From 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 9 Nov 2023 23:44:30 +0000 Subject: [PATCH] JAL-4059 Fix up Jsmol calls and delete html files from JS zips in build.gradle. Improve closure-compiler core creation with merged swingjs. Change startup file for core example page. Add querystringnamepspace to example pages. Remove unnecessary core lists. --- build.gradle | 81 +- src/jalview/bin/JalviewJS2.java | 7 +- utils/jalviewjs/_j2sclasslist.txt | 1152 ++++++++++++++++++++ .../chromium_test/jalview_bin_Jalview-stderr.html | 3 +- utils/jalviewjs/classlists/jalview.txt | 791 -------------- utils/jalviewjs/classlists/jvexamplefile.txt | 1031 ------------------ utils/jalviewjs/coretemplate.html | 3 +- .../site-resources/jalview_bin_JalviewJS_core.html | 3 +- utils/jalviewjs/some_commands.txt | 19 + 9 files changed, 1242 insertions(+), 1848 deletions(-) delete mode 100644 utils/jalviewjs/classlists/jalview.txt delete mode 100644 utils/jalviewjs/classlists/jvexamplefile.txt create mode 100644 utils/jalviewjs/some_commands.txt diff --git a/build.gradle b/build.gradle index 4b43a77..fe7e4e4 100644 --- a/build.gradle +++ b/build.gradle @@ -563,6 +563,7 @@ ext { } jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib") jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs") + jalviewjsTransferSiteMergeDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_merge") jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core") jalviewjsJalviewCoreHtmlFile = string("") jalviewjsJalviewCoreName = string(jalviewjs_core_name) @@ -3400,6 +3401,8 @@ task jalviewjsTransferUnzipSwingJs { copy { from zipTree(file_zip) into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" + exclude "**.html" + exclude "**.htm" } } @@ -3416,6 +3419,22 @@ task jalviewjsTransferUnzipLib { copy { from zipTree(file_zip) into "${jalviewDir}/${jalviewjsTransferSiteLibDir}" + exclude "**.html" + exclude "**.htm" + + // The following replace() is needed due to a mismatch in Jmol calls to + // colorPtToFFRGB$javajs_util_T3d when only colorPtToFFRGB$javajs_util_T3 is defined + // in the SwingJS.zip (github or the one distributed with JSmol) + if (file_zip.getName().equals("Jmol-SwingJS.zip")) { + filter { line -> + def l = "" + while(!line.equals(l)) { + line = line.replace('colorPtToFFRGB$javajs_util_T3d', 'colorPtToFFRGB$javajs_util_T3') + l = line + } + return line + } + } } } } @@ -3431,8 +3450,6 @@ task jalviewjsTransferUnzipAllLibs { } - - task jalviewjsCreateJ2sSettings(type: WriteProperties) { group "JalviewJS" description "Create the alternative j2s file from the j2s.* properties" @@ -3679,6 +3696,37 @@ DEBUG: ${eclipseDebug} } +task jalviewjsMergeJs (type: Sync) { + dependsOn jalviewjsTransferUnzipAllLibs + dependsOn jalviewjsTranspile + + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}") + // merge swingjs lib last + inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}") + // merge jalview files very last + inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteJsDir}") + + def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}" + + from inputFiles + into outputDir + def outputFiles = [] + rename { filename -> + outputFiles += "${outputDir}/${filename}" + null + } + preserve { + include "**" + } + + // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite) + duplicatesStrategy "INCLUDE" + + outputs.files outputFiles + inputs.files inputFiles +} + + def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) { def stdout = new ByteArrayOutputStream() @@ -3693,6 +3741,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin def coreTop = file(prefixFile) def coreBottom = file(suffixFile) + def missingFiles = [] coreFile.getParentFile().mkdirs() coreFile.createNewFile() coreFile.write( coreTop.getText("UTF-8") ) @@ -3706,6 +3755,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin msg = "...file '"+f.getPath()+"' does not exist, skipping" println(msg) logOutFile.append(msg+"\n") + missingFiles += f } } coreFile.append( coreBottom.getText("UTF-8") ) @@ -3748,6 +3798,11 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin } } msg = "--" + if (missingFiles.size() > 0) { + msg += "\n!!! These files were listed but missing:\n" + missingFiles.each { file -> msg += "!!! " + file.getPath() + "\n" } + msg = "--" + } println(msg) logOutFile.append(msg+"\n") } @@ -3758,11 +3813,12 @@ task jalviewjsBuildAllCores { description "Build the core js lib closures listed in the classlists dir" dependsOn jalviewjsTranspile dependsOn jalviewjsTransferUnzipSwingJs + dependsOn jalviewjsMergeJs - def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}" - def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}" - def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}" - def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}" + def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}" + def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}" + def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}" + def jsDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_js_subdir}" def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core" def prefixFile = "${jsDir}/core/coretop2.js" def suffixFile = "${jsDir}/core/corebottom2.js" @@ -3823,19 +3879,6 @@ task jalviewjsBuildAllCores { outputs.file(zjsfile) } - // _stevesoft core. add any cores without a classlist here (and the inputs and outputs) - def stevesoftClasslistName = "_stevesoft" - def stevesoftClasslist = [ - 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js", - 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js", - 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"), - 'name': stevesoftClasslistName - ] - jalviewjsCoreClasslists += stevesoftClasslist - inputs.files(stevesoftClasslist['list']) - outputs.file(stevesoftClasslist['jsfile']) - outputs.file(stevesoftClasslist['zjsfile']) - // _all core def allClasslistName = "_all" def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js") diff --git a/src/jalview/bin/JalviewJS2.java b/src/jalview/bin/JalviewJS2.java index b0a9ba0..579cfbb 100644 --- a/src/jalview/bin/JalviewJS2.java +++ b/src/jalview/bin/JalviewJS2.java @@ -20,13 +20,13 @@ */ package jalview.bin; -import jalview.util.Platform; - import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import javax.swing.Timer; +import jalview.util.Platform; + /** * Entry point for JalviewJS development. * @@ -44,8 +44,7 @@ public class JalviewJS2 * @j2sNative * * J2S.thisApplet.__Info.args = - * ["open","examples/uniref50.fa","features", - * "examples/exampleFeatures.txt"]; + * ["--open","examples/exampleFile_2_7.jar"]; */ } diff --git a/utils/jalviewjs/_j2sclasslist.txt b/utils/jalviewjs/_j2sclasslist.txt index f1f2064..3471709 100644 --- a/utils/jalviewjs/_j2sclasslist.txt +++ b/utils/jalviewjs/_j2sclasslist.txt @@ -1,13 +1,33 @@ +com/github/reinert/jjschema/Attributes.js +com/stevesoft/pat/AmpersandRule.js com/stevesoft/pat/Any.js +com/stevesoft/pat/BackG.js +com/stevesoft/pat/BackMatch.js +com/stevesoft/pat/BackRefRule.js +com/stevesoft/pat/Backup.js +com/stevesoft/pat/BasicStringBufferLike.js +com/stevesoft/pat/Bits.js com/stevesoft/pat/Boundary.js com/stevesoft/pat/Bracket.js com/stevesoft/pat/Branch.js com/stevesoft/pat/CaseMgr.js +com/stevesoft/pat/ChangeRule.js +com/stevesoft/pat/CodeRule.js +com/stevesoft/pat/Ctrl.js +com/stevesoft/pat/Custom.js +com/stevesoft/pat/CustomEndpoint.js +com/stevesoft/pat/DirFileRegex.js com/stevesoft/pat/DotMulti.js com/stevesoft/pat/End.js com/stevesoft/pat/FastBracket.js com/stevesoft/pat/FastChar.js com/stevesoft/pat/FastMulti.js +com/stevesoft/pat/FileRegex.js +com/stevesoft/pat/Group.js +com/stevesoft/pat/LeftRule.js +com/stevesoft/pat/Multi.js +com/stevesoft/pat/MultiMin.js +com/stevesoft/pat/Multi_stage2.js com/stevesoft/pat/NUnicodeAlpha.js com/stevesoft/pat/NUnicodeCurrency.js com/stevesoft/pat/NUnicodeDigit.js @@ -16,24 +36,47 @@ com/stevesoft/pat/NUnicodePunct.js com/stevesoft/pat/NUnicodeW.js com/stevesoft/pat/NUnicodeWhite.js com/stevesoft/pat/NoPattern.js +com/stevesoft/pat/NonDirFileRegex.js +com/stevesoft/pat/NotImplementedError.js com/stevesoft/pat/NullPattern.js +com/stevesoft/pat/NullRule.js com/stevesoft/pat/Or.js com/stevesoft/pat/OrMark.js +com/stevesoft/pat/PartialBuffer.js com/stevesoft/pat/Pattern.js com/stevesoft/pat/PatternSub.js +com/stevesoft/pat/PopRule.js +com/stevesoft/pat/Prop.js com/stevesoft/pat/Pthings.js +com/stevesoft/pat/PushRule.js +com/stevesoft/pat/RBuffer.js com/stevesoft/pat/Range.js com/stevesoft/pat/RegOpt.js com/stevesoft/pat/RegRes.js +com/stevesoft/pat/RegSyntax.js +com/stevesoft/pat/RegSyntaxError.js com/stevesoft/pat/Regex.js +com/stevesoft/pat/RegexReader.js +com/stevesoft/pat/RegexTokenizer.js +com/stevesoft/pat/RegexWriter.js com/stevesoft/pat/ReplaceRule.js +com/stevesoft/pat/Replacer.js +com/stevesoft/pat/RightRule.js com/stevesoft/pat/Rthings.js +com/stevesoft/pat/RuleHolder.js com/stevesoft/pat/Skip.js +com/stevesoft/pat/Skip2.js +com/stevesoft/pat/SkipBMH.js +com/stevesoft/pat/Skipped.js +com/stevesoft/pat/SpecialRule.js com/stevesoft/pat/Start.js com/stevesoft/pat/StrPos.js +com/stevesoft/pat/StringBufferLike.js com/stevesoft/pat/StringLike.js com/stevesoft/pat/StringRule.js com/stevesoft/pat/SubMark.js +com/stevesoft/pat/TransPat.js +com/stevesoft/pat/Transformer.js com/stevesoft/pat/UniValidator.js com/stevesoft/pat/UnicodeAlpha.js com/stevesoft/pat/UnicodeCurrency.js @@ -45,48 +88,180 @@ com/stevesoft/pat/UnicodeUpper.js com/stevesoft/pat/UnicodeW.js com/stevesoft/pat/UnicodeWhite.js com/stevesoft/pat/Validator.js +com/stevesoft/pat/WantMoreTextReplaceRule.js +com/stevesoft/pat/lookAhead.js com/stevesoft/pat/oneChar.js com/stevesoft/pat/parsePerl.js com/stevesoft/pat/patInf.js com/stevesoft/pat/patInt.js +com/stevesoft/pat/wrap/CharArrayBufferWrap.js +com/stevesoft/pat/wrap/CharArrayWrap.js +com/stevesoft/pat/wrap/RandomAccessFileWrap.js +com/stevesoft/pat/wrap/StringBufferWrap.js com/stevesoft/pat/wrap/StringWrap.js +com/stevesoft/pat/wrap/WriterWrap.js core/package.js +ext/edu/ucsf/rbvi/strucviz2/ChimUtils.js +ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.js +ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.js +ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.js +ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.js +ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.js +ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.js +ext/edu/ucsf/rbvi/strucviz2/StructureManager.js +ext/edu/ucsf/rbvi/strucviz2/StructureSettings.js +ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.js +ext/vamsas/IRegistry.js +ext/vamsas/IRegistryService.js +ext/vamsas/IRegistryServiceLocator.js +ext/vamsas/Jpred.js +ext/vamsas/JpredService.js +ext/vamsas/JpredServiceLocator.js +ext/vamsas/JpredSoapBindingStub.js +ext/vamsas/MuscleWS.js +ext/vamsas/MuscleWSService.js +ext/vamsas/MuscleWSServiceLocator.js +ext/vamsas/MuscleWSSoapBindingStub.js +ext/vamsas/RegistryServiceSoapBindingStub.js +ext/vamsas/SeqSearchI.js +ext/vamsas/SeqSearchServiceLocator.js +ext/vamsas/SeqSearchServiceService.js +ext/vamsas/SeqSearchServiceSoapBindingStub.js +ext/vamsas/ServiceHandle.js +ext/vamsas/ServiceHandles.js +intervalstore/api/IntervalI.js +intervalstore/api/IntervalStoreI.js +intervalstore/impl/BinarySearcher.js +intervalstore/impl/IntervalStore.js +intervalstore/impl/NCList.js +intervalstore/impl/NCNode.js jalview/analysis/AAFrequency.js jalview/analysis/AlignSeq.js +jalview/analysis/AlignmentAnnotationUtils.js +jalview/analysis/AlignmentSorter.js +jalview/analysis/AlignmentUtils.js jalview/analysis/AnnotationSorter.js +jalview/analysis/AverageDistanceEngine.js +jalview/analysis/AverageDistanceTree.js +jalview/analysis/CodingUtils.js +jalview/analysis/CodonComparator.js jalview/analysis/Conservation.js jalview/analysis/CrossRef.js +jalview/analysis/Dna.js +jalview/analysis/Finder.js jalview/analysis/GeneticCodeI.js jalview/analysis/GeneticCodes.js +jalview/analysis/Grouping.js +jalview/analysis/NJTree.js +jalview/analysis/PCA.js +jalview/analysis/ParseProperties.js +jalview/analysis/Rna.js +jalview/analysis/SecStrConsensus.js +jalview/analysis/SeqsetUtils.js jalview/analysis/SequenceIdMatcher.js +jalview/analysis/StructureFrequency.js +jalview/analysis/TreeBuilder.js +jalview/analysis/TreeEngine.js jalview/analysis/TreeModel.js +jalview/analysis/WUSSParseException.js jalview/analysis/scoremodels/DistanceScoreModel.js jalview/analysis/scoremodels/FeatureDistanceModel.js jalview/analysis/scoremodels/PIDModel.js jalview/analysis/scoremodels/ScoreMatrix.js jalview/analysis/scoremodels/ScoreModels.js +jalview/analysis/scoremodels/SimilarityParams.js jalview/analysis/scoremodels/SimilarityScoreModel.js +jalview/analysis/scoremodels/SmithWatermanModel.js +jalview/analytics/Plausible.js jalview/api/AlignCalcManagerI.js jalview/api/AlignCalcWorkerI.js +jalview/api/AlignExportSettingsI.js jalview/api/AlignViewControllerGuiI.js jalview/api/AlignViewControllerI.js jalview/api/AlignViewportI.js +jalview/api/AlignmentColsCollectionI.js +jalview/api/AlignmentRowsCollectionI.js jalview/api/AlignmentViewPanel.js jalview/api/BuildDetailsI.js +jalview/api/ComplexAlignFile.js +jalview/api/DBRefEntryI.js +jalview/api/FeatureColourI.js jalview/api/FeatureRenderer.js +jalview/api/FeatureSettingsControllerI.js +jalview/api/FeatureSettingsModelI.js +jalview/api/FeaturesDisplayedI.js +jalview/api/FeaturesSourceI.js +jalview/api/FinderI.js jalview/api/OOMHandlerI.js +jalview/api/RendererListenerI.js +jalview/api/RotatableCanvasI.js jalview/api/SequenceRenderer.js +jalview/api/SequenceStructureBinding.js +jalview/api/SiftsClientI.js +jalview/api/SplitContainerI.js jalview/api/StructureSelectionManagerProvider.js jalview/api/ViewStyleI.js jalview/api/analysis/PairwiseScoreModelI.js jalview/api/analysis/ScoreModelI.js +jalview/api/analysis/SimilarityParamsI.js +jalview/api/structures/JalviewStructureDisplayI.js +jalview/appletgui/APopupMenu.js +jalview/appletgui/AlignFrame.js +jalview/appletgui/AlignViewport.js +jalview/appletgui/AlignmentPanel.js +jalview/appletgui/AnnotationColourChooser.js +jalview/appletgui/AnnotationColumnChooser.js +jalview/appletgui/AnnotationLabels.js +jalview/appletgui/AnnotationPanel.js +jalview/appletgui/AnnotationRowFilter.js +jalview/appletgui/AppletJmol.js +jalview/appletgui/AppletJmolBinding.js +jalview/appletgui/CutAndPasteTransfer.js +jalview/appletgui/EditNameDialog.js +jalview/appletgui/EmbmenuFrame.js +jalview/appletgui/ExtJmol.js +jalview/appletgui/FeatureColourChooser.js +jalview/appletgui/FeatureRenderer.js +jalview/appletgui/FeatureSettings.js +jalview/appletgui/Finder.js +jalview/appletgui/FontChooser.js +jalview/appletgui/IdCanvas.js +jalview/appletgui/IdPanel.js +jalview/appletgui/IdwidthAdjuster.js +jalview/appletgui/JVDialog.js +jalview/appletgui/OverviewCanvas.js +jalview/appletgui/OverviewPanel.js +jalview/appletgui/PCAPanel.js +jalview/appletgui/PaintRefresher.js +jalview/appletgui/PairwiseAlignPanel.js +jalview/appletgui/RedundancyPanel.js +jalview/appletgui/RotatableCanvas.js +jalview/appletgui/ScalePanel.js +jalview/appletgui/SeqCanvas.js +jalview/appletgui/SeqPanel.js +jalview/appletgui/SequenceRenderer.js +jalview/appletgui/SliderPanel.js +jalview/appletgui/SplitFrame.js +jalview/appletgui/TitledPanel.js +jalview/appletgui/Tooltip.js +jalview/appletgui/TreeCanvas.js +jalview/appletgui/TreePanel.js +jalview/appletgui/UserDefinedColours.js jalview/bin/ArgsParser.js jalview/bin/BuildDetails.js jalview/bin/Cache.js jalview/bin/Commands.js jalview/bin/Console.js +jalview/bin/GetMemory.js +jalview/bin/HiDPISetting.js jalview/bin/Jalview.js +jalview/bin/JalviewJS2.js +jalview/bin/JalviewLite.js +jalview/bin/JalviewLiteURLRetrieve.js jalview/bin/JalviewTaskbar.js +jalview/bin/Launcher.js +jalview/bin/MemorySetting.js +jalview/bin/ScreenInfo.js jalview/bin/argparser/Arg.js jalview/bin/argparser/ArgParser.js jalview/bin/argparser/ArgValue.js @@ -94,119 +269,450 @@ jalview/bin/argparser/ArgValues.js jalview/bin/argparser/ArgValuesMap.js jalview/bin/argparser/BootstrapArgs.js jalview/bin/argparser/SubVals.js +jalview/bin/groovy/JalviewObject.js jalview/bin/groovy/JalviewObjectI.js +jalview/commands/ChangeCaseCommand.js +jalview/commands/CommandI.js +jalview/commands/EditCommand.js +jalview/commands/OrderCommand.js +jalview/commands/RemoveGapColCommand.js +jalview/commands/RemoveGapsCommand.js +jalview/commands/SlideSequencesCommand.js +jalview/commands/TrimRegionCommand.js jalview/controller/AlignViewController.js +jalview/controller/FeatureSettingsController.js +jalview/controller/FeatureSettingsControllerGuiI.js jalview/datamodel/ASequence.js jalview/datamodel/ASequenceI.js +jalview/datamodel/AlignExportSettingsAdapter.js +jalview/datamodel/AlignedCodon.js +jalview/datamodel/AlignedCodonFrame.js jalview/datamodel/Alignment.js jalview/datamodel/AlignmentAnnotation.js +jalview/datamodel/AlignmentExportData.js jalview/datamodel/AlignmentI.js +jalview/datamodel/AlignmentOrder.js +jalview/datamodel/AlignmentView.js +jalview/datamodel/AllColsCollection.js +jalview/datamodel/AllColsIterator.js +jalview/datamodel/AllRowsCollection.js +jalview/datamodel/AllRowsIterator.js jalview/datamodel/AnnotatedCollectionI.js jalview/datamodel/Annotation.js jalview/datamodel/BinaryNode.js +jalview/datamodel/BinarySequence.js +jalview/datamodel/CigarArray.js +jalview/datamodel/CigarBase.js +jalview/datamodel/CigarCigar.js +jalview/datamodel/CigarSimple.js jalview/datamodel/ColumnSelection.js +jalview/datamodel/ContactListI.js +jalview/datamodel/ContactListImpl.js +jalview/datamodel/ContactListProviderI.js jalview/datamodel/ContactMapHolder.js jalview/datamodel/ContactMapHolderI.js +jalview/datamodel/ContactMatrix.js +jalview/datamodel/ContactMatrixI.js +jalview/datamodel/ContactRange.js +jalview/datamodel/ContiguousI.js +jalview/datamodel/DBRefEntry.js jalview/datamodel/DBRefSource.js +jalview/datamodel/FeatureProperties.js +jalview/datamodel/FloatContactMatrix.js +jalview/datamodel/GeneLociI.js +jalview/datamodel/GeneLocus.js +jalview/datamodel/GraphLine.js +jalview/datamodel/GroupSet.js +jalview/datamodel/GroupSetHolder.js +jalview/datamodel/GroupSetI.js jalview/datamodel/HiddenColumns.js jalview/datamodel/HiddenColumnsCursor.js jalview/datamodel/HiddenCursorPosition.js jalview/datamodel/HiddenSequences.js +jalview/datamodel/IncompleteCodonException.js +jalview/datamodel/MappedFeatures.js +jalview/datamodel/Mapping.js +jalview/datamodel/MappingType.js +jalview/datamodel/NodeTransformI.js jalview/datamodel/PDBEntry.js +jalview/datamodel/Point.js jalview/datamodel/Profile.js jalview/datamodel/ProfileI.js jalview/datamodel/Profiles.js jalview/datamodel/ProfilesI.js +jalview/datamodel/Provenance.js +jalview/datamodel/ProvenanceEntry.js +jalview/datamodel/Range.js 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+jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.js +jalview/datamodel/annotations/AnnotationRowBuilder.js +jalview/datamodel/features/FeatureAttributeType.js +jalview/datamodel/features/FeatureAttributes.js +jalview/datamodel/features/FeatureLocationI.js +jalview/datamodel/features/FeatureMatcher.js +jalview/datamodel/features/FeatureMatcherI.js +jalview/datamodel/features/FeatureMatcherSet.js +jalview/datamodel/features/FeatureMatcherSetI.js +jalview/datamodel/features/FeatureSource.js +jalview/datamodel/features/FeatureSourceI.js +jalview/datamodel/features/FeatureSources.js +jalview/datamodel/features/FeatureStore.js jalview/datamodel/features/SequenceFeatures.js jalview/datamodel/features/SequenceFeaturesI.js +jalview/exceptions/JalviewException.js +jalview/ext/android/ContainerHelpers.js +jalview/ext/android/SparseDoubleArray.js +jalview/ext/android/SparseIntArray.js +jalview/ext/android/SparseShortArray.js +jalview/ext/ensembl/EnsemblCdna.js 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jalview/schemes/ResidueProperties.js jalview/schemes/ScoreColourScheme.js @@ -225,67 +733,295 @@ jalview/schemes/SunsetColourScheme.js jalview/schemes/TCoffeeColourScheme.js jalview/schemes/TaylorColourScheme.js jalview/schemes/TurnColourScheme.js +jalview/schemes/UserColourScheme.js jalview/schemes/ZappoColourScheme.js +jalview/structure/AlignmentViewPanelListener.js +jalview/structure/AtomSpec.js +jalview/structure/AtomSpecModel.js jalview/structure/CommandListener.js +jalview/structure/SecondaryStructureListener.js jalview/structure/SelectionListener.js jalview/structure/SelectionSource.js jalview/structure/SequenceListener.js +jalview/structure/StructureCommand.js +jalview/structure/StructureCommandI.js +jalview/structure/StructureCommandsBase.js +jalview/structure/StructureCommandsI.js jalview/structure/StructureImportSettings.js +jalview/structure/StructureListener.js +jalview/structure/StructureMapping.js +jalview/structure/StructureMappingcommandSet.js 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+jalview/ws/params/ValueConstrainI.js +jalview/ws/params/WsParamSetI.js +jalview/ws/params/simple/BooleanOption.js +jalview/ws/params/simple/IntegerParameter.js +jalview/ws/params/simple/Option.js +jalview/ws/params/simple/Parameter.js +jalview/ws/params/simple/StringChoiceParameter.js +jalview/ws/rest/AlignmentProcessor.js +jalview/ws/rest/HttpResultSet.js +jalview/ws/rest/InputType.js +jalview/ws/rest/NoValidInputDataException.js +jalview/ws/rest/RestClient.js +jalview/ws/rest/RestJob.js +jalview/ws/rest/RestJobThread.js +jalview/ws/rest/RestServiceDescription.js +jalview/ws/rest/params/Alignment.js +jalview/ws/rest/params/AnnotationFile.js +jalview/ws/rest/params/JobConstant.js +jalview/ws/rest/params/SeqGroupIndexVector.js +jalview/ws/rest/params/SeqIdVector.js +jalview/ws/rest/params/SeqVector.js +jalview/ws/rest/params/Tree.js jalview/ws/seqfetcher/ASequenceFetcher.js jalview/ws/seqfetcher/DbSourceProxy.js jalview/ws/seqfetcher/DbSourceProxyImpl.js +jalview/ws/sifts/MappingOutputPojo.js +jalview/ws/sifts/SiftsClient.js +jalview/ws/sifts/SiftsException.js jalview/ws/sifts/SiftsSettings.js +jalview/ws/uimodel/AlignAnalysisUIText.js +jalview/ws/utils/UrlDownloadClient.js +jalview/xml/binding/embl/EntrySetType.js +jalview/xml/binding/embl/EntryType.js +jalview/xml/binding/embl/ObjectFactory.js +jalview/xml/binding/embl/ROOT.js +jalview/xml/binding/embl/XrefType.js +jalview/xml/binding/jalview/AlcodonFrame.js jalview/xml/binding/jalview/Annotation.js +jalview/xml/binding/jalview/AnnotationColourScheme.js jalview/xml/binding/jalview/AnnotationElement.js +jalview/xml/binding/jalview/DoubleMatrix.js +jalview/xml/binding/jalview/DoubleVector.js +jalview/xml/binding/jalview/Feature.js +jalview/xml/binding/jalview/FeatureMatcher.js +jalview/xml/binding/jalview/FeatureMatcherSet.js +jalview/xml/binding/jalview/FilterBy.js jalview/xml/binding/jalview/JalviewModel.js +jalview/xml/binding/jalview/JalviewUserColours.js +jalview/xml/binding/jalview/MapListType.js +jalview/xml/binding/jalview/MapOnAMatrixType.js +jalview/xml/binding/jalview/Mapping.js +jalview/xml/binding/jalview/MatrixType.js +jalview/xml/binding/jalview/NoValueColour.js +jalview/xml/binding/jalview/ObjectFactory.js +jalview/xml/binding/jalview/PcaDataType.js jalview/xml/binding/jalview/Pdbentry.js +jalview/xml/binding/jalview/Property.js jalview/xml/binding/jalview/Sequence.js jalview/xml/binding/jalview/SequenceSet.js jalview/xml/binding/jalview/SequenceType.js +jalview/xml/binding/jalview/ThresholdType.js jalview/xml/binding/jalview/VAMSAS.js jalview/xml/binding/jalview/WebServiceParameterSet.js +jalview/xml/binding/jalview/package-info.js +jalview/xml/binding/sifts/Alignment.js +jalview/xml/binding/sifts/EntityType.js +jalview/xml/binding/sifts/Entry.js +jalview/xml/binding/sifts/ObjectFactory.js +jalview/xml/binding/sifts/package-info.js +jalview/xml/binding/uniprot/CitationType.js +jalview/xml/binding/uniprot/CofactorType.js +jalview/xml/binding/uniprot/CommentType.js +jalview/xml/binding/uniprot/ConsortiumType.js +jalview/xml/binding/uniprot/DbReferenceType.js +jalview/xml/binding/uniprot/Entry.js +jalview/xml/binding/uniprot/EventType.js +jalview/xml/binding/uniprot/EvidenceType.js +jalview/xml/binding/uniprot/EvidencedStringType.js +jalview/xml/binding/uniprot/FeatureType.js +jalview/xml/binding/uniprot/GeneLocationType.js +jalview/xml/binding/uniprot/GeneNameType.js +jalview/xml/binding/uniprot/GeneType.js +jalview/xml/binding/uniprot/ImportedFromType.js +jalview/xml/binding/uniprot/InteractantType.js +jalview/xml/binding/uniprot/IsoformType.js +jalview/xml/binding/uniprot/KeywordType.js +jalview/xml/binding/uniprot/LocationType.js +jalview/xml/binding/uniprot/MoleculeType.js +jalview/xml/binding/uniprot/NameListType.js +jalview/xml/binding/uniprot/ObjectFactory.js +jalview/xml/binding/uniprot/OrganismNameType.js +jalview/xml/binding/uniprot/OrganismType.js +jalview/xml/binding/uniprot/PersonType.js +jalview/xml/binding/uniprot/PhysiologicalReactionType.js +jalview/xml/binding/uniprot/PositionType.js +jalview/xml/binding/uniprot/PropertyType.js +jalview/xml/binding/uniprot/ProteinExistenceType.js +jalview/xml/binding/uniprot/ProteinType.js +jalview/xml/binding/uniprot/ReactionType.js +jalview/xml/binding/uniprot/ReferenceType.js +jalview/xml/binding/uniprot/SequenceType.js +jalview/xml/binding/uniprot/SourceDataType.js +jalview/xml/binding/uniprot/SourceType.js +jalview/xml/binding/uniprot/StatusType.js +jalview/xml/binding/uniprot/SubcellularLocationType.js +jalview/xml/binding/uniprot/Uniprot.js +jalview/xml/binding/uniprot/package-info.js java/applet/AppletContext.js java/applet/AppletStub.js java/applet/JSApplet.js @@ -297,6 +1033,7 @@ java/awt/Adjustable.js java/awt/AlphaComposite.js java/awt/BasicStroke.js java/awt/BorderLayout.js +java/awt/CardLayout.js java/awt/Color.js java/awt/Component.js java/awt/ComponentOrientation.js @@ -315,10 +1052,15 @@ java/awt/FlowLayout.js java/awt/FocusTraversalPolicy.js java/awt/Font.js java/awt/FontMetrics.js +java/awt/Graphics.js +java/awt/Graphics2D.js java/awt/GraphicsCallback.js java/awt/GraphicsConfiguration.js java/awt/GraphicsDevice.js java/awt/GraphicsEnvironment.js +java/awt/GridBagConstraints.js +java/awt/GridBagLayout.js +java/awt/GridBagLayoutInfo.js java/awt/GridLayout.js java/awt/Image.js java/awt/Insets.js @@ -384,6 +1126,7 @@ java/awt/event/MouseEvent.js java/awt/event/MouseListener.js java/awt/event/MouseMotionAdapter.js java/awt/event/MouseMotionListener.js +java/awt/event/MouseWheelEvent.js java/awt/event/MouseWheelListener.js java/awt/event/TextListener.js java/awt/event/WindowAdapter.js @@ -392,6 +1135,7 @@ java/awt/event/WindowFocusListener.js java/awt/event/WindowListener.js java/awt/event/WindowStateListener.js java/awt/font/FontRenderContext.js +java/awt/font/TextAttribute.js java/awt/geom/AffineTransform.js java/awt/geom/Dimension2D.js java/awt/geom/Path2D.js @@ -425,13 +1169,23 @@ java/beans/PropertyChangeEvent.js java/beans/PropertyChangeListener.js java/beans/PropertyChangeSupport.js java/io/BufferedInputStream.js +java/io/BufferedWriter.js java/io/DataInput.js java/io/DataInputStream.js java/io/File.js +java/io/FileOutputStream.js +java/io/FileReader.js +java/io/FileSystem.js java/io/FilenameFilter.js java/io/FilterInputStream.js +java/io/FilterOutputStream.js +java/io/InputStream.js java/io/InputStreamReader.js java/io/ObjectStreamField.js +java/io/OutputStreamWriter.js +java/io/PrintStream.js +java/io/StringWriter.js +java/io/Writer.js java/lang/AbstractStringBuilder.js java/lang/ApplicationShutdownHooks.js java/lang/Class.js @@ -454,10 +1208,18 @@ java/math/BigInteger.js java/math/MathContext.js java/net/ContentHandler.js java/net/HttpURLConnection.js +java/net/URI.js java/net/URL.js java/net/URLConnection.js +java/net/URLEncoder.js java/net/URLStreamHandler.js java/net/URLStreamHandlerFactory.js +java/net/UnknownHostException.js +java/nio/file/FileSystem.js +java/nio/file/FileSystems.js +java/nio/file/Path.js +java/nio/file/Watchable.js +java/nio/file/spi/FileSystemProvider.js java/security/AccessController.js java/security/PrivilegedAction.js java/security/PrivilegedExceptionAction.js @@ -502,6 +1264,7 @@ java/util/IdentityHashMap.js java/util/Iterator.js java/util/JumboEnumSet.js java/util/LinkedHashMap.js +java/util/LinkedHashSet.js java/util/LinkedList.js java/util/List.js java/util/ListIterator.js @@ -513,6 +1276,7 @@ java/util/Objects.js java/util/Properties.js java/util/PropertyResourceBundle.js java/util/Queue.js +java/util/Random.js java/util/RandomAccess.js java/util/RegularEnumSet.js java/util/ServiceLoader.js @@ -526,13 +1290,18 @@ java/util/TimeZone.js java/util/TreeMap.js java/util/TreeSet.js java/util/Vector.js +java/util/WeakHashMap.js java/util/concurrent/AbstractExecutorService.js java/util/concurrent/BlockingQueue.js +java/util/concurrent/Callable.js java/util/concurrent/Executor.js java/util/concurrent/ExecutorService.js java/util/concurrent/Executors.js +java/util/concurrent/Future.js +java/util/concurrent/FutureTask.js java/util/concurrent/LinkedBlockingQueue.js java/util/concurrent/RejectedExecutionHandler.js +java/util/concurrent/RunnableFuture.js java/util/concurrent/Semaphore.js java/util/concurrent/ThreadFactory.js java/util/concurrent/ThreadPoolExecutor.js @@ -577,18 +1346,39 @@ java/util/zip/InflaterInputStream.js java/util/zip/ZipConstants.js java/util/zip/ZipEntry.js java/util/zip/ZipInputStream.js +javajs/api/BytePoster.js javajs/api/GenericLineReader.js +javajs/api/GenericOutputChannel.js javajs/api/JSONEncodable.js +javajs/async/SwingJSUtils.js +javajs/util/A4d.js javajs/util/AjaxURLConnection.js javajs/util/AjaxURLStreamHandler.js javajs/util/AjaxURLStreamHandlerFactory.js +javajs/util/BS.js javajs/util/Base64.js +javajs/util/CU.js +javajs/util/DF.js javajs/util/Encoding.js javajs/util/JSThread.js +javajs/util/LimitedLineReader.js javajs/util/Lst.js +javajs/util/M3.js +javajs/util/M34.js +javajs/util/M34d.js +javajs/util/M3d.js +javajs/util/M4d.js +javajs/util/OC.js +javajs/util/P3d.js +javajs/util/P3i.js +javajs/util/P4d.js javajs/util/PT.js javajs/util/Rdr.js javajs/util/SB.js +javajs/util/T3d.js +javajs/util/T3i.js +javajs/util/T4d.js +javajs/util/V3d.js javax/net/ssl/HttpsURLConnection.js javax/swing/AbstractAction.js javax/swing/AbstractButton.js @@ -614,6 +1404,7 @@ javax/swing/DefaultComboBoxModel.js javax/swing/DefaultDesktopManager.js javax/swing/DefaultListCellRenderer.js javax/swing/DefaultListSelectionModel.js +javax/swing/DefaultRowSorter.js javax/swing/DefaultSingleSelectionModel.js javax/swing/DesktopManager.js javax/swing/DropMode.js @@ -639,6 +1430,7 @@ javax/swing/JList.js javax/swing/JMenu.js javax/swing/JMenuBar.js javax/swing/JMenuItem.js +javax/swing/JOptionPane.js javax/swing/JPanel.js javax/swing/JPopupMenu.js javax/swing/JProgressBar.js @@ -648,6 +1440,7 @@ javax/swing/JScrollBar.js javax/swing/JScrollPane.js javax/swing/JSeparator.js javax/swing/JTabbedPane.js +javax/swing/JTable.js javax/swing/JTextArea.js javax/swing/JTextField.js javax/swing/JToggleButton.js @@ -669,11 +1462,13 @@ javax/swing/Popup.js javax/swing/PopupFactory.js javax/swing/RepaintManager.js javax/swing/RootPaneContainer.js +javax/swing/RowSorter.js javax/swing/ScrollPaneConstants.js javax/swing/ScrollPaneLayout.js javax/swing/Scrollable.js javax/swing/SingleSelectionModel.js javax/swing/SizeRequirements.js +javax/swing/SortOrder.js javax/swing/SortingFocusTraversalPolicy.js javax/swing/Spring.js javax/swing/SpringLayout.js @@ -701,8 +1496,10 @@ javax/swing/event/AncestorEvent.js javax/swing/event/AncestorListener.js javax/swing/event/CaretEvent.js javax/swing/event/CaretListener.js +javax/swing/event/CellEditorListener.js javax/swing/event/ChangeEvent.js javax/swing/event/ChangeListener.js +javax/swing/event/DocumentEvent.js javax/swing/event/DocumentListener.js javax/swing/event/EventListenerList.js javax/swing/event/HyperlinkListener.js @@ -711,11 +1508,21 @@ javax/swing/event/InternalFrameEvent.js javax/swing/event/InternalFrameListener.js javax/swing/event/ListDataEvent.js javax/swing/event/ListDataListener.js +javax/swing/event/ListSelectionEvent.js javax/swing/event/ListSelectionListener.js javax/swing/event/MenuEvent.js javax/swing/event/MenuKeyListener.js javax/swing/event/MenuListener.js javax/swing/event/MouseInputListener.js +javax/swing/event/RowSorterEvent.js +javax/swing/event/RowSorterListener.js +javax/swing/event/SwingPropertyChangeSupport.js +javax/swing/event/TableColumnModelEvent.js +javax/swing/event/TableColumnModelListener.js +javax/swing/event/TableModelEvent.js +javax/swing/event/TableModelListener.js +javax/swing/event/UndoableEditEvent.js +javax/swing/event/UndoableEditListener.js javax/swing/filechooser/FileFilter.js javax/swing/filechooser/FileView.js javax/swing/plaf/ActionMapUIResource.js @@ -730,6 +1537,16 @@ javax/swing/plaf/InsetsUIResource.js javax/swing/plaf/UIResource.js javax/swing/plaf/basic/BasicBorders.js javax/swing/plaf/basic/BasicGraphicsUtils.js +javax/swing/table/AbstractTableModel.js +javax/swing/table/DefaultTableCellRenderer.js +javax/swing/table/DefaultTableColumnModel.js +javax/swing/table/DefaultTableModel.js +javax/swing/table/JTableHeader.js +javax/swing/table/TableCellRenderer.js +javax/swing/table/TableColumn.js +javax/swing/table/TableColumnModel.js +javax/swing/table/TableModel.js +javax/swing/table/TableRowSorter.js javax/swing/text/AbstractDocument.js javax/swing/text/AttributeSet.js javax/swing/text/BoxView.js @@ -748,15 +1565,20 @@ javax/swing/text/PlainDocument.js javax/swing/text/PlainView.js javax/swing/text/Position.js javax/swing/text/Segment.js +javax/swing/text/SegmentCache.js javax/swing/text/SimpleAttributeSet.js javax/swing/text/Style.js javax/swing/text/StyleConstants.js javax/swing/text/StyleContext.js javax/swing/text/TabExpander.js javax/swing/text/TextAction.js +javax/swing/text/Utilities.js javax/swing/text/View.js javax/swing/text/WrappedPlainView.js javax/swing/tree/TreeNode.js +javax/swing/undo/AbstractUndoableEdit.js +javax/swing/undo/CompoundEdit.js +javax/swing/undo/UndoableEdit.js javax/xml/bind/ContextFinder.js javax/xml/bind/GetPropertyAction.js javax/xml/bind/JAXBContext.js @@ -775,7 +1597,284 @@ javax/xml/namespace/QName.js javax/xml/stream/XMLInputFactory.js javax/xml/stream/XMLStreamConstants.js javax/xml/stream/XMLStreamReader.js +mc_view/AppletPDBCanvas.js +mc_view/AppletPDBViewer.js +mc_view/Atom.js +mc_view/Bond.js +mc_view/MCMatrix.js +mc_view/PDBCanvas.js +mc_view/PDBChain.js +mc_view/PDBfile.js +mc_view/Residue.js +mc_view/Zsort.js +net/miginfocom/layout/AC.js +net/miginfocom/layout/AnimSpec.js +net/miginfocom/layout/BoundSize.js +net/miginfocom/layout/CC.js +net/miginfocom/layout/ComponentWrapper.js +net/miginfocom/layout/ConstraintParser.js +net/miginfocom/layout/ContainerWrapper.js +net/miginfocom/layout/DimConstraint.js +net/miginfocom/layout/Grid.js +net/miginfocom/layout/LC.js +net/miginfocom/layout/LayoutUtil.js +net/miginfocom/layout/LinkHandler.js +net/miginfocom/layout/PlatformDefaults.js +net/miginfocom/layout/ResizeConstraint.js +net/miginfocom/layout/UnitValue.js +net/miginfocom/swing/MigLayout.js +net/miginfocom/swing/SwingComponentWrapper.js +net/miginfocom/swing/SwingContainerWrapper.js org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js +org/jibble/epsgraphics/EpsDocument.js +org/jibble/epsgraphics/EpsException.js +org/jibble/epsgraphics/EpsGraphics2D.js +org/jmol/adapter/readers/pdb/PdbReader.js +org/jmol/adapter/smarter/Atom.js +org/jmol/adapter/smarter/AtomIterator.js +org/jmol/adapter/smarter/AtomSetCollection.js +org/jmol/adapter/smarter/AtomSetCollectionReader.js +org/jmol/adapter/smarter/AtomSetObject.js +org/jmol/adapter/smarter/Bond.js +org/jmol/adapter/smarter/Resolver.js +org/jmol/adapter/smarter/SmarterJmolAdapter.js +org/jmol/adapter/smarter/Structure.js +org/jmol/adapter/smarter/StructureIterator.js +org/jmol/api/AtomIndexIterator.js +org/jmol/api/EventManager.js +org/jmol/api/FontManager.js +org/jmol/api/GenericFileInterface.js +org/jmol/api/GenericMouseInterface.js +org/jmol/api/GenericPlatform.js +org/jmol/api/Interface.js +org/jmol/api/JmolAdapter.js +org/jmol/api/JmolAdapterAtomIterator.js +org/jmol/api/JmolAdapterStructureIterator.js +org/jmol/api/JmolCallbackListener.js +org/jmol/api/JmolGraphicsInterface.js +org/jmol/api/JmolMeasurementClient.js +org/jmol/api/JmolRendererInterface.js +org/jmol/api/JmolRepaintManager.js +org/jmol/api/JmolScriptEvaluator.js +org/jmol/api/JmolScriptFunction.js +org/jmol/api/JmolScriptManager.js +org/jmol/api/JmolSelectionListener.js +org/jmol/api/JmolStatusListener.js +org/jmol/api/JmolViewer.js +org/jmol/api/PlatformViewer.js +org/jmol/api/SymmetryInterface.js +org/jmol/api/Translator.js +org/jmol/atomdata/AtomDataServer.js +org/jmol/atomdata/RadiusData.js +org/jmol/awt/AwtFile.js +org/jmol/awt/AwtFont.js +org/jmol/awt/Display.js +org/jmol/awt/Image.js +org/jmol/awt/Mouse.js +org/jmol/awt/Platform.js +org/jmol/bspt/Bspf.js +org/jmol/bspt/Bspt.js +org/jmol/bspt/CubeIterator.js +org/jmol/bspt/Element.js +org/jmol/bspt/Leaf.js +org/jmol/bspt/Node.js +org/jmol/c/CBK.js +org/jmol/c/FIL.js +org/jmol/c/PAL.js +org/jmol/c/STER.js +org/jmol/c/STR.js +org/jmol/c/VDW.js +org/jmol/dssx/Bridge.js +org/jmol/dssx/DSSP.js +org/jmol/g3d/CylinderRenderer.js +org/jmol/g3d/G3DRenderer.js +org/jmol/g3d/Graphics3D.js +org/jmol/g3d/HermiteRenderer.js +org/jmol/g3d/LineRenderer.js +org/jmol/g3d/Pixelator.js +org/jmol/g3d/Platform3D.js +org/jmol/g3d/PrecisionRenderer.js +org/jmol/g3d/SphereRenderer.js +org/jmol/g3d/TextRenderer.js +org/jmol/g3d/TextString.js +org/jmol/g3d/TriangleRenderer.js +org/jmol/i18n/GT.js +org/jmol/i18n/Language.js +org/jmol/i18n/Resource.js +org/jmol/io/FileReader.js +org/jmol/modelset/Atom.js +org/jmol/modelset/AtomCollection.js 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+org/json/simple/ItemList.js +org/json/simple/JSONArray.js +org/json/simple/JSONAware.js +org/json/simple/JSONObject.js +org/json/simple/JSONStreamAware.js +org/json/simple/JSONValue.js +org/json/simple/parser/ContainerFactory.js +org/json/simple/parser/ContentHandler.js +org/json/simple/parser/JSONParser.js +org/json/simple/parser/ParseException.js +org/json/simple/parser/Yylex.js +org/json/simple/parser/Yytoken.js +org/stackoverflowusers/file/WindowsShortcut.js org/xml/sax/AttributeList.js org/xml/sax/Attributes.js org/xml/sax/ContentHandler.js @@ -799,12 +1898,18 @@ sun/awt/image/DataStealer.js sun/awt/image/IntegerComponentRaster.js sun/awt/image/IntegerInterleavedRaster.js sun/awt/image/SunWritableRaster.js +sun/font/AttributeValues.js +sun/font/EAttribute.js sun/font/FontDesignMetrics.js sun/java2d/StateTrackable.js sun/java2d/StateTrackableDelegate.js sun/swing/DefaultLookup.js +sun/swing/StringUIClientPropertyKey.js sun/swing/SwingLazyValue.js +sun/swing/SwingUtilities2.js sun/swing/UIAction.js +sun/swing/UIClientPropertyKey.js +sun/swing/table/DefaultTableCellHeaderRenderer.js sun/text/resources/en/FormatData_en_GB.js sun/util/calendar/AbstractCalendar.js sun/util/calendar/BaseCalendar.js @@ -829,6 +1934,7 @@ swingjs/JSApp.js swingjs/JSAppletThread.js swingjs/JSAppletViewer.js swingjs/JSDummyApplet.js +swingjs/JSFileSystem.js swingjs/JSFocusPeer.js swingjs/JSFontMetrics.js swingjs/JSFrameViewer.js @@ -837,6 +1943,7 @@ swingjs/JSGraphicsConfiguration.js swingjs/JSGraphicsEnvironment.js swingjs/JSImage.js swingjs/JSImagekit.js +swingjs/JSKeyEvent.js swingjs/JSMenuManager.js swingjs/JSMouse.js swingjs/JSScreenDevice.js @@ -846,11 +1953,13 @@ swingjs/JSUtil.js swingjs/api/Interface.js swingjs/api/JSUtilI.js swingjs/api/js/DOMNode.js +swingjs/api/js/HTML5Applet.js swingjs/api/js/HTML5Canvas.js swingjs/api/js/HTML5CanvasContext2D.js swingjs/api/js/JSFunction.js swingjs/api/js/JSInterface.js swingjs/jquery/JQueryUI.js +swingjs/json/JSON.js swingjs/jzlib/Adler32.js swingjs/jzlib/CRC32.js swingjs/jzlib/Checksum.js @@ -863,7 +1972,9 @@ swingjs/jzlib/InflaterInputStream.js swingjs/jzlib/ZStream.js swingjs/plaf/BasicComboBoxEditor.js swingjs/plaf/BasicComboBoxRenderer.js +swingjs/plaf/BasicHTML.js swingjs/plaf/ButtonListener.js +swingjs/plaf/CellHolder.js swingjs/plaf/DefaultMenuLayout.js swingjs/plaf/HTML5LookAndFeel.js swingjs/plaf/JSAppletUI.js @@ -899,6 +2010,8 @@ swingjs/plaf/JSScrollPaneUI.js swingjs/plaf/JSSeparatorUI.js swingjs/plaf/JSSliderUI.js swingjs/plaf/JSTabbedPaneUI.js +swingjs/plaf/JSTableHeaderUI.js +swingjs/plaf/JSTableUI.js swingjs/plaf/JSTextAreaUI.js swingjs/plaf/JSTextFieldUI.js swingjs/plaf/JSTextUI.js @@ -917,4 +2030,43 @@ swingjs/xml/JSSAXAttributes.js swingjs/xml/JSSAXParser.js swingjs/xml/JSXMLGregorianCalendarImpl.js swingjs/xml/JSXMLInputFactory.js +swingjs/xml/JSXMLStreamReader.js swingjs/xml/JSXMLStreamReader.jscore/package.js +uk/ac/ebi/picr/model/CrossReference.js +uk/ac/ebi/picr/model/CrossReference_Helper.js +uk/ac/ebi/picr/model/UPEntry.js +uk/ac/ebi/picr/model/UPEntry_Helper.js +uk/ac/ebi/www/Data.js +uk/ac/ebi/www/InputParams.js +uk/ac/ebi/www/WSFile.js +uk/ac/ebi/www/WSWUBlast.js +uk/ac/ebi/www/WSWUBlastService.js +uk/ac/ebi/www/WSWUBlastServiceLocator.js +uk/ac/ebi/www/WSWUBlastSoapBindingStub.js +uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.js +uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.js +uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.js +uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.js +vamsas/IMsaWS.js +vamsas/objects/simple/Alignment.js +vamsas/objects/simple/Alignment_Helper.js +vamsas/objects/simple/JpredResult.js +vamsas/objects/simple/JpredResult_Helper.js +vamsas/objects/simple/MsaResult.js +vamsas/objects/simple/MsaResult_Helper.js +vamsas/objects/simple/Msfalignment.js +vamsas/objects/simple/Msfalignment_Helper.js +vamsas/objects/simple/Object.js +vamsas/objects/simple/Object_Helper.js +vamsas/objects/simple/Result.js +vamsas/objects/simple/Result_Helper.js +vamsas/objects/simple/Secstructpred.js +vamsas/objects/simple/Secstructpred_Helper.js +vamsas/objects/simple/SeqSearchResult.js +vamsas/objects/simple/SeqSearchResult_Helper.js +vamsas/objects/simple/Sequence.js +vamsas/objects/simple/SequenceSet.js +vamsas/objects/simple/SequenceSet_Helper.js +vamsas/objects/simple/Sequence_Helper.js +vamsas/objects/simple/WsJobId.js +vamsas/objects/simple/WsJobId_Helper.js diff --git a/utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html b/utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html index 1c95aa1..b11b2cf 100644 --- a/utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html +++ b/utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html @@ -15,7 +15,8 @@ Info = { serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php', j2sPath: 'swingjs/j2s', console: window.console, - allowjavascript: true + allowjavascript: true, + querystringnamespace: "" } diff --git a/utils/jalviewjs/classlists/jalview.txt b/utils/jalviewjs/classlists/jalview.txt deleted file mode 100644 index 5d60006..0000000 --- a/utils/jalviewjs/classlists/jalview.txt +++ /dev/null @@ -1,791 +0,0 @@ -jalview/analysis/AAFrequency.js -jalview/analysis/AlignSeq.js -jalview/analysis/AlignmentAnnotationUtils.js -jalview/analysis/AlignmentUtils.js -jalview/analysis/AnnotationSorter.js -jalview/analysis/Conservation.js -jalview/analysis/CrossRef.js -jalview/analysis/NJTree.js -jalview/analysis/SeqsetUtils.js -jalview/analysis/TreeBuilder.js -jalview/analysis/TreeModel.js -jalview/analysis/scoremodels/DistanceScoreModel.js -jalview/analysis/scoremodels/FeatureDistanceModel.js -jalview/analysis/scoremodels/PIDModel.js -jalview/analysis/scoremodels/ScoreMatrix.js -jalview/analysis/scoremodels/ScoreModels.js -jalview/analysis/scoremodels/SimilarityParams.js 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-org/jmol/modelsetbio/Monomer.js -org/jmol/modelsetbio/ProteinStructure.js -org/jmol/modelsetbio/Sheet.js -org/jmol/modelsetbio/Turn.js -org/jmol/render/BallsRenderer.js -org/jmol/render/BbcageRenderer.js -org/jmol/render/CageRenderer.js -org/jmol/render/FontLineShapeRenderer.js -org/jmol/render/FrankRenderer.js -org/jmol/render/HoverRenderer.js -org/jmol/render/LabelsRenderer.js -org/jmol/render/MeasuresRenderer.js -org/jmol/render/RepaintManager.js -org/jmol/render/ShapeRenderer.js -org/jmol/render/SticksRenderer.js -org/jmol/render/TextRenderer.js -org/jmol/render/UccageRenderer.js -org/jmol/renderbio/BioShapeRenderer.js -org/jmol/renderbio/CartoonRenderer.js -org/jmol/renderbio/RocketsRenderer.js -org/jmol/renderbio/StrandsRenderer.js -org/jmol/script/ContextToken.js -org/jmol/script/SV.js -org/jmol/script/ScriptCompiler.js -org/jmol/script/ScriptContext.js -org/jmol/script/ScriptError.js -org/jmol/script/ScriptEval.js -org/jmol/script/ScriptExpr.js -org/jmol/script/ScriptFlowContext.js -org/jmol/script/ScriptFunction.js -org/jmol/script/ScriptManager.js -org/jmol/script/ScriptMathProcessor.js -org/jmol/script/ScriptParam.js -org/jmol/script/ScriptQueueThread.js -org/jmol/script/ScriptTokenParser.js -org/jmol/script/T.js -org/jmol/scriptext/CmdExt.js -org/jmol/scriptext/MathExt.js -org/jmol/scriptext/ScriptExt.js -org/jmol/shape/AtomShape.js -org/jmol/shape/Balls.js -org/jmol/shape/Bbcage.js -org/jmol/shape/Echo.js -org/jmol/shape/FontLineShape.js -org/jmol/shape/Frank.js -org/jmol/shape/Hover.js -org/jmol/shape/Labels.js -org/jmol/shape/Measures.js -org/jmol/shape/Mesh.js -org/jmol/shape/Shape.js -org/jmol/shape/Sticks.js -org/jmol/shape/TextShape.js -org/jmol/shape/Uccage.js -org/jmol/shapebio/BioShape.js -org/jmol/shapebio/BioShapeCollection.js -org/jmol/shapebio/Cartoon.js -org/jmol/shapebio/Rockets.js -org/jmol/symmetry/Symmetry.js -org/jmol/symmetry/SymmetryInfo.js -org/jmol/symmetry/UnitCell.js -org/jmol/thread/HoverWatcherThread.js -org/jmol/thread/JmolThread.js -org/jmol/thread/TimeoutThread.js -org/jmol/util/BSUtil.js -org/jmol/util/BoxInfo.js -org/jmol/util/C.js -org/jmol/util/ColorEncoder.js -org/jmol/util/CommandHistory.js -org/jmol/util/DefaultLogger.js -org/jmol/util/Edge.js -org/jmol/util/Elements.js -org/jmol/util/Escape.js -org/jmol/util/Font.js -org/jmol/util/GData.js -org/jmol/util/Geodesic.js -org/jmol/util/Int2IntHash.js -org/jmol/util/Int2IntHashEntry.js -org/jmol/util/Logger.js -org/jmol/util/LoggerInterface.js -org/jmol/util/MeshSurface.js -org/jmol/util/Node.js -org/jmol/util/Normix.js -org/jmol/util/Point3fi.js -org/jmol/util/Rectangle.js -org/jmol/util/Rgb16.js -org/jmol/util/Shader.js -org/jmol/util/SimpleEdge.js -org/jmol/util/SimpleNode.js -org/jmol/util/SimpleUnitCell.js -org/jmol/util/TempArray.js -org/jmol/viewer/ActionManager.js -org/jmol/viewer/AnimationManager.js -org/jmol/viewer/ColorManager.js -org/jmol/viewer/FileManager.js -org/jmol/viewer/Gesture.js -org/jmol/viewer/GlobalSettings.js -org/jmol/viewer/JC.js -org/jmol/viewer/ModelManager.js -org/jmol/viewer/MotionPoint.js -org/jmol/viewer/MouseState.js -org/jmol/viewer/SelectionManager.js -org/jmol/viewer/ShapeManager.js -org/jmol/viewer/StateManager.js -org/jmol/viewer/StatusManager.js -org/jmol/viewer/TransformManager.js -org/jmol/viewer/Viewer.js -org/jmol/viewer/binding/Binding.js -org/jmol/viewer/binding/JmolBinding.js -org/json/simple/parser/ParseException.js -org/xml/sax/AttributeList.js -org/xml/sax/Attributes.js -org/xml/sax/ContentHandler.js -org/xml/sax/InputSource.js -org/xml/sax/Parser.js -org/xml/sax/XMLReader.js -org/xml/sax/ext/Attributes2.js -sun/awt/AWTAutoShutdown.js -sun/awt/AppContext.js -sun/awt/CausedFocusEvent.js -sun/awt/ComponentFactory.js -sun/awt/EventQueueItem.js -sun/awt/MostRecentKeyValue.js -sun/awt/MostRecentThreadAppContext.js -sun/awt/PaintEventDispatcher.js -sun/awt/PostEventQueue.js -sun/awt/RequestFocusController.js -sun/awt/SunGraphicsCallback.js -sun/awt/SunToolkit.js -sun/awt/image/DataStealer.js -sun/awt/image/IntegerComponentRaster.js -sun/awt/image/IntegerInterleavedRaster.js -sun/awt/image/OffScreenImageSource.js -sun/awt/image/SunWritableRaster.js -sun/font/AttributeValues.js -sun/font/EAttribute.js -sun/font/FontDesignMetrics.js -sun/java2d/StateTrackable.js -sun/java2d/StateTrackableDelegate.js -sun/net/www/MessageHeader.js -sun/swing/DefaultLookup.js -sun/swing/StringUIClientPropertyKey.js -sun/swing/SwingLazyValue.js -sun/swing/SwingUtilities2.js -sun/swing/UIAction.js -sun/swing/UIClientPropertyKey.js -sun/swing/table/DefaultTableCellHeaderRenderer.js -sun/text/resources/FormatData.js -sun/text/resources/en/FormatData_en.js -sun/text/resources/en/FormatData_en_GB.js -sun/text/resources/en/FormatData_en_US.js -sun/util/calendar/AbstractCalendar.js -sun/util/calendar/BaseCalendar.js -sun/util/calendar/CalendarDate.js -sun/util/calendar/CalendarSystem.js -sun/util/calendar/CalendarUtils.js -sun/util/calendar/Gregorian.js -sun/util/calendar/ZoneInfo.js -sun/util/calendar/ZoneInfoFile.js -sun/util/locale/BaseLocale.js -sun/util/locale/LanguageTag.js -sun/util/locale/LocaleUtils.js -sun/util/locale/provider/AuxLocaleProviderAdapter.js -sun/util/locale/provider/AvailableLanguageTags.js -sun/util/locale/provider/CalendarDataProviderImpl.js -sun/util/locale/provider/CalendarDataUtility.js -sun/util/locale/provider/CalendarProviderImpl.js -sun/util/locale/provider/DateFormatProviderImpl.js -sun/util/locale/provider/JRELocaleProviderAdapter.js -sun/util/locale/provider/LocaleDataMetaInfo.js -sun/util/locale/provider/LocaleProviderAdapter.js -sun/util/locale/provider/LocaleResources.js -sun/util/locale/provider/LocaleServiceProviderPool.js -sun/util/locale/provider/ResourceBundleBasedAdapter.js -sun/util/locale/provider/SPILocaleProviderAdapter.js -sun/util/resources/LocaleData.js -sun/util/resources/ParallelListResourceBundle.js -sun/util/spi/CalendarProvider.js -swingjs/JSApp.js -swingjs/JSAppletThread.js -swingjs/JSAppletViewer.js -swingjs/JSDummyApplet.js -swingjs/JSFileSystem.js -swingjs/JSFocusPeer.js -swingjs/JSFontMetrics.js -swingjs/JSFrameViewer.js -swingjs/JSGraphics2D.js -swingjs/JSGraphicsConfiguration.js -swingjs/JSGraphicsEnvironment.js -swingjs/JSImage.js -swingjs/JSImagekit.js -swingjs/JSKeyEvent.js -swingjs/JSMenuManager.js -swingjs/JSMouse.js -swingjs/JSScreenDevice.js -swingjs/JSThreadGroup.js -swingjs/JSToolkit.js -swingjs/JSUtil.js -swingjs/a2s/A2SContainer.js -swingjs/a2s/Dialog.js -swingjs/api/Interface.js -swingjs/api/JSUtilI.js -swingjs/api/js/DOMNode.js -swingjs/api/js/HTML5Canvas.js -swingjs/api/js/HTML5CanvasContext2D.js -swingjs/api/js/JSFunction.js -swingjs/api/js/JSInterface.js -swingjs/jquery/JQueryUI.js -swingjs/json/JSON.js -swingjs/jzlib/Adler32.js -swingjs/jzlib/CRC32.js -swingjs/jzlib/Checksum.js -swingjs/jzlib/InfBlocks.js -swingjs/jzlib/InfCodes.js -swingjs/jzlib/InfTree.js -swingjs/jzlib/Inflate.js -swingjs/jzlib/Inflater.js -swingjs/jzlib/InflaterInputStream.js -swingjs/jzlib/ZStream.js -swingjs/plaf/BasicComboBoxEditor.js -swingjs/plaf/BasicComboBoxRenderer.js -swingjs/plaf/BasicHTML.js -swingjs/plaf/ButtonListener.js -swingjs/plaf/CellHolder.js -swingjs/plaf/DefaultMenuLayout.js -swingjs/plaf/HTML5LookAndFeel.js -swingjs/plaf/JSAppletUI.js -swingjs/plaf/JSButtonUI.js -swingjs/plaf/JSCheckBoxMenuItemUI.js -swingjs/plaf/JSCheckBoxUI.js -swingjs/plaf/JSComboBoxUI.js -swingjs/plaf/JSComboPopupList.js -swingjs/plaf/JSComponentUI.js -swingjs/plaf/JSDesktopIconUI.js -swingjs/plaf/JSDesktopPaneUI.js -swingjs/plaf/JSDialogUI.js -swingjs/plaf/JSEventHandler.js -swingjs/plaf/JSFrameUI.js -swingjs/plaf/JSGraphicsUtils.js -swingjs/plaf/JSInternalFrameUI.js -swingjs/plaf/JSLabelUI.js -swingjs/plaf/JSLayeredPaneUI.js -swingjs/plaf/JSLightweightUI.js -swingjs/plaf/JSListUI.js -swingjs/plaf/JSMenuBarUI.js -swingjs/plaf/JSMenuItemUI.js -swingjs/plaf/JSMenuUI.js -swingjs/plaf/JSOptionPaneUI.js -swingjs/plaf/JSPanelUI.js -swingjs/plaf/JSPopupMenuSeparatorUI.js -swingjs/plaf/JSPopupMenuUI.js -swingjs/plaf/JSPopupUI.js -swingjs/plaf/JSProgressBarUI.js -swingjs/plaf/JSRadioButtonMenuItemUI.js -swingjs/plaf/JSRadioButtonUI.js -swingjs/plaf/JSRootPaneUI.js -swingjs/plaf/JSScrollBarUI.js -swingjs/plaf/JSScrollPaneUI.js -swingjs/plaf/JSSeparatorUI.js -swingjs/plaf/JSSliderUI.js -swingjs/plaf/JSTabbedPaneUI.js -swingjs/plaf/JSTableHeaderUI.js -swingjs/plaf/JSTableUI.js -swingjs/plaf/JSTextAreaUI.js -swingjs/plaf/JSTextFieldUI.js -swingjs/plaf/JSTextUI.js -swingjs/plaf/JSToolTipUI.js -swingjs/plaf/JSViewportUI.js -swingjs/plaf/JSWindowUI.js -swingjs/plaf/LazyActionMap.js -swingjs/plaf/Resizer.js -swingjs/plaf/TextListener.js -swingjs/xml/JSJAXBClass.js -swingjs/xml/JSJAXBContext.js -swingjs/xml/JSJAXBContextFactory.js -swingjs/xml/JSJAXBField.js -swingjs/xml/JSJAXBUnmarshaller.js -swingjs/xml/JSSAXAttributes.js -swingjs/xml/JSSAXParser.js -swingjs/xml/JSXMLGregorianCalendarImpl.js -swingjs/xml/JSXMLInputFactory.js -swingjs/xml/JSXMLStreamReader.js diff --git a/utils/jalviewjs/coretemplate.html b/utils/jalviewjs/coretemplate.html index 7d802f2..b27080b 100644 --- a/utils/jalviewjs/coretemplate.html +++ b/utils/jalviewjs/coretemplate.html @@ -15,7 +15,8 @@ Info = { serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php', j2sPath: 'swingjs/j2s', console:'sysoutdiv', - allowjavascript: true + allowjavascript: true, + querystringnamespace: "" } diff --git a/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html index 27fd9a4..cce8ce8 100644 --- a/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html +++ b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html @@ -16,7 +16,8 @@ Info = { serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php', j2sPath: 'swingjs/j2s', console:'sysoutdiv', - allowjavascript: true + allowjavascript: true, + querystringnamespace: "" } diff --git a/utils/jalviewjs/some_commands.txt b/utils/jalviewjs/some_commands.txt new file mode 100644 index 0000000..b7a122c --- /dev/null +++ b/utils/jalviewjs/some_commands.txt @@ -0,0 +1,19 @@ +java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp ./tools/closure-compiler-v20230802.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level ADVANCED --warning_level QUIET --charset UTF-8 --js='./build/jalviewjs/site/swingjs/**.js' --js='!**/DatabaseReaction.js' --js='!**/FileTime.js' --js='!**/ChoiceFormat.js' --js='!**/TableView.js' --js='!**/JSVApplet.js' --js='!**/NativeMDLReactionReader.js' --js='!**/AsyncCallback.js' --js='!**/_ES6/jsutil.js' --js='!**/org/jmol/inchi/InChIJS.js' --js='!**/j2s/swingjs/JSUtil2.js' --js='!**/j2s/core/*.js' --js='!**/js/core/*' --js_output_file ./coreall-advanced.z.js > errors.txt + +grep JSC_UNDEFINED_VARIABLE errors.txt | perl -n -e 'm/.* variable (\S+) is undeclared/ && print "var $1;\n";' > externs.txt + +java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp ./tools/closure-compiler-v20230802.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level ADVANCED --warning_level QUIET --charset UTF-8 --js='./build/jalviewjs/site/swingjs/**.js' --js='!**/DatabaseReaction.js' --js='!**/FileTime.js' --js='!**/ChoiceFormat.js' --js='!**/TableView.js' --js='!**/JSVApplet.js' --js='!**/NativeMDLReactionReader.js' --js='!**/AsyncCallback.js' --js='!**/_ES6/jsutil.js' --js='!**/org/jmol/inchi/InChIJS.js' --js='!**/j2s/swingjs/JSUtil2.js' --js='!**/j2s/core/*.js' --js='!**/js/core/*' --js_output_file ./coreall-advanced.z.js --externs=./externs.txt + +java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp ./tools/closure-compiler-v20230802.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE --warning_level QUIET --charset UTF-8 --js='./build/jalviewjs/site/swingjs/**.js' --js='!**/DatabaseReaction.js' --js='!**/FileTime.js' --js='!**/ChoiceFormat.js' --js='!**/TableView.js' --js='!**/JSVApplet.js' --js='!**/NativeMDLReactionReader.js' --js='!**/AsyncCallback.js' --js='!**/_ES6/jsutil.js' --js='!**/org/jmol/inchi/InChIJS.js' --js='!**/j2s/swingjs/JSUtil2.js' --js='!**/j2s/core/*.js' --js='!**/js/core/*' --js_output_file ./coreall-simple.z.js --externs=./externs.txt + +cat ./build/jalviewjs/site/swingjs/j2s/com/actelion/research/chem/io/NativeMDLReactionReader.js ./build/jalviewjs/site/swingjs/j2s/com/actelion/research/chem/reaction/DatabaseReaction.js ./build/jalviewjs/site/swingjs/j2s/java/nio/file/attribute/FileTime.js ./build/jalviewjs/site/swingjs/j2s/java/text/ChoiceFormat.js ./build/jalviewjs/site/swingjs/j2s/javax/swing/text/html/TableView.js ./build/jalviewjs/site/swingjs/j2s/jme/js/AsyncCallback.js ./build/jalviewjs/site/swingjs/j2s/jspecview/appletjs/JSVApplet.js > problems1.js + +cat ./build/jalviewjs/site/swingjs/j2s/resources/_ES6/jsutil.js ./build/jalviewjs/site/swingjs/j2s/_ES6/jsutil.js ./build/jalviewjs/site/swingjs/j2s/org/jmol/inchi/InChIJS.js ./build/jalviewjs/site/swingjs/j2s/swingjs/JSUtil2.js > problems2.js + +cat ./build/jalviewjs/site/swingjs/js/core/coretop2.js ./coreall-simple.z.js ./problems1.js ./problems2.js ./build/jalviewjs/site/swingjs/js/core/corebottom2.js > ./build/jalviewjs/site/swingjs/j2s/core/coreall.z.js + + +-- + + +perl -p -i -e 's/colorPtToFFRGB\$javajs_util_T3d/colorPtToFFRGB\$javajs_util_T3/' $(grep -rl 'colorPtToFFRGB$javajs_util_T3d' ./build/jalviewjs/site/swingjs/j2s/) -- 1.7.10.2