna.java
create mode 100644 src/jalview/gui/AppVarnaBinding.java
create mode 100644 src/jalview/gui/ChimeraViewFrame.java
delete mode 100644 src/jalview/gui/ConservationThread.java
create mode 100644 src/jalview/gui/CutAndPasteHtmlTransfer.java
create mode 100644 src/jalview/gui/HTMLOptions.java
create mode 100644 src/jalview/gui/Help.java
create mode 100644 src/jalview/gui/JDatabaseTree.java
create mode 100644 src/jalview/gui/JalviewChimeraBindingModel.java
create mode 100644 src/jalview/gui/MenuChooser.java
create mode 100644 src/jalview/gui/PDBSearchPanel.java
create mode 100644 src/jalview/gui/ProgressBar.java
create mode 100644 src/jalview/gui/SVGOptions.java
delete mode 100644 src/jalview/gui/ScriptWindow.java
create mode 100644 src/jalview/gui/SplitFrame.java
create mode 100644 src/jalview/gui/StructureChooser.java
create mode 100644 src/jalview/gui/StructureViewer.java
create mode 100644 src/jalview/gui/StructureViewerBase.java
create mode 100644 src/jalview/httpserver/AbstractRequestHandler.java
create mode 100644 src/jalview/httpserver/HttpServer.java
create mode 100644 src/jalview/io/BioJsHTMLOutput.java
create mode 100644 src/jalview/io/Gff3File.java
create mode 100644 src/jalview/io/HtmlFile.java
create mode 100644 src/jalview/io/HtmlSvgOutput.java
create mode 100644 src/jalview/io/InputStreamParser.java
create mode 100644 src/jalview/io/JSONFile.java
create mode 100644 src/jalview/io/PhylipFile.java
create mode 100644 src/jalview/io/RnamlFile.java
create mode 100644 src/jalview/io/SequenceAnnotationReport.java
create mode 100644 src/jalview/io/TCoffeeScoreFile.java
create mode 100644 src/jalview/jbgui/GAlignExportSettings.java
create mode 100644 src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
create mode 100644 src/jalview/jbgui/GPDBSearchPanel.java
create mode 100644 src/jalview/jbgui/GRnaStructureViewer.java
create mode 100644 src/jalview/jbgui/GSplitFrame.java
create mode 100644 src/jalview/jbgui/GStructureChooser.java
create mode 100644 src/jalview/jbgui/PDBDocFieldPreferences.java
create mode 100644 src/jalview/json/binding/biojs/BioJSReleasePojo.java
create mode 100644 src/jalview/json/binding/biojs/BioJSRepositoryPojo.java
create mode 100644 src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
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create mode 100644 src/jalview/json/binding/biojson/v1/JalviewBioJsColorSchemeMapper.java
create mode 100644 src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
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create mode 100644 src/jalview/renderer/AnnotationRenderer.java
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create mode 100644 src/jalview/schemabinding/version2/AnnotationColourScheme.java
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create mode 100644 src/jalview/schemabinding/version2/RnaViewer.java
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create mode 100644 src/jalview/schemes/RNAHelicesColour.java
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create mode 100644 src/jalview/util/ColorUtils.java
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create mode 100644 src/jalview/util/ReverseListIterator.java
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create mode 100644 src/jalview/viewmodel/AlignmentViewport.java
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create mode 100644 src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
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create mode 100644 src/jalview/ws/jws2/AAConClient.java
create mode 100644 src/jalview/ws/jws2/AADisorderClient.java
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create mode 100644 src/jalview/ws/jws2/JPred301Client.java
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create mode 100644 src/jalview/ws/jws2/RNAalifoldClient.java
create mode 100644 src/jalview/ws/jws2/SequenceAnnotationWSClient.java
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create mode 100644 src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
create mode 100644 src/jalview/ws/params/AutoCalcSetting.java
create mode 100644 src/jalview/ws/uimodel/AlignAnalysisUIText.java
create mode 100644 src/jalview/ws/uimodel/PDBRestRequest.java
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