[jalview] 02/03: Merge tag 'upstream/2.10.1.dfsg'
Ximin Luo
infinity0 at debian.org
Sat Dec 10 15:13:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
infinity0 pushed a commit to branch master
in repository jalview.
commit e643aaa940725d05c9e2c5827d9b05f7bd0cdb6b
Merge: ef4e6f6 7eb4c6f
Author: Ximin Luo <infinity0 at debian.org>
Date: Sat Dec 10 16:11:32 2016 +0100
Merge tag 'upstream/2.10.1.dfsg'
Upstream version 2.10.1.dfsg
# gpg: Signature made Sat 10 Dec 2016 16:11:29 CET
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# gpg: Good signature from "Ximin Luo <infinity0 at pwned.gg>" [ultimate]
# gpg: aka "Ximin Luo <infinity0 at torproject.org>" [ultimate]
# gpg: aka "Ximin Luo <infinity0 at freenetproject.org>" [ultimate]
# gpg: aka "Ximin Luo <infinity0 at debian.org>" [ultimate]
# gpg: aka "Satoshi Nakamoto (www.bitcoin.org) <satoshin at gmx.com>" [ultimate]
JalviewApplet.jpx | 150 +-
JalviewX.jpx | 94 +-
README | 2 +-
build.xml | 1439 ++--
doc/AddingGroovySupport.html | 27 +-
doc/AnnotationPostAnalysis.txt | 59 +
doc/JalviewRNASupport.html | 84 +
doc/UnitTesting.html | 110 +
doc/biojsmsa-templates.html | 101 +
doc/building.html | 50 +-
doc/developing.html | 103 +-
doc/i18n.html | 96 +
doc/index.html | 327 +-
doc/newdmobj.html | 73 +-
help/help.hs | 104 +-
help/help.jhm | 62 +-
help/helpTOC.html | 46 +-
help/helpTOC.xml | 270 +-
help/html/Jalview_Logo.png | Bin 0 -> 15420 bytes
help/html/calculations/consensus.html | 80 +-
help/html/calculations/conservation.html | 98 +-
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 | 71 +
help/html/calculations/scorematrices.html | 1664 +++++
help/html/calculations/sorting.html | 139 +-
help/html/calculations/structureconsensus.html | 63 +
help/html/calculations/tree.html | 177 +-
help/html/calculations/treeviewer.html | 209 +-
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 | 127 +-
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 | 69 +-
help/html/colourSchemes/helix.html | 97 +-
help/html/colourSchemes/hydrophobic.html | 104 +-
help/html/colourSchemes/index.html | 646 +-
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 | 150 +-
.../features/AnnotationColumnSelectionWithSM.gif | Bin 0 -> 42694 bytes
.../AnnotationColumnSelectionWithoutSM.gif | Bin 0 -> 37778 bytes
help/html/features/annotation.html | 297 +-
help/html/features/annotationsFormat.html | 559 +-
help/html/features/bioJsonFormat.html | 82 +
help/html/features/biojsmsa.html | 58 +
help/html/features/chimera.html | 244 +
help/html/features/clarguments.html | 423 +-
help/html/features/codingfeatures.html | 72 +-
help/html/features/columnFilterByAnnotation.html | 91 +
help/html/features/commandline.html | 91 +-
help/html/features/creatinFeatures.html | 84 +-
help/html/features/cursorMode.html | 123 +-
help/html/features/dasfeatures.html | 101 +-
help/html/features/dassettings.html | 90 +-
help/html/features/editingFeatures.html | 64 +-
help/html/features/ensemblsequencefetcher.html | 96 +
help/html/features/featuresFormat.html | 312 +-
help/html/features/featureschemes.html | 139 +-
help/html/features/featuresettings.html | 173 +-
help/html/features/groovy.html | 210 +-
help/html/features/hiddenRegions.html | 176 +-
help/html/features/jalarchive.html | 43 +-
help/html/features/jmol.html | 496 +-
help/html/features/mmcif.html | 55 +
help/html/features/multipleViews.html | 135 +-
help/html/features/newkeystrokes.html | 76 +-
help/html/features/overview.html | 38 +-
help/html/features/pdbseqfetcher.png | Bin 0 -> 198431 bytes
help/html/features/pdbsequencefetcher.html | 102 +
help/html/features/pdbviewer.html | 295 +-
help/html/features/preferences.html | 466 +-
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 | 214 +-
help/html/features/selectfetchdb.gif | Bin 0 -> 19522 bytes
help/html/features/seqfeatures.html | 156 +-
help/html/features/seqfetch.html | 143 +-
help/html/features/seqfetcher.gif | Bin 8702 -> 11434 bytes
help/html/features/seqmappings.html | 89 +-
help/html/features/sifts_mapping_output.png | Bin 0 -> 123157 bytes
help/html/features/siftsmapping.html | 90 +
help/html/features/splitView.html | 162 +
help/html/features/structurechooser.html | 134 +
help/html/features/uniprotqueryfields.html | 391 +
help/html/features/uniprotseqfetcher.png | Bin 0 -> 215964 bytes
help/html/features/uniprotsequencefetcher.html | 169 +
help/html/features/varna.html | 93 +
help/html/features/viewingpdbs.html | 264 +-
help/html/features/wrap.html | 637 +-
help/html/features/xsspannotation.html | 94 +
help/html/groovy/featureCounter.html | 269 +
help/html/index.html | 106 +-
help/html/io/export.html | 110 +-
help/html/io/exportseqreport.html | 58 +
help/html/io/fileformats.html | 130 +-
help/html/io/index.html | 139 +-
help/html/io/modellerpir.html | 75 +-
help/html/io/seqreport.gif | Bin 0 -> 25151 bytes
help/html/io/tcoffeescores.html | 84 +
help/html/jalviewjnlp.html | 78 -
help/html/keys.html | 580 +-
help/html/memory.html | 211 +-
help/html/menus/alignmentMenu.html | 1197 +--
help/html/menus/alwannotation.html | 90 +
help/html/menus/alwannotationpanel.html | 121 +
help/html/menus/alwannotations.html | 87 -
help/html/menus/alwcalculate.html | 193 +-
help/html/menus/alwcolour.html | 89 +-
help/html/menus/alwedit.html | 178 +-
help/html/menus/alwfile.html | 212 +-
help/html/menus/alwformat.html | 116 +-
help/html/menus/alwselect.html | 94 +-
help/html/menus/alwview.html | 129 +-
help/html/menus/desktopMenu.html | 233 +-
help/html/menus/index.html | 55 +-
help/html/menus/popupMenu.html | 321 +-
help/html/menus/wsmenu.html | 162 +-
help/html/misc/aaproperties.html | 80 +-
help/html/misc/aminoAcids.html | 529 +-
help/html/misc/geneticCode.html | 153 +-
help/html/na/index.html | 123 +
help/html/privacy.html | 124 +-
help/html/releases.html | 3901 +++++++---
help/html/vamsas/index.html | 255 +-
help/html/webServices/AACon.html | 73 +
help/html/webServices/JABAWS.html | 105 +-
help/html/webServices/RNAalifold.html | 86 +
help/html/webServices/RNAalifoldAnnotationRows.png | Bin 0 -> 31732 bytes
help/html/webServices/dbreffetcher.html | 176 +-
help/html/webServices/index.html | 152 +-
help/html/webServices/jnet.html | 216 +-
help/html/webServices/msaclient.html | 128 +-
help/html/webServices/newsreader.html | 77 +-
help/html/webServices/proteinDisorder.html | 250 +
help/html/webServices/shmr.html | 101 +-
help/html/webServices/urllinks.html | 172 +-
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 | 143 +-
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 | 297 +-
resources/fts/pdb_data_columns.txt | 130 +
resources/fts/uniprot_data_columns.txt | 175 +
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/blank_16x16_placeholder.png | Bin 0 -> 2873 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 | 1277 ++++
resources/lang/Messages_es.properties | 1278 ++++
resources/so-xp-simple.obo.zip | Bin 0 -> 144326 bytes
resources/uniprot_mapping.xml | 9 +-
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 | 731 +-
schemas/jalviewJvV1.xsd | 325 +-
schemas/sifts/alignment.xsd | 155 +
schemas/sifts/dataTypes.xsd | 154 +
schemas/sifts/eFamily.xsd | 154 +
schemas/vamsas.xsd | 18 +-
schemas/vamsasJvV1.xsd | 183 +-
src/MCview/AppletPDBCanvas.java | 283 +-
src/MCview/AppletPDBViewer.java | 87 +-
src/MCview/Atom.java | 75 +-
src/MCview/Bond.java | 33 +-
src/MCview/MCMatrix.java | 13 +-
src/MCview/PDBCanvas.java | 284 +-
src/MCview/PDBChain.java | 520 +-
src/MCview/PDBViewer.java | 267 +-
src/MCview/PDBfile.java | 233 +-
src/MCview/Residue.java | 34 +-
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 | 10 +-
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 | 1043 +++
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java | 372 +
.../edu/ucsf/rbvi/strucviz2/ChimeraManager.java | 889 +++
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java | 623 ++
.../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 | 992 +++
.../edu/ucsf/rbvi/strucviz2/StructureSettings.java | 62 +
.../ucsf/rbvi/strucviz2/port/ListenerThreads.java | 334 +
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 | 758 +-
src/jalview/analysis/AlignSeq.java | 458 +-
src/jalview/analysis/AlignmentAnnotationUtils.java | 243 +
src/jalview/analysis/AlignmentSorter.java | 291 +-
src/jalview/analysis/AlignmentUtils.java | 2984 ++++++++
src/jalview/analysis/AnnotationSorter.java | 416 ++
src/jalview/analysis/CodingUtils.java | 139 +
src/jalview/analysis/CodonComparator.java | 111 +
src/jalview/analysis/Conservation.java | 597 +-
src/jalview/analysis/CrossRef.java | 1702 +++--
src/jalview/analysis/Dna.java | 1685 +++--
src/jalview/analysis/Finder.java | 125 +-
src/jalview/analysis/Grouping.java | 147 +-
src/jalview/analysis/NJTree.java | 457 +-
src/jalview/analysis/PCA.java | 140 +-
src/jalview/analysis/ParseProperties.java | 56 +-
src/jalview/analysis/Rna.java | 503 ++
src/jalview/analysis/SecStrConsensus.java | 254 +
src/jalview/analysis/SeqsetUtils.java | 48 +-
src/jalview/analysis/SequenceIdMatcher.java | 199 +-
src/jalview/analysis/StructureFrequency.java | 486 ++
src/jalview/analysis/WUSSParseException.java | 43 +
.../analysis/scoremodels/FeatureScoreModel.java | 161 +
.../analysis/scoremodels/PIDScoreModel.java | 75 +
.../scoremodels/PairwiseSeqScoreModel.java | 80 +
src/jalview/analysis/scoremodels/SWScoreModel.java | 94 +
src/jalview/api/AlignCalcManagerI.java | 164 +
src/jalview/api/AlignCalcWorkerI.java | 60 +
src/jalview/api/AlignExportSettingI.java | 73 +
src/jalview/api/AlignViewControllerGuiI.java | 65 +
src/jalview/api/AlignViewControllerI.java | 112 +
src/jalview/api/AlignViewportI.java | 448 ++
src/jalview/api/AlignmentViewPanel.java | 57 +-
src/jalview/api/BuildDetailsI.java | 30 +
src/jalview/api/ComplexAlignFile.java | 68 +
src/jalview/api/DBRefEntryI.java | 114 +
src/jalview/api/FeatureColourI.java | 181 +
src/jalview/api/FeatureRenderer.java | 146 +-
src/jalview/api/FeatureSettingsControllerI.java | 28 +
src/jalview/api/FeatureSettingsModelI.java | 95 +
src/jalview/api/FeaturesDisplayedI.java | 49 +
src/jalview/api/FeaturesSourceI.java | 28 +
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/SiftsClientI.java | 132 +
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 | 884 ++-
src/jalview/appletgui/AlignFrame.java | 7861 +++++++++++---------
src/jalview/appletgui/AlignViewport.java | 1727 +----
src/jalview/appletgui/AlignmentPanel.java | 732 +-
src/jalview/appletgui/AnnotationColourChooser.java | 206 +-
src/jalview/appletgui/AnnotationColumnChooser.java | 954 +++
src/jalview/appletgui/AnnotationLabels.java | 331 +-
src/jalview/appletgui/AnnotationPanel.java | 1029 +--
src/jalview/appletgui/AnnotationRowFilter.java | 173 +
src/jalview/appletgui/AppletJmol.java | 257 +-
src/jalview/appletgui/AppletJmolBinding.java | 110 +-
src/jalview/appletgui/CutAndPasteTransfer.java | 385 +-
src/jalview/appletgui/EditNameDialog.java | 20 +-
src/jalview/appletgui/EmbmenuFrame.java | 586 +-
src/jalview/appletgui/ExtJmol.java | 107 +-
src/jalview/appletgui/FeatureColourChooser.java | 147 +-
src/jalview/appletgui/FeatureRenderer.java | 999 +--
src/jalview/appletgui/FeatureSettings.java | 486 +-
src/jalview/appletgui/Finder.java | 116 +-
src/jalview/appletgui/FontChooser.java | 369 +-
src/jalview/appletgui/IdCanvas.java | 125 +-
src/jalview/appletgui/IdPanel.java | 99 +-
src/jalview/appletgui/IdwidthAdjuster.java | 51 +-
src/jalview/appletgui/JVDialog.java | 50 +-
src/jalview/appletgui/OverviewPanel.java | 122 +-
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 | 361 +-
src/jalview/appletgui/SeqCanvas.java | 334 +-
src/jalview/appletgui/SeqPanel.java | 650 +-
src/jalview/appletgui/SequenceRenderer.java | 157 +-
src/jalview/appletgui/SliderPanel.java | 114 +-
src/jalview/appletgui/SplitFrame.java | 236 +
src/jalview/appletgui/TitledPanel.java | 95 +
src/jalview/appletgui/Tooltip.java | 478 +-
src/jalview/appletgui/TreeCanvas.java | 162 +-
src/jalview/appletgui/TreePanel.java | 113 +-
src/jalview/appletgui/UserDefinedColours.java | 174 +-
src/jalview/bin/ArgsParser.java | 117 +
src/jalview/bin/BuildDetails.java | 75 +
src/jalview/bin/Cache.java | 429 +-
src/jalview/bin/Jalview.java | 950 +--
src/jalview/bin/JalviewLite.java | 5722 +++++++-------
src/jalview/bin/JalviewLiteURLRetrieve.java | 22 +-
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 | 703 +-
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 | 155 +-
src/jalview/controller/AlignViewController.java | 467 ++
.../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 | 114 +
src/jalview/datamodel/AlignedCodonFrame.java | 1101 ++-
src/jalview/datamodel/Alignment.java | 1118 ++-
src/jalview/datamodel/AlignmentAnnotation.java | 785 +-
src/jalview/datamodel/AlignmentExportData.java | 83 +
src/jalview/datamodel/AlignmentI.java | 282 +-
src/jalview/datamodel/AlignmentOrder.java | 56 +-
src/jalview/datamodel/AlignmentView.java | 2423 +++---
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 | 1307 ++--
src/jalview/datamodel/CigarCigar.java | 125 +-
src/jalview/datamodel/CigarSimple.java | 67 +-
src/jalview/datamodel/ColumnSelection.java | 3061 ++++----
src/jalview/datamodel/DBRefEntry.java | 226 +-
src/jalview/datamodel/DBRefSource.java | 257 +-
src/jalview/datamodel/FeatureProperties.java | 120 +-
src/jalview/datamodel/GraphLine.java | 29 +-
src/jalview/datamodel/HiddenSequences.java | 193 +-
.../datamodel/IncompleteCodonException.java | 33 +
src/jalview/datamodel/Mapping.java | 406 +-
src/jalview/datamodel/MappingType.java | 83 +
src/jalview/datamodel/NodeTransformI.java | 13 +-
src/jalview/datamodel/PDBEntry.java | 382 +-
src/jalview/datamodel/Profile.java | 163 +
src/jalview/datamodel/ProfileI.java | 87 +
src/jalview/datamodel/Profiles.java | 63 +
src/jalview/datamodel/ProfilesI.java | 32 +
src/jalview/datamodel/Provenance.java | 15 +-
src/jalview/datamodel/ProvenanceEntry.java | 13 +-
src/jalview/datamodel/ResidueCount.java | 641 ++
src/jalview/datamodel/RnaViewerModel.java | 64 +
src/jalview/datamodel/SearchResultMatchI.java | 50 +
src/jalview/datamodel/SearchResults.java | 328 +-
src/jalview/datamodel/SearchResultsI.java | 104 +
.../datamodel/SecondaryStructureAnnotation.java | 52 +
src/jalview/datamodel/SeqCigar.java | 261 +-
src/jalview/datamodel/Sequence.java | 781 +-
src/jalview/datamodel/SequenceCollectionI.java | 67 +
src/jalview/datamodel/SequenceDummy.java | 63 +
src/jalview/datamodel/SequenceFeature.java | 322 +-
src/jalview/datamodel/SequenceGroup.java | 518 +-
src/jalview/datamodel/SequenceI.java | 217 +-
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 | 59 -
src/jalview/datamodel/xdb/embl/EmblEntry.java | 1137 +--
src/jalview/datamodel/xdb/embl/EmblError.java | 18 +-
src/jalview/datamodel/xdb/embl/EmblFeature.java | 48 +-
.../datamodel/xdb/embl/EmblFeatureLocElement.java | 116 -
.../datamodel/xdb/embl/EmblFeatureLocations.java | 168 -
src/jalview/datamodel/xdb/embl/EmblFile.java | 115 +-
src/jalview/datamodel/xdb/embl/EmblSequence.java | 59 +-
src/jalview/datamodel/xdb/embl/Qualifier.java | 21 +-
src/jalview/exceptions/JalviewException.java | 45 +
.../exceptions/NoFileSelectedException.java | 30 +
src/jalview/ext/android/ContainerHelpers.java | 108 +
src/jalview/ext/android/SparseIntArray.java | 432 ++
src/jalview/ext/android/SparseShortArray.java | 442 ++
src/jalview/ext/ensembl/EnsemblCdna.java | 131 +
src/jalview/ext/ensembl/EnsemblCds.java | 138 +
src/jalview/ext/ensembl/EnsemblFeatures.java | 160 +
src/jalview/ext/ensembl/EnsemblGene.java | 615 ++
src/jalview/ext/ensembl/EnsemblGenome.java | 115 +
src/jalview/ext/ensembl/EnsemblGenomes.java | 65 +
src/jalview/ext/ensembl/EnsemblInfo.java | 91 +
src/jalview/ext/ensembl/EnsemblLookup.java | 180 +
src/jalview/ext/ensembl/EnsemblProtein.java | 147 +
src/jalview/ext/ensembl/EnsemblRestClient.java | 567 ++
src/jalview/ext/ensembl/EnsemblSeqProxy.java | 955 +++
.../ext/ensembl/EnsemblSequenceFetcher.java | 133 +
src/jalview/ext/ensembl/EnsemblSymbol.java | 159 +
src/jalview/ext/ensembl/EnsemblXref.java | 224 +
src/jalview/ext/ensembl/Species.java | 52 +
src/jalview/ext/htsjdk/HtsContigDb.java | 232 +
src/jalview/ext/jmol/JalviewJmolBinding.java | 3015 ++++----
src/jalview/ext/jmol/JmolCommands.java | 338 +-
src/jalview/ext/jmol/JmolParser.java | 658 ++
src/jalview/ext/paradise/Annotate3D.java | 255 +
src/jalview/ext/rbvi/chimera/ChimeraCommands.java | 293 +
src/jalview/ext/rbvi/chimera/ChimeraListener.java | 149 +
.../ext/rbvi/chimera/JalviewChimeraBinding.java | 1127 +++
src/jalview/ext/so/SequenceOntology.java | 474 ++
src/jalview/ext/varna/JalviewVarnaBinding.java | 35 +
src/jalview/ext/varna/RnaModel.java | 52 +
src/jalview/ext/varna/VarnaCommands.java | 170 +
src/jalview/fts/api/FTSData.java | 46 +
src/jalview/fts/api/FTSDataColumnI.java | 161 +
src/jalview/fts/api/FTSRestClientI.java | 139 +
src/jalview/fts/api/GFTSPanelI.java | 140 +
.../fts/core/DecimalFormatTableCellRenderer.java | 80 +
src/jalview/fts/core/FTSDataColumnPreferences.java | 338 +
src/jalview/fts/core/FTSRestClient.java | 506 ++
src/jalview/fts/core/FTSRestRequest.java | 190 +
src/jalview/fts/core/FTSRestResponse.java | 174 +
src/jalview/fts/core/GFTSPanel.java | 992 +++
src/jalview/fts/service/pdb/PDBFTSPanel.java | 279 +
src/jalview/fts/service/pdb/PDBFTSRestClient.java | 426 ++
.../fts/service/uniprot/UniProtFTSRestClient.java | 323 +
.../fts/service/uniprot/UniprotFTSPanel.java | 238 +
src/jalview/gui/AlignExportSettings.java | 118 +
src/jalview/gui/AlignFrame.java | 3384 +++++----
src/jalview/gui/AlignViewport.java | 2425 ++----
src/jalview/gui/AlignmentPanel.java | 1255 ++--
src/jalview/gui/AnnotationChooser.java | 657 ++
src/jalview/gui/AnnotationColourChooser.java | 531 +-
src/jalview/gui/AnnotationColumnChooser.java | 922 +++
src/jalview/gui/AnnotationExporter.java | 628 +-
src/jalview/gui/AnnotationLabels.java | 990 ++-
src/jalview/gui/AnnotationPanel.java | 1518 ++--
src/jalview/gui/AnnotationRowFilter.java | 407 +
src/jalview/gui/AppJmol.java | 1123 ++-
src/jalview/gui/AppJmolBinding.java | 146 +-
src/jalview/gui/AppVarna.java | 752 ++
src/jalview/gui/AppVarnaBinding.java | 577 ++
src/jalview/gui/AssociatePdbFileWithSeq.java | 107 +-
src/jalview/gui/BlogReader.java | 121 +-
src/jalview/gui/ChimeraViewFrame.java | 1147 +++
src/jalview/gui/ConservationThread.java | 103 -
src/jalview/gui/Console.java | 42 +-
src/jalview/gui/CrossRefAction.java | 312 +
src/jalview/gui/CutAndPasteHtmlTransfer.java | 252 +
src/jalview/gui/CutAndPasteTransfer.java | 215 +-
src/jalview/gui/DasSourceBrowser.java | 1826 +++--
src/jalview/gui/Desktop.java | 1861 +++--
src/jalview/gui/EPSOptions.java | 47 +-
src/jalview/gui/EditNameDialog.java | 30 +-
src/jalview/gui/FeatureColourChooser.java | 233 +-
src/jalview/gui/FeatureRenderer.java | 1209 +--
src/jalview/gui/FeatureSettings.java | 884 ++-
src/jalview/gui/Finder.java | 220 +-
src/jalview/gui/FontChooser.java | 173 +-
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 | 164 +-
src/jalview/gui/IdPanel.java | 338 +-
src/jalview/gui/IdwidthAdjuster.java | 50 +-
src/jalview/gui/JDatabaseTree.java | 596 ++
src/jalview/gui/Jalview2XML.java | 4913 ++++++++----
src/jalview/gui/Jalview2XML_V1.java | 976 +--
src/jalview/gui/JalviewAppender.java | 13 +-
src/jalview/gui/JalviewChangeSupport.java | 32 +-
src/jalview/gui/JalviewChimeraBindingModel.java | 144 +
src/jalview/gui/JalviewDialog.java | 102 +-
src/jalview/gui/JvSwingUtils.java | 184 +-
src/jalview/gui/MenuChooser.java | 99 +
src/jalview/gui/OOMWarning.java | 177 +-
src/jalview/gui/OptsAndParamsPage.java | 224 +-
src/jalview/gui/OptsParametersContainerI.java | 26 +-
src/jalview/gui/OverviewPanel.java | 169 +-
src/jalview/gui/PCAPanel.java | 476 +-
src/jalview/gui/PaintRefresher.java | 134 +-
src/jalview/gui/PairwiseAlignPanel.java | 50 +-
src/jalview/gui/PopupMenu.java | 1420 ++--
src/jalview/gui/Preferences.java | 715 +-
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 | 443 +-
src/jalview/gui/ScriptWindow.java | 732 --
src/jalview/gui/SeqCanvas.java | 312 +-
src/jalview/gui/SeqPanel.java | 1090 +--
src/jalview/gui/SequenceFetcher.java | 1090 +--
src/jalview/gui/SequenceRenderer.java | 196 +-
src/jalview/gui/SliderPanel.java | 96 +-
src/jalview/gui/SplashScreen.java | 304 +-
src/jalview/gui/SplitFrame.java | 756 ++
src/jalview/gui/StructureChooser.java | 1178 +++
src/jalview/gui/StructureViewer.java | 248 +
src/jalview/gui/StructureViewerBase.java | 555 ++
src/jalview/gui/TextColourChooser.java | 103 +-
src/jalview/gui/TreeCanvas.java | 311 +-
src/jalview/gui/TreePanel.java | 211 +-
src/jalview/gui/UserDefinedColours.java | 322 +-
src/jalview/gui/UserQuestionnaireCheck.java | 34 +-
src/jalview/gui/VamsasApplication.java | 69 +-
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 | 192 +-
src/jalview/io/AlignmentProperties.java | 35 +-
src/jalview/io/AnnotationFile.java | 3291 ++++----
src/jalview/io/AppletFormatAdapter.java | 472 +-
src/jalview/io/BLCFile.java | 28 +-
src/jalview/io/BioJsHTMLOutput.java | 315 +
src/jalview/io/ClansFile.java | 57 +-
src/jalview/io/ClustalFile.java | 79 +-
src/jalview/io/DBRefFile.java | 91 +-
src/jalview/io/FastaFile.java | 78 +-
src/jalview/io/FeaturesFile.java | 2181 +++---
src/jalview/io/FileLoader.java | 206 +-
src/jalview/io/FileParse.java | 272 +-
src/jalview/io/FormatAdapter.java | 141 +-
src/jalview/io/HTMLOutput.java | 456 +-
src/jalview/io/HtmlFile.java | 193 +
src/jalview/io/HtmlSvgOutput.java | 307 +
src/jalview/io/IdentifyFile.java | 268 +-
src/jalview/io/InputStreamParser.java | 57 +
src/jalview/io/JPredFile.java | 39 +-
src/jalview/io/JSONFile.java | 895 +++
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 | 121 +-
src/jalview/io/MatrixFile.java | 69 +-
src/jalview/io/ModellerDescription.java | 98 +-
src/jalview/io/NewickFile.java | 48 +-
src/jalview/io/PDBFeatureSettings.java | 85 +
src/jalview/io/PIRFile.java | 25 +-
src/jalview/io/PfamFile.java | 124 +-
src/jalview/io/PhylipFile.java | 329 +
src/jalview/io/PileUpfile.java | 40 +-
src/jalview/io/RnamlFile.java | 244 +
src/jalview/io/SequenceAnnotationReport.java | 469 ++
src/jalview/io/SimpleBlastFile.java | 28 +-
src/jalview/io/StockholmFile.java | 1781 +++--
src/jalview/io/StructureFile.java | 508 ++
src/jalview/io/TCoffeeScoreFile.java | 651 ++
src/jalview/io/VamsasAppDatastore.java | 191 +-
src/jalview/io/WSWUBlastClient.java | 67 +-
src/jalview/io/gff/ExonerateHelper.java | 365 +
src/jalview/io/gff/Gff2Helper.java | 71 +
src/jalview/io/gff/Gff3Helper.java | 425 ++
src/jalview/io/gff/GffConstants.java | 43 +
src/jalview/io/gff/GffHelperBase.java | 426 ++
src/jalview/io/gff/GffHelperFactory.java | 89 +
src/jalview/io/gff/GffHelperI.java | 63 +
src/jalview/io/gff/InterProScanHelper.java | 138 +
src/jalview/io/gff/SequenceOntologyFactory.java | 48 +
src/jalview/io/gff/SequenceOntologyI.java | 80 +
src/jalview/io/gff/SequenceOntologyLite.java | 240 +
src/jalview/io/packed/DataProvider.java | 47 +-
src/jalview/io/packed/JalviewDataset.java | 290 +-
src/jalview/io/packed/ParsePackedSet.java | 70 +-
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 | 23 +-
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 | 724 +-
src/jalview/io/vamsas/Sequencemapping.java | 60 +-
src/jalview/io/vamsas/Tree.java | 82 +-
src/jalview/javascript/JSFunctionExec.java | 544 +-
src/jalview/javascript/JalviewLiteJsApi.java | 166 +-
src/jalview/javascript/JsCallBack.java | 26 +-
src/jalview/javascript/JsSelectionSender.java | 50 +-
src/jalview/javascript/MouseOverListener.java | 39 +-
.../javascript/MouseOverStructureListener.java | 629 +-
src/jalview/jbgui/GAlignExportSettings.java | 192 +
src/jalview/jbgui/GAlignFrame.java | 2273 ++++--
src/jalview/jbgui/GAlignmentPanel.java | 26 +-
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java | 275 +
src/jalview/jbgui/GCutAndPasteTransfer.java | 63 +-
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/GPairwiseAlignPanel.java | 28 +-
src/jalview/jbgui/GPreferences.java | 1606 ++--
src/jalview/jbgui/GRestInputParamEditDialog.java | 118 +-
src/jalview/jbgui/GRestServiceEditorPane.java | 273 +-
src/jalview/jbgui/GRnaStructureViewer.java | 43 +
src/jalview/jbgui/GSequenceLink.java | 85 +-
src/jalview/jbgui/GSliderPanel.java | 43 +-
src/jalview/jbgui/GSplitFrame.java | 224 +
src/jalview/jbgui/GStructureChooser.java | 819 ++
src/jalview/jbgui/GStructureViewer.java | 313 +-
src/jalview/jbgui/GTreePanel.java | 72 +-
src/jalview/jbgui/GUserDefinedColours.java | 72 +-
src/jalview/jbgui/GWebserviceInfo.java | 45 +-
src/jalview/jbgui/GWsPreferences.java | 121 +-
.../json/binding/biojs/BioJSReleasePojo.java | 66 +
.../json/binding/biojs/BioJSRepositoryPojo.java | 111 +
.../biojson/v1/AlignmentAnnotationPojo.java | 149 +
.../json/binding/biojson/v1/AlignmentPojo.java | 158 +
.../biojson/v1/AnnotationDisplaySettingPojo.java | 118 +
.../json/binding/biojson/v1/AnnotationPojo.java | 101 +
.../binding/biojson/v1/ColourSchemeMapper.java | 111 +
.../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 | 1622 ++++
src/jalview/renderer/AwtRenderPanelI.java | 62 +
src/jalview/renderer/ScaleRenderer.java | 132 +
.../renderer/seqfeatures/FeatureRenderer.java | 465 ++
src/jalview/rest/RestHandler.java | 115 +
src/jalview/schemabinding/version2/.castor.cdr | 45 -
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 | 1842 +++--
.../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 | 529 +-
.../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 | 276 +-
.../version2/descriptors/GroupDescriptor.java | 443 +-
.../descriptors/HiddenColumnsDescriptor.java | 440 +-
.../version2/descriptors/JGroupDescriptor.java | 2162 +++---
.../version2/descriptors/JSeqDescriptor.java | 1146 +--
.../descriptors/JalviewModelDescriptor.java | 600 +-
.../JalviewModelSequenceDescriptor.java | 815 +-
.../descriptors/JalviewUserColoursDescriptor.java | 541 +-
.../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 | 277 +-
.../descriptors/UserColoursDescriptor.java | 445 +-
.../version2/descriptors/VAMSASDescriptor.java | 471 +-
.../descriptors/VamsasModelDescriptor.java | 276 +-
.../version2/descriptors/ViewportDescriptor.java | 4612 +++++++-----
.../WebServiceParameterSetDescriptor.java | 693 +-
src/jalview/schemes/AnnotationColourGradient.java | 318 +-
src/jalview/schemes/Blosum62ColourScheme.java | 48 +-
src/jalview/schemes/BuriedColourScheme.java | 19 +-
src/jalview/schemes/ClustalxColourScheme.java | 227 +-
src/jalview/schemes/ColourSchemeI.java | 103 +-
src/jalview/schemes/ColourSchemeProperty.java | 180 +-
src/jalview/schemes/Consensus.java | 13 +-
src/jalview/schemes/CovariationColourScheme.java | 124 +
src/jalview/schemes/FeatureColour.java | 696 ++
src/jalview/schemes/FeatureSettingsAdapter.java | 68 +
src/jalview/schemes/FollowerColourScheme.java | 69 +
src/jalview/schemes/GraduatedColor.java | 295 -
src/jalview/schemes/HelixColourScheme.java | 19 +-
src/jalview/schemes/HydrophobicColourScheme.java | 19 +-
src/jalview/schemes/NucleotideColourScheme.java | 24 +-
src/jalview/schemes/PIDColourScheme.java | 45 +-
.../schemes/PurinePyrimidineColourScheme.java | 90 +
src/jalview/schemes/RNAHelicesColour.java | 205 +
src/jalview/schemes/RNAHelicesColourChooser.java | 137 +
.../schemes/RNAInteractionColourScheme.java | 85 +
src/jalview/schemes/ResidueColourScheme.java | 271 +-
src/jalview/schemes/ResidueProperties.java | 2662 +++++--
src/jalview/schemes/ScoreColourScheme.java | 25 +-
src/jalview/schemes/ScoreMatrix.java | 259 +-
src/jalview/schemes/StrandColourScheme.java | 19 +-
src/jalview/schemes/TCoffeeColourScheme.java | 144 +
src/jalview/schemes/TaylorColourScheme.java | 15 +-
src/jalview/schemes/TurnColourScheme.java | 19 +-
src/jalview/schemes/UserColourScheme.java | 54 +-
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 | 23 +-
src/jalview/structure/StructureImportSettings.java | 153 +
src/jalview/structure/StructureListener.java | 71 +-
src/jalview/structure/StructureMapping.java | 112 +-
.../structure/StructureMappingcommandSet.java | 49 +-
.../structure/StructureSelectionManager.java | 1284 +++-
src/jalview/structure/VamsasListener.java | 75 +-
src/jalview/structure/VamsasSource.java | 30 +-
.../structures/models/AAStructureBindingModel.java | 680 ++
.../models/SequenceStructureBindingModel.java | 72 +
src/jalview/util/AWTConsole.java | 35 +-
src/jalview/util/ArrayUtils.java | 47 +
src/jalview/util/BrowserLauncher.java | 194 +-
src/jalview/util/CaseInsensitiveString.java | 77 +
src/jalview/util/ColorUtils.java | 194 +
src/jalview/util/Comparison.java | 294 +-
src/jalview/util/DBRefUtils.java | 575 +-
src/jalview/util/DnaUtils.java | 153 +
src/jalview/util/Format.java | 93 +-
src/jalview/util/GroupUrlLink.java | 59 +-
src/jalview/util/HttpUtils.java | 67 +
src/jalview/util/ImageMaker.java | 251 +-
src/jalview/util/LinkedIdentityHashSet.java | 143 +
src/jalview/util/MapList.java | 942 ++-
src/jalview/util/MappingUtils.java | 937 +++
src/jalview/util/MessageManager.java | 127 +
src/jalview/util/ParseHtmlBodyAndLinks.java | 185 +-
src/jalview/util/Platform.java | 184 +-
src/jalview/util/QuickSort.java | 561 +-
src/jalview/util/ReverseListIterator.java | 63 +
src/jalview/util/ShiftList.java | 297 +-
src/jalview/util/SparseCount.java | 174 +
src/jalview/util/StringUtils.java | 406 +
src/jalview/util/TableSorter.java | 1213 +--
src/jalview/util/UrlConstants.java | 55 +
src/jalview/util/UrlLink.java | 1018 ++-
src/jalview/util/jarInputStreamProvider.java | 93 +-
src/jalview/viewmodel/AlignmentViewport.java | 2875 +++++++
src/jalview/viewmodel/PCAModel.java | 246 +
.../AnnotationFilterParameter.java | 122 +
.../seqfeatures/FeatureRendererModel.java | 947 +++
.../seqfeatures/FeatureRendererSettings.java | 110 +
.../seqfeatures/FeatureSettingsModel.java | 28 +
.../viewmodel/seqfeatures/FeaturesDisplayed.java | 114 +
src/jalview/viewmodel/styles/ViewStyle.java | 1097 +++
src/jalview/workers/AlignCalcManager.java | 399 +
src/jalview/workers/AlignCalcWorker.java | 139 +
.../workers/AlignmentAnnotationFactory.java | 148 +
src/jalview/workers/AnnotationProviderI.java | 37 +
src/jalview/workers/AnnotationWorker.java | 144 +
src/jalview/workers/ColumnCounterWorker.java | 244 +
src/jalview/workers/ComplementConsensusThread.java | 118 +
src/jalview/workers/ConsensusThread.java | 220 +
src/jalview/workers/ConservationThread.java | 140 +
src/jalview/workers/FeatureCounterI.java | 83 +
src/jalview/workers/StrucConsensusThread.java | 170 +
src/jalview/ws/AWSThread.java | 111 +-
src/jalview/ws/AWsJob.java | 13 +-
src/jalview/ws/DBRefFetcher.java | 1578 ++--
src/jalview/ws/DasSequenceFeatureFetcher.java | 1829 ++---
src/jalview/ws/EnfinEnvision2OneWay.java | 709 --
src/jalview/ws/HttpClientUtils.java | 169 +
src/jalview/ws/JobStateSummary.java | 36 +-
src/jalview/ws/SequenceFetcher.java | 582 +-
src/jalview/ws/SequenceFetcherFactory.java | 52 +
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 | 88 -
src/jalview/ws/dbsources/EmblCdsSource.java | 101 +
src/jalview/ws/dbsources/EmblSource.java | 259 +-
src/jalview/ws/dbsources/EmblXmlSource.java | 301 +-
src/jalview/ws/dbsources/GeneDbSource.java | 265 +-
src/jalview/ws/dbsources/Pdb.java | 504 +-
src/jalview/ws/dbsources/Pfam.java | 315 +-
src/jalview/ws/dbsources/PfamFull.java | 142 +-
src/jalview/ws/dbsources/PfamSeed.java | 140 +-
src/jalview/ws/dbsources/Rfam.java | 119 +
src/jalview/ws/dbsources/RfamFull.java | 85 +
src/jalview/ws/dbsources/RfamSeed.java | 89 +
src/jalview/ws/dbsources/Uniprot.java | 312 +-
src/jalview/ws/dbsources/UniprotName.java | 46 +
src/jalview/ws/dbsources/UnprotName.java | 41 -
src/jalview/ws/dbsources/Xfam.java | 95 +
.../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 | 523 +-
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 | 205 +-
src/jalview/ws/jws1/JWS1Thread.java | 21 +-
src/jalview/ws/jws1/MsaWSClient.java | 61 +-
src/jalview/ws/jws1/MsaWSThread.java | 90 +-
src/jalview/ws/jws1/SeqSearchWSClient.java | 64 +-
src/jalview/ws/jws1/SeqSearchWSThread.java | 95 +-
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 | 299 +
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 | 377 +-
src/jalview/ws/jws2/Jws2Discoverer.java | 758 +-
src/jalview/ws/jws2/MsaWSClient.java | 278 +-
src/jalview/ws/jws2/MsaWSThread.java | 401 +-
src/jalview/ws/jws2/ParameterUtils.java | 34 +-
src/jalview/ws/jws2/RNAalifoldClient.java | 404 +
.../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 | 793 +-
src/jalview/ws/seqfetcher/DbSourceProxy.java | 312 +-
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 297 +-
src/jalview/ws/sifts/MappingOutputPojo.java | 137 +
src/jalview/ws/sifts/SiftsClient.java | 1094 +++
src/jalview/ws/sifts/SiftsException.java | 32 +
src/jalview/ws/sifts/SiftsSettings.java | 78 +
src/jalview/ws/uimodel/AlignAnalysisUIText.java | 133 +
src/jalview/xml/binding/sifts/Alignment.java | 2310 ++++++
src/jalview/xml/binding/sifts/EntityType.java | 62 +
src/jalview/xml/binding/sifts/Entry.java | 2818 +++++++
src/jalview/xml/binding/sifts/ObjectFactory.java | 319 +
src/jalview/xml/binding/sifts/package-info.java | 9 +
.../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 +-
1123 files changed, 234438 insertions(+), 122373 deletions(-)
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