[jalview] branch master updated (18b273b -> 2363bb7)
Markus Koschany
apo at moszumanska.debian.org
Fri Apr 8 21:58:57 UTC 2016
This is an automated email from the git hooks/post-receive script.
apo pushed a change to branch master
in repository jalview.
from 18b273b Vcs-fields: Use https.
new be818c2 Remove trailing whitespace
new 2363bb7 Imported Debian patch 2.7.dfsg-5
The 2 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 | 21 +-
debian/control | 5 +-
debian/copyright | 49 +-
debian/jalview.classpath | 1 +
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/rules | 3 -
debian/upstream/edam | 45 -
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 15420 -> 0 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 27629 -> 0 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 13891 -> 0 bytes
.../html/colourSchemes/annotationColourSetting.jpg | Bin 0 -> 43293 bytes
help/html/colourSchemes/annotationColouring.html | 124 +-
help/html/colourSchemes/annotationColours.gif | Bin 23564 -> 0 bytes
help/html/colourSchemes/annotationColours.jpg | Bin 0 -> 107885 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 137157 -> 0 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 34699 -> 0 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 42343 -> 0 bytes
help/html/colourSchemes/userDefined_java7.gif | Bin 38939 -> 0 bytes
help/html/colourSchemes/zappo.html | 90 +-
help/html/editing/index.html | 152 +-
.../features/AnnotationColumnSelectionWithSM.gif | Bin 42694 -> 0 bytes
.../AnnotationColumnSelectionWithoutSM.gif | Bin 37778 -> 0 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 97462 -> 0 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 29766 -> 0 bytes
help/html/features/schooser_main.png | Bin 58895 -> 0 bytes
help/html/features/search.html | 201 +-
help/html/features/selectfetchdb.gif | Bin 41486 -> 0 bytes
help/html/features/seqfeatures.html | 157 +-
help/html/features/seqfetch.html | 135 +-
help/html/features/seqfetcher.gif | Bin 11434 -> 8702 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 25151 -> 0 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 31732 -> 0 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 23662 -> 18473 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 53903 -> 0 bytes
resources/images/JalviewLogo_big.png | Bin 4539 -> 0 bytes
resources/images/Jalview_Logo.png | Bin 15420 -> 0 bytes
resources/images/Jalview_Logo_small.png | Bin 1687 -> 0 bytes
resources/images/dna.png | Bin 895 -> 0 bytes
resources/images/error.png | Bin 633 -> 0 bytes
resources/images/good.png | Bin 965 -> 0 bytes
resources/images/loading.gif | Bin 1849 -> 0 bytes
resources/images/logo.gif | Bin 14501 -> 615 bytes
resources/images/logo_big.gif | Bin 16656 -> 6804 bytes
resources/images/logo_big_v2.gif | Bin 6804 -> 0 bytes
resources/images/logo_v2.gif | Bin 615 -> 0 bytes
resources/images/protein.png | Bin 524 -> 0 bytes
resources/images/sugar.png | Bin 542 -> 0 bytes
resources/images/warning.gif | Bin 239 -> 0 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 | 3007 +++-----
src/jalview/gui/AlignViewport.java | 2423 ++++--
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 | 4137 ++++-------
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 +-
1040 files changed, 116832 insertions(+), 193634 deletions(-)
create mode 100644 debian/jalview.classpath
create mode 100755 debian/new-upstream
delete mode 100644 debian/patches/drop-lib
delete mode 100644 debian/patches/encoding-fix
delete mode 100644 debian/patches/testng
delete mode 100644 debian/upstream/edam
delete mode 100644 doc/AnnotationPostAnalysis.txt
delete mode 100644 doc/JalviewRNASupport.html
delete mode 100644 doc/UnitTesting.html
delete mode 100644 doc/biojsmsa-templates.html
delete mode 100644 doc/i18n.html
delete mode 100644 help/html/Jalview_Logo.png
delete mode 100644 help/html/calculations/pcaviewer.gif
delete mode 100644 help/html/calculations/referenceseq.html
delete mode 100644 help/html/calculations/scorematrices.html
delete mode 100644 help/html/calculations/structureconsensus.html
delete mode 100644 help/html/colourSchemes/annotationColourSetting.gif
create mode 100644 help/html/colourSchemes/annotationColourSetting.jpg
delete mode 100644 help/html/colourSchemes/annotationColours.gif
create mode 100644 help/html/colourSchemes/annotationColours.jpg
delete mode 100644 help/html/colourSchemes/colbytcoffee.png
delete mode 100644 help/html/colourSchemes/purinepyrimidine.html
delete mode 100644 help/html/colourSchemes/rnahelicesColouring.html
delete mode 100644 help/html/colourSchemes/rnahelicescoloring.png
delete mode 100644 help/html/colourSchemes/userDefined_java6.gif
delete mode 100644 help/html/colourSchemes/userDefined_java7.gif
delete mode 100644 help/html/features/AnnotationColumnSelectionWithSM.gif
delete mode 100644 help/html/features/AnnotationColumnSelectionWithoutSM.gif
delete mode 100644 help/html/features/bioJsonFormat.html
delete mode 100644 help/html/features/biojsmsa.html
delete mode 100644 help/html/features/chimera.html
delete mode 100644 help/html/features/columnFilterByAnnotation.html
delete mode 100644 help/html/features/pdbseqfetcher.png
delete mode 100644 help/html/features/pdbsequencefetcher.html
delete mode 100644 help/html/features/schooser_enter-id.png
delete mode 100644 help/html/features/schooser_main.png
delete mode 100644 help/html/features/selectfetchdb.gif
delete mode 100644 help/html/features/splitView.html
delete mode 100644 help/html/features/structurechooser.html
delete mode 100644 help/html/features/varna.html
delete mode 100644 help/html/features/xsspannotation.html
delete mode 100644 help/html/io/exportseqreport.html
delete mode 100644 help/html/io/seqreport.gif
delete mode 100644 help/html/io/tcoffeescores.html
create mode 100644 help/html/jalviewjnlp.html
delete mode 100644 help/html/menus/alwannotation.html
delete mode 100644 help/html/menus/alwannotationpanel.html
create mode 100644 help/html/menus/alwannotations.html
delete mode 100644 help/html/na/index.html
delete mode 100644 help/html/webServices/AACon.html
delete mode 100644 help/html/webServices/RNAalifold.html
delete mode 100644 help/html/webServices/RNAalifoldAnnotationRows.png
delete mode 100644 help/html/webServices/proteinDisorder.html
delete mode 100644 resources/authors.props
delete mode 100644 resources/images/JalviewLogo_Huge.png
delete mode 100644 resources/images/JalviewLogo_big.png
delete mode 100644 resources/images/Jalview_Logo.png
delete mode 100644 resources/images/Jalview_Logo_small.png
delete mode 100644 resources/images/dna.png
delete mode 100644 resources/images/error.png
delete mode 100644 resources/images/good.png
delete mode 100644 resources/images/loading.gif
delete mode 100644 resources/images/logo_big_v2.gif
delete mode 100644 resources/images/logo_v2.gif
delete mode 100644 resources/images/protein.png
delete mode 100644 resources/images/sugar.png
delete mode 100644 resources/images/warning.gif
delete mode 100644 resources/lang/Messages.properties
delete mode 100644 resources/lang/Messages_es.properties
delete mode 100644 src/com/github/reinert/jjschema/Attributes.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java
delete mode 100644 src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java
delete mode 100644 src/jalview/analysis/AlignmentAnnotationUtils.java
delete mode 100644 src/jalview/analysis/AlignmentUtils.java
delete mode 100644 src/jalview/analysis/AnnotationSorter.java
delete mode 100644 src/jalview/analysis/CodingUtils.java
delete mode 100644 src/jalview/analysis/CodonComparator.java
delete mode 100644 src/jalview/analysis/Rna.java
delete mode 100644 src/jalview/analysis/SecStrConsensus.java
delete mode 100644 src/jalview/analysis/StructureFrequency.java
delete mode 100644 src/jalview/analysis/WUSSParseException.java
delete mode 100644 src/jalview/analysis/scoremodels/FeatureScoreModel.java
delete mode 100644 src/jalview/analysis/scoremodels/PIDScoreModel.java
delete mode 100644 src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
delete mode 100644 src/jalview/analysis/scoremodels/SWScoreModel.java
delete mode 100644 src/jalview/api/AlignCalcManagerI.java
delete mode 100644 src/jalview/api/AlignCalcWorkerI.java
delete mode 100644 src/jalview/api/AlignExportSettingI.java
delete mode 100644 src/jalview/api/AlignViewControllerGuiI.java
delete mode 100644 src/jalview/api/AlignViewControllerI.java
delete mode 100644 src/jalview/api/AlignViewportI.java
delete mode 100644 src/jalview/api/BuildDetailsI.java
delete mode 100644 src/jalview/api/ComplexAlignFile.java
delete mode 100644 src/jalview/api/FeatureSettingsControllerI.java
delete mode 100644 src/jalview/api/FeatureSettingsModelI.java
delete mode 100644 src/jalview/api/FeaturesDisplayedI.java
delete mode 100644 src/jalview/api/OOMHandlerI.java
delete mode 100644 src/jalview/api/RotatableCanvasI.java
delete mode 100644 src/jalview/api/SplitContainerI.java
delete mode 100644 src/jalview/api/ViewStyleI.java
delete mode 100644 src/jalview/api/analysis/ScoreModelI.java
delete mode 100644 src/jalview/api/analysis/ViewBasedAnalysisI.java
delete mode 100644 src/jalview/api/structures/JalviewStructureDisplayI.java
delete mode 100644 src/jalview/appletgui/AnnotationColumnChooser.java
delete mode 100644 src/jalview/appletgui/AnnotationRowFilter.java
delete mode 100644 src/jalview/appletgui/SplitFrame.java
delete mode 100644 src/jalview/appletgui/TitledPanel.java
delete mode 100644 src/jalview/bin/BuildDetails.java
delete mode 100644 src/jalview/controller/AlignViewController.java
delete mode 100644 src/jalview/controller/FeatureSettingsController.java
delete mode 100644 src/jalview/controller/FeatureSettingsControllerGuiI.java
delete mode 100644 src/jalview/datamodel/ASequence.java
delete mode 100644 src/jalview/datamodel/ASequenceI.java
delete mode 100644 src/jalview/datamodel/AlignedCodon.java
delete mode 100644 src/jalview/datamodel/AlignmentExportData.java
delete mode 100644 src/jalview/datamodel/AnnotatedCollectionI.java
delete mode 100644 src/jalview/datamodel/IncompleteCodonException.java
delete mode 100644 src/jalview/datamodel/RnaViewerModel.java
delete mode 100644 src/jalview/datamodel/SecondaryStructureAnnotation.java
delete mode 100644 src/jalview/datamodel/SequenceCollectionI.java
delete mode 100644 src/jalview/datamodel/SequenceDummy.java
delete mode 100644 src/jalview/datamodel/StructureViewerModel.java
delete mode 100644 src/jalview/exceptions/JalviewException.java
delete mode 100644 src/jalview/exceptions/NoFileSelectedException.java
delete mode 100644 src/jalview/ext/jmol/PDBFileWithJmol.java
delete mode 100644 src/jalview/ext/paradise/Annotate3D.java
delete mode 100644 src/jalview/ext/rbvi/chimera/ChimeraCommands.java
delete mode 100644 src/jalview/ext/rbvi/chimera/ChimeraListener.java
delete mode 100644 src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
delete mode 100644 src/jalview/ext/varna/JalviewVarnaBinding.java
delete mode 100644 src/jalview/ext/varna/RnaModel.java
delete mode 100644 src/jalview/ext/varna/VarnaCommands.java
delete mode 100644 src/jalview/gui/AlignExportSettings.java
delete mode 100644 src/jalview/gui/AnnotationChooser.java
delete mode 100644 src/jalview/gui/AnnotationColumnChooser.java
delete mode 100644 src/jalview/gui/AnnotationRowFilter.java
delete mode 100644 src/jalview/gui/AppVarna.java
delete mode 100644 src/jalview/gui/AppVarnaBinding.java
delete mode 100644 src/jalview/gui/ChimeraViewFrame.java
create mode 100644 src/jalview/gui/ConservationThread.java
delete mode 100644 src/jalview/gui/CutAndPasteHtmlTransfer.java
delete mode 100644 src/jalview/gui/HTMLOptions.java
delete mode 100644 src/jalview/gui/Help.java
delete mode 100644 src/jalview/gui/JDatabaseTree.java
delete mode 100644 src/jalview/gui/JalviewChimeraBindingModel.java
delete mode 100644 src/jalview/gui/MenuChooser.java
delete mode 100644 src/jalview/gui/PDBSearchPanel.java
delete mode 100644 src/jalview/gui/ProgressBar.java
delete mode 100644 src/jalview/gui/SVGOptions.java
create mode 100644 src/jalview/gui/ScriptWindow.java
delete mode 100644 src/jalview/gui/SplitFrame.java
delete mode 100644 src/jalview/gui/StructureChooser.java
delete mode 100644 src/jalview/gui/StructureViewer.java
delete mode 100644 src/jalview/gui/StructureViewerBase.java
delete mode 100644 src/jalview/httpserver/AbstractRequestHandler.java
delete mode 100644 src/jalview/httpserver/HttpServer.java
delete mode 100644 src/jalview/io/BioJsHTMLOutput.java
delete mode 100644 src/jalview/io/Gff3File.java
delete mode 100644 src/jalview/io/HtmlFile.java
delete mode 100644 src/jalview/io/HtmlSvgOutput.java
delete mode 100644 src/jalview/io/InputStreamParser.java
delete mode 100644 src/jalview/io/JSONFile.java
delete mode 100644 src/jalview/io/PhylipFile.java
delete mode 100644 src/jalview/io/RnamlFile.java
delete mode 100644 src/jalview/io/SequenceAnnotationReport.java
delete mode 100644 src/jalview/io/TCoffeeScoreFile.java
delete mode 100644 src/jalview/jbgui/GAlignExportSettings.java
delete mode 100644 src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
delete mode 100644 src/jalview/jbgui/GPDBSearchPanel.java
delete mode 100644 src/jalview/jbgui/GRnaStructureViewer.java
delete mode 100644 src/jalview/jbgui/GSplitFrame.java
delete mode 100644 src/jalview/jbgui/GStructureChooser.java
delete mode 100644 src/jalview/jbgui/PDBDocFieldPreferences.java
delete mode 100644 src/jalview/json/binding/biojs/BioJSReleasePojo.java
delete mode 100644 src/jalview/json/binding/biojs/BioJSRepositoryPojo.java
delete mode 100644 src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
delete mode 100644 src/jalview/json/binding/biojson/v1/AlignmentPojo.java
delete mode 100644 src/jalview/json/binding/biojson/v1/AnnotationPojo.java
delete mode 100644 src/jalview/json/binding/biojson/v1/JalviewBioJsColorSchemeMapper.java
delete mode 100644 src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
delete mode 100644 src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
delete mode 100644 src/jalview/json/binding/biojson/v1/SequencePojo.java
delete mode 100644 src/jalview/math/AlignmentDimension.java
delete mode 100644 src/jalview/renderer/AnnotationRenderer.java
delete mode 100644 src/jalview/renderer/AwtRenderPanelI.java
delete mode 100644 src/jalview/renderer/seqfeatures/FeatureRenderer.java
delete mode 100644 src/jalview/rest/RestHandler.java
delete mode 100644 src/jalview/schemabinding/version2/AnnotationColourScheme.java
delete mode 100644 src/jalview/schemabinding/version2/CalcIdParam.java
delete mode 100644 src/jalview/schemabinding/version2/RnaViewer.java
delete mode 100644 src/jalview/schemabinding/version2/SecondaryStructure.java
delete mode 100644 src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java
delete mode 100644 src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java
delete mode 100644 src/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.java
delete mode 100644 src/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.java
delete mode 100644 src/jalview/schemes/CovariationColourScheme.java
delete mode 100644 src/jalview/schemes/FollowerColourScheme.java
delete mode 100644 src/jalview/schemes/PurinePyrimidineColourScheme.java
delete mode 100644 src/jalview/schemes/RNAHelicesColour.java
delete mode 100644 src/jalview/schemes/RNAHelicesColourChooser.java
delete mode 100644 src/jalview/schemes/RNAInteractionColourScheme.java
delete mode 100644 src/jalview/schemes/TCoffeeColourScheme.java
delete mode 100644 src/jalview/structure/AtomSpec.java
delete mode 100644 src/jalview/structure/CommandListener.java
delete mode 100644 src/jalview/structure/SecondaryStructureListener.java
delete mode 100644 src/jalview/structures/models/AAStructureBindingModel.java
delete mode 100644 src/jalview/structures/models/SequenceStructureBindingModel.java
delete mode 100644 src/jalview/util/ColorUtils.java
delete mode 100644 src/jalview/util/MappingUtils.java
delete mode 100644 src/jalview/util/MessageManager.java
delete mode 100644 src/jalview/util/ReverseListIterator.java
delete mode 100644 src/jalview/util/StringUtils.java
delete mode 100644 src/jalview/viewmodel/AlignmentViewport.java
delete mode 100644 src/jalview/viewmodel/PCAModel.java
delete mode 100644 src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java
delete mode 100644 src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
delete mode 100644 src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
delete mode 100644 src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java
delete mode 100644 src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
delete mode 100644 src/jalview/viewmodel/styles/ViewStyle.java
delete mode 100644 src/jalview/workers/AlignCalcManager.java
delete mode 100644 src/jalview/workers/AlignCalcWorker.java
delete mode 100644 src/jalview/workers/ComplementConsensusThread.java
delete mode 100644 src/jalview/workers/ConsensusThread.java
delete mode 100644 src/jalview/workers/ConservationThread.java
delete mode 100644 src/jalview/workers/StrucConsensusThread.java
create mode 100644 src/jalview/ws/EnfinEnvision2OneWay.java
delete mode 100644 src/jalview/ws/HttpClientUtils.java
create mode 100644 src/jalview/ws/dbsources/DasSequenceSource.java
delete mode 100644 src/jalview/ws/dbsources/PDBRestClient.java
delete mode 100644 src/jalview/ws/dbsources/Rfam.java
delete mode 100644 src/jalview/ws/dbsources/RfamFull.java
delete mode 100644 src/jalview/ws/dbsources/RfamSeed.java
delete mode 100644 src/jalview/ws/dbsources/Xfam.java
create mode 100644 src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
delete mode 100644 src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
delete mode 100644 src/jalview/ws/dbsources/das/api/jalviewSourceI.java
delete mode 100644 src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
delete mode 100644 src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
delete mode 100644 src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
delete mode 100644 src/jalview/ws/jws1/Annotate3D.java
delete mode 100644 src/jalview/ws/jws2/AAConClient.java
delete mode 100644 src/jalview/ws/jws2/AADisorderClient.java
delete mode 100644 src/jalview/ws/jws2/AbstractJabaCalcWorker.java
delete mode 100644 src/jalview/ws/jws2/JPred301Client.java
delete mode 100644 src/jalview/ws/jws2/JabawsCalcWorker.java
delete mode 100644 src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
delete mode 100644 src/jalview/ws/jws2/RNAalifoldClient.java
delete mode 100644 src/jalview/ws/jws2/SequenceAnnotationWSClient.java
delete mode 100644 src/jalview/ws/jws2/dm/AAConSettings.java
delete mode 100644 src/jalview/ws/jws2/jabaws2/Jws2Instance.java
delete mode 100644 src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
delete mode 100644 src/jalview/ws/params/AutoCalcSetting.java
delete mode 100644 src/jalview/ws/uimodel/AlignAnalysisUIText.java
delete mode 100644 src/jalview/ws/uimodel/PDBRestRequest.java
delete mode 100644 src/jalview/ws/uimodel/PDBRestResponse.java
create mode 100644 src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
create mode 100644 src/org/biojava/dasobert/das/DAS_Feature_Handler.java
create mode 100644 src/org/biojava/dasobert/das/DAS_Sequence_Handler.java
create mode 100644 src/org/biojava/dasobert/das/FeatureThread.java
create mode 100644 src/org/biojava/dasobert/das/SequenceThread.java
create mode 100644 src/org/biojava/dasobert/das2/Das2Capability.java
create mode 100644 src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
create mode 100644 src/org/biojava/dasobert/das2/Das2Source.java
create mode 100644 src/org/biojava/dasobert/das2/Das2SourceImpl.java
create mode 100644 src/org/biojava/dasobert/das2/DasSourceConverter.java
create mode 100644 src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
create mode 100644 src/org/biojava/dasobert/das2/io/DasSourceReader.java
create mode 100644 src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
create mode 100644 src/org/biojava/dasobert/dasregistry/Das1Source.java
create mode 100644 src/org/biojava/dasobert/dasregistry/Das2Validator.java
create mode 100644 src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
create mode 100644 src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
create mode 100644 src/org/biojava/dasobert/dasregistry/DasSource.java
create mode 100644 src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
create mode 100644 src/org/biojava/dasobert/eventmodel/AbstractDasEvent.java
create mode 100644 src/org/biojava/dasobert/eventmodel/FeatureEvent.java
create mode 100644 src/org/biojava/dasobert/eventmodel/FeatureListener.java
create mode 100644 src/org/biojava/dasobert/eventmodel/ObjectListener.java
create mode 100644 src/org/biojava/dasobert/eventmodel/SequenceEvent.java
create mode 100644 src/org/biojava/dasobert/eventmodel/SequenceListener.java
create mode 100644 src/org/biojava/dasobert/feature/AbstractFeatureTrack.java
create mode 100644 src/org/biojava/dasobert/feature/AbstractSegment.java
create mode 100644 src/org/biojava/dasobert/feature/FeatureComparator.java
create mode 100644 src/org/biojava/dasobert/feature/FeatureMapComparator.java
create mode 100644 src/org/biojava/dasobert/feature/FeatureTrack.java
create mode 100644 src/org/biojava/dasobert/feature/FeatureTrackConverter.java
create mode 100644 src/org/biojava/dasobert/feature/FeatureTrackImpl.java
create mode 100644 src/org/biojava/dasobert/feature/HistogramFeature.java
create mode 100644 src/org/biojava/dasobert/feature/HistogramSegment.java
create mode 100644 src/org/biojava/dasobert/feature/Segment.java
create mode 100644 src/org/biojava/dasobert/feature/SegmentComparator.java
create mode 100644 src/org/biojava/dasobert/feature/SegmentImpl.java
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-java/jalview.git
More information about the pkg-java-commits
mailing list