source.jalview.org Git - jalview.git/commit

git://source.jalview.org / jalview.git / commit

author	Ben Soares <bsoares@dundee.ac.uk>
	Fri, 30 Aug 2019 16:19:52 +0000 (17:19 +0100)
committer	Ben Soares <bsoares@dundee.ac.uk>
	Fri, 30 Aug 2019 16:19:52 +0000 (17:19 +0100)
commit	a83adb45bdf9554e270921b4baad94defd314b36
tree	66dd653cd158b0e3ec7fcaa738c2f3c23cd37a8b	tree \| snapshot
parent	d4ec118f86b5c9dee801e743c46aaacc7bb521d1	commit \| diff

JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from the applet branch. AND IT WORKS (sometimes)

344 files changed:

README		diff \| blob \| history
build.gradle		diff \| blob \| history
gradle.properties		diff \| blob \| history
src/com/stevesoft/pat/RegOpt.java		diff \| blob \| history
src/com/stevesoft/pat/Regex.java		diff \| blob \| history
src/com/stevesoft/pat/RegexReader.java		diff \| blob \| history
src/com/stevesoft/pat/RegexTokenizer.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java		diff \| blob \| history
src/ext/vamsas/JpredSoapBindingStub.java	[changed mode: 0755->0644]	diff \| blob \| history
src/ext/vamsas/MuscleWSSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/RegistryServiceSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/SeqSearchServiceSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/ServiceHandle.java		diff \| blob \| history
src/intervalstore/api/IntervalI.java	[new file with mode: 0644]	blob
src/intervalstore/api/IntervalStoreI.java	[new file with mode: 0644]	blob
src/intervalstore/impl/BinarySearcher.java	[new file with mode: 0644]	blob
src/intervalstore/impl/IntervalStore.java	[new file with mode: 0644]	blob
src/intervalstore/impl/NCList.java	[new file with mode: 0644]	blob
src/intervalstore/impl/NCListBuilder.java	[new file with mode: 0644]	blob
src/intervalstore/impl/NCNode.java	[new file with mode: 0644]	blob
src/intervalstore/nonc/IntervalStore.java	[new file with mode: 0644]	blob
src/jalview/analysis/AlignmentSorter.java		diff \| blob \| history
src/jalview/analysis/Conservation.java		diff \| blob \| history
src/jalview/analysis/CrossRef.java		diff \| blob \| history
src/jalview/analysis/Finder.java		diff \| blob \| history
src/jalview/analysis/GeneticCodes.java		diff \| blob \| history
src/jalview/analysis/ParseProperties.java		diff \| blob \| history
src/jalview/analysis/SeqsetUtils.java		diff \| blob \| history
src/jalview/analysis/StructureFrequency.java		diff \| blob \| history
src/jalview/analysis/scoremodels/FeatureDistanceModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/ScoreMatrix.java		diff \| blob \| history
src/jalview/analysis/scoremodels/ScoreModels.java		diff \| blob \| history
src/jalview/analysis/scoremodels/SimilarityParams.java		diff \| blob \| history
src/jalview/api/AlignFrameI.java	[new file with mode: 0644]	blob
src/jalview/api/AlignViewportI.java		diff \| blob \| history
src/jalview/api/AlignmentColsCollectionI.java		diff \| blob \| history
src/jalview/api/AlignmentViewPanel.java		diff \| blob \| history
src/jalview/api/FeatureColourI.java		diff \| blob \| history
src/jalview/api/FeatureRenderer.java		diff \| blob \| history
src/jalview/api/JalviewApp.java	[new file with mode: 0644]	blob
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignViewport.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/appletgui/AnnotationLabels.java		diff \| blob \| history
src/jalview/appletgui/AnnotationPanel.java		diff \| blob \| history
src/jalview/appletgui/EmbmenuFrame.java		diff \| blob \| history
src/jalview/appletgui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/FontChooser.java		diff \| blob \| history
src/jalview/appletgui/IdPanel.java		diff \| blob \| history
src/jalview/appletgui/OverviewCanvas.java		diff \| blob \| history
src/jalview/appletgui/OverviewPanel.java		diff \| blob \| history
src/jalview/appletgui/ScalePanel.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/appletgui/TreePanel.java		diff \| blob \| history
src/jalview/bin/AppletParams.java	[new file with mode: 0644]	blob
src/jalview/bin/ApplicationSingletonProvider.java	[new file with mode: 0644]	blob
src/jalview/bin/ArgsParser.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewAppLoader.java	[new file with mode: 0644]	blob
src/jalview/bin/JalviewJS2.java		diff \| blob \| history
src/jalview/bin/JalviewJSApi.java	[new file with mode: 0644]	blob
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/bin/JalviewTaskbar.java	[deleted file]	blob \| history
src/jalview/bin/Launcher.java	[deleted file]	blob \| history
src/jalview/bin/MemorySetting.java	[deleted file]	blob \| history
src/jalview/commands/ChangeCaseCommand.java		diff \| blob \| history
src/jalview/controller/AlignViewController.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AlignmentI.java		diff \| blob \| history
src/jalview/datamodel/AllColsCollection.java		diff \| blob \| history
src/jalview/datamodel/BinarySequence.java		diff \| blob \| history
src/jalview/datamodel/ColumnSelection.java		diff \| blob \| history
src/jalview/datamodel/DBRefEntry.java		diff \| blob \| history
src/jalview/datamodel/DBRefSource.java		diff \| blob \| history
src/jalview/datamodel/HiddenColumns.java		diff \| blob \| history
src/jalview/datamodel/PDBEntry.java		diff \| blob \| history
src/jalview/datamodel/ResidueCount.java		diff \| blob \| history
src/jalview/datamodel/SecondaryStructureAnnotation.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceFeature.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/datamodel/VisibleColsCollection.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureAttributes.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureSources.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureStore.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureStoreI.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/FeatureStoreImpl.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/FeatureStoreJS.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/SequenceFeatures.java		diff \| blob \| history
src/jalview/datamodel/features/SequenceFeaturesI.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblCdna.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblCds.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblGene.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblInfo.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblMap.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblProtein.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblRestClient.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSeqProxy.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java		diff \| blob \| history
src/jalview/ext/htsjdk/VCFReader.java		diff \| blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/paradise/Annotate3D.java		diff \| blob \| history
src/jalview/ext/so/SequenceOntology.java		diff \| blob \| history
src/jalview/fts/core/FTSRestRequest.java		diff \| blob \| history
src/jalview/fts/service/pdb/PDBFTSRestClient.java		diff \| blob \| history
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java		diff \| blob \| history
src/jalview/gui/APQHandlers.java	[deleted file]	blob \| history
src/jalview/gui/AlignExportOptions.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AlignmentPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationColumnChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/AppVarna.java		diff \| blob \| history
src/jalview/gui/AppVarnaBinding.java		diff \| blob \| history
src/jalview/gui/AssociatePdbFileWithSeq.java		diff \| blob \| history
src/jalview/gui/BlogReader.java		diff \| blob \| history
src/jalview/gui/CalculationChooser.java		diff \| blob \| history
src/jalview/gui/ChimeraViewFrame.java		diff \| blob \| history
src/jalview/gui/ColourMenuHelper.java		diff \| blob \| history
src/jalview/gui/ComboBoxTooltipRenderer.java		diff \| blob \| history
src/jalview/gui/Console.java		diff \| blob \| history
src/jalview/gui/CrossRefAction.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/FeatureEditor.java		diff \| blob \| history
src/jalview/gui/FeatureRenderer.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/FeatureTypeSettings.java		diff \| blob \| history
src/jalview/gui/Finder.java		diff \| blob \| history
src/jalview/gui/FontChooser.java		diff \| blob \| history
src/jalview/gui/IdCanvas.java		diff \| blob \| history
src/jalview/gui/IdPanel.java		diff \| blob \| history
src/jalview/gui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/gui/JalviewAppender.java		diff \| blob \| history
src/jalview/gui/JalviewDialog.java		diff \| blob \| history
src/jalview/gui/JvSwingUtils.java		diff \| blob \| history
src/jalview/gui/LineartOptions.java		diff \| blob \| history
src/jalview/gui/MenuChooser.java	[deleted file]	blob \| history
src/jalview/gui/OOMWarning.java		diff \| blob \| history
src/jalview/gui/OverviewCanvas.java		diff \| blob \| history
src/jalview/gui/OverviewPanel.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/PromptUserConfig.java		diff \| blob \| history
src/jalview/gui/RotatableCanvas.java		diff \| blob \| history
src/jalview/gui/ScalePanel.java		diff \| blob \| history
src/jalview/gui/SeqCanvas.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SequenceRenderer.java		diff \| blob \| history
src/jalview/gui/SliderPanel.java		diff \| blob \| history
src/jalview/gui/SplashScreen.java		diff \| blob \| history
src/jalview/gui/SplitFrame.java		diff \| blob \| history
src/jalview/gui/StructureChooser.java		diff \| blob \| history
src/jalview/gui/StructureViewer.java		diff \| blob \| history
src/jalview/gui/StructureViewerBase.java		diff \| blob \| history
src/jalview/gui/UserDefinedColours.java		diff \| blob \| history
src/jalview/gui/UserQuestionnaireCheck.java		diff \| blob \| history
src/jalview/gui/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/WebserviceInfo.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/gui/WsParamSetManager.java		diff \| blob \| history
src/jalview/gui/WsPreferences.java		diff \| blob \| history
src/jalview/httpserver/HttpServer.java		diff \| blob \| history
src/jalview/io/AlignFile.java		diff \| blob \| history
src/jalview/io/AnnotationFile.java		diff \| blob \| history
src/jalview/io/BackupFilenameParts.java		diff \| blob \| history
src/jalview/io/BackupFiles.java		diff \| blob \| history
src/jalview/io/BackupFilesPresetEntry.java	[deleted file]	blob \| history
src/jalview/io/FeaturesFile.java		diff \| blob \| history
src/jalview/io/FileFormats.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/FormatAdapter.java		diff \| blob \| history
src/jalview/io/HTMLOutput.java		diff \| blob \| history
src/jalview/io/HtmlSvgOutput.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/IntKeyStringValueEntry.java	[deleted file]	blob \| history
src/jalview/io/JPredFile.java		diff \| blob \| history
src/jalview/io/JalviewFileFilter.java		diff \| blob \| history
src/jalview/io/JnetAnnotationMaker.java		diff \| blob \| history
src/jalview/io/ModellerDescription.java		diff \| blob \| history
src/jalview/io/NewickFile.java		diff \| blob \| history
src/jalview/io/PIRFile.java		diff \| blob \| history
src/jalview/io/RnamlFile.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/TCoffeeScoreFile.java		diff \| blob \| history
src/jalview/io/VamsasAppDatastore.java		diff \| blob \| history
src/jalview/io/WSWUBlastClient.java		diff \| blob \| history
src/jalview/io/cache/AppCache.java		diff \| blob \| history
src/jalview/io/cache/JvCacheableInputBox.java		diff \| blob \| history
src/jalview/io/gff/Gff3Helper.java		diff \| blob \| history
src/jalview/io/gff/InterProScanHelper.java		diff \| blob \| history
src/jalview/io/gff/SequenceOntologyFactory.java		diff \| blob \| history
src/jalview/io/vamsas/DatastoreRegistry.java		diff \| blob \| history
src/jalview/io/vamsas/Rangetype.java		diff \| blob \| history
src/jalview/io/vamsas/Sequencefeature.java		diff \| blob \| history
src/jalview/io/vamsas/Sequencemapping.java		diff \| blob \| history
src/jalview/io/vamsas/Tree.java		diff \| blob \| history
src/jalview/io/vcf/VCFLoader.java		diff \| blob \| history
src/jalview/javascript/JSFunctionExec.java		diff \| blob \| history
src/jalview/javascript/JalviewLiteJsApi.java		diff \| blob \| history
src/jalview/javascript/JsSelectionSender.java		diff \| blob \| history
src/jalview/javascript/MouseOverListener.java		diff \| blob \| history
src/jalview/javascript/MouseOverStructureListener.java		diff \| blob \| history
src/jalview/javascript/json/JSON.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GAlignmentPanel.java		diff \| blob \| history
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java		diff \| blob \| history
src/jalview/jbgui/GCutAndPasteTransfer.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GPCAPanel.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GRnaStructureViewer.java		diff \| blob \| history
src/jalview/jbgui/GSequenceLink.java		diff \| blob \| history
src/jalview/jbgui/GSliderPanel.java		diff \| blob \| history
src/jalview/jbgui/GSplitFrame.java		diff \| blob \| history
src/jalview/jbgui/GStructureChooser.java		diff \| blob \| history
src/jalview/jbgui/GStructureViewer.java		diff \| blob \| history
src/jalview/jbgui/GTreePanel.java		diff \| blob \| history
src/jalview/project/Jalview2XML.java		diff \| blob \| history
src/jalview/renderer/OverviewRenderer.java		diff \| blob \| history
src/jalview/renderer/OverviewResColourFinder.java		diff \| blob \| history
src/jalview/renderer/ResidueColourFinder.java		diff \| blob \| history
src/jalview/renderer/ResidueShader.java		diff \| blob \| history
src/jalview/renderer/ResidueShaderI.java		diff \| blob \| history
src/jalview/renderer/seqfeatures/FeatureColourFinder.java		diff \| blob \| history
src/jalview/renderer/seqfeatures/FeatureRenderer.java		diff \| blob \| history
src/jalview/rest/RestHandler.java		diff \| blob \| history
src/jalview/schemes/AnnotationColourGradient.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeProperty.java		diff \| blob \| history
src/jalview/schemes/ColourSchemes.java		diff \| blob \| history
src/jalview/schemes/Consensus.java		diff \| blob \| history
src/jalview/schemes/FeatureColour.java		diff \| blob \| history
src/jalview/schemes/RNAHelicesColour.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/structure/StructureImportSettings.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/structures/models/AAStructureBindingModel.java		diff \| blob \| history
src/jalview/urls/IdOrgSettings.java		diff \| blob \| history
src/jalview/urls/IdentifiersUrlProvider.java		diff \| blob \| history
src/jalview/util/BrowserLauncher.java		diff \| blob \| history
src/jalview/util/ColorUtils.java		diff \| blob \| history
src/jalview/util/DBRefUtils.java		diff \| blob \| history
src/jalview/util/GroupUrlLink.java		diff \| blob \| history
src/jalview/util/MessageManager.java		diff \| blob \| history
src/jalview/util/Platform.java		diff \| blob \| history
src/jalview/util/ShortcutKeyMaskExWrapper.java	[deleted file]	blob \| history
src/jalview/util/UrlLink.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/OverviewDimensions.java		diff \| blob \| history
src/jalview/viewmodel/OverviewDimensionsHideHidden.java		diff \| blob \| history
src/jalview/viewmodel/OverviewDimensionsShowHidden.java		diff \| blob \| history
src/jalview/viewmodel/ViewportRanges.java		diff \| blob \| history
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java		diff \| blob \| history
src/jalview/workers/AlignCalcManager.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/SequenceFetcher.java		diff \| blob \| history
src/jalview/ws/SequenceFetcherFactory.java		diff \| blob \| history
src/jalview/ws/dbsources/EmblCdsSource.java		diff \| blob \| history
src/jalview/ws/dbsources/EmblSource.java		diff \| blob \| history
src/jalview/ws/dbsources/Pdb.java		diff \| blob \| history
src/jalview/ws/dbsources/PfamFull.java		diff \| blob \| history
src/jalview/ws/dbsources/PfamSeed.java		diff \| blob \| history
src/jalview/ws/dbsources/Uniprot.java		diff \| blob \| history
src/jalview/ws/jws1/Discoverer.java		diff \| blob \| history
src/jalview/ws/jws1/JPredClient.java		diff \| blob \| history
src/jalview/ws/jws1/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/jws1/SeqSearchWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/AAConClient.java		diff \| blob \| history
src/jalview/ws/jws2/AADisorderClient.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Client.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Discoverer.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/RNAalifoldClient.java		diff \| blob \| history
src/jalview/ws/jws2/SequenceAnnotationWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2Instance.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java		diff \| blob \| history
src/jalview/ws/rest/HttpResultSet.java		diff \| blob \| history
src/jalview/ws/rest/RestClient.java		diff \| blob \| history
src/jalview/ws/seqfetcher/ASequenceFetcher.java		diff \| blob \| history
src/jalview/ws/seqfetcher/DbSourceProxy.java		diff \| blob \| history
src/jalview/ws/seqfetcher/DbSourceProxyRoot.java	[new file with mode: 0644]	blob
src/jalview/ws/sifts/SiftsClient.java		diff \| blob \| history
src/jalview/ws/sifts/SiftsSettings.java		diff \| blob \| history
src/jalview/xml/binding/jalview/JalviewModelType.java	[deleted file]	blob \| history
src/mc_view/PDBfile.java		diff \| blob \| history
src/org/jibble/epsgraphics/EpsGraphics2D.java		diff \| blob \| history
src/uk/ac/ebi/www/InputParams.java		diff \| blob \| history
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java		diff \| blob \| history
utils/jalviewjs/SwingJS-site.zip		diff \| blob \| history
utils/jalviewjs/eclipse/dropins/net.sf.j2s.core.jar		diff \| blob \| history
utils/jalviewjs/site-resources/applets-nocore.html	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/applets.html	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/css/ie6.css	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/css/ie7.css	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/css/reset.css	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/css/style.css	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/1gaq.txt	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/2GIS.pdb	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/3W5V.pdb	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/backupfilestest.fa	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/biojsonschema.json	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/dna_interleaved.phy	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/dna_sequential.phy	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/estrogenReceptorCdna.fa	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/estrogenReceptorCdna_aln.fa	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/estrogenReceptorCdna_frag.fa	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/estrogenReceptorProtein.aln	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/estrogenReceptorProtein.fa	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/estrogenReceptorProtein_aln.fa	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/estrogenReceptorProtein_frag.fa	[new file with mode: 0644]	blob
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utils/jalviewjs/site-resources/examples/ferredoxin.nw	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/jpred_msa.fasta	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/jpred_msa.seq.concise	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/plantfdx.annotations	[new file with mode: 0644]	blob
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utils/jalviewjs/site-resources/examples/unfolded_RF00031.aln	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/uniref50.score_ascii	[new file with mode: 0644]	blob
utils/jalviewjs/site-resources/examples/uniref50_mz.fa	[new file with mode: 0644]	blob
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utils/jalviewjs/site-resources/jalview_embedded_example1.html	[new file with mode: 0644]	blob
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utils/jalviewjs/site-resources/javascript/facebox-1.3.js	[new file with mode: 0644]	blob
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