JAL-4059 Fix up Jsmol calls and delete html files from JS zips in build.gradle. ...

diff --git a/build.gradle b/build.gradle
index 4b43a77..fe7e4e4 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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
+jalview/datamodel/RangeElementsIterator.js
+jalview/datamodel/RangeIterator.js
 jalview/datamodel/ResidueCount.js
+jalview/datamodel/RnaViewerModel.js
+jalview/datamodel/SearchResultMatchI.js
 jalview/datamodel/SearchResults.js
 jalview/datamodel/SearchResultsI.js
+jalview/datamodel/SecondaryStructureAnnotation.js
+jalview/datamodel/SeqCigar.js
+jalview/datamodel/SeqDistanceContactMatrix.js
 jalview/datamodel/Sequence.js
 jalview/datamodel/SequenceCollectionI.js
 jalview/datamodel/SequenceCursor.js
+jalview/datamodel/SequenceDummy.js
+jalview/datamodel/SequenceFeature.js
 jalview/datamodel/SequenceGroup.js
 jalview/datamodel/SequenceI.js
 jalview/datamodel/SequenceNode.js
+jalview/datamodel/SequencePoint.js
+jalview/datamodel/StartRegionIterator.js
+jalview/datamodel/StructureViewerModel.js
+jalview/datamodel/VisibleColsCollection.js
+jalview/datamodel/VisibleContigsIterator.js
+jalview/datamodel/VisibleRowsCollection.js
+jalview/datamodel/VisibleRowsIterator.js
+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
+jalview/ext/ensembl/EnsemblCds.js
 jalview/ext/ensembl/EnsemblData.js
+jalview/ext/ensembl/EnsemblFeatures.js
 jalview/ext/ensembl/EnsemblGene.js
+jalview/ext/ensembl/EnsemblGenome.js
+jalview/ext/ensembl/EnsemblGenomes.js
+jalview/ext/ensembl/EnsemblInfo.js
+jalview/ext/ensembl/EnsemblLookup.js
+jalview/ext/ensembl/EnsemblMap.js
+jalview/ext/ensembl/EnsemblProtein.js
 jalview/ext/ensembl/EnsemblRestClient.js
 jalview/ext/ensembl/EnsemblSeqProxy.js
 jalview/ext/ensembl/EnsemblSequenceFetcher.js
+jalview/ext/ensembl/EnsemblSymbol.js
+jalview/ext/ensembl/EnsemblXref.js
+jalview/ext/ensembl/Species.js
+jalview/ext/htsjdk/HtsContigDb.js
+jalview/ext/htsjdk/VCFReader.js
+jalview/ext/jmol/JalviewJmolBinding.js
+jalview/ext/jmol/JmolCommands.js
+jalview/ext/jmol/JmolParser.js
+jalview/ext/paradise/Annotate3D.js
+jalview/ext/pymol/PymolCommands.js
+jalview/ext/pymol/PymolManager.js
+jalview/ext/rbvi/chimera/ChimeraCommands.js
+jalview/ext/rbvi/chimera/ChimeraListener.js
+jalview/ext/rbvi/chimera/ChimeraXCommands.js
+jalview/ext/rbvi/chimera/ChimeraXManager.js
+jalview/ext/rbvi/chimera/JalviewChimeraBinding.js
+jalview/ext/so/SequenceOntology.js
+jalview/ext/varna/JalviewVarnaBinding.js
+jalview/ext/varna/RnaModel.js
+jalview/ext/varna/VarnaCommands.js
+jalview/fts/api/FTSData.js
+jalview/fts/api/FTSDataColumnI.js
+jalview/fts/api/FTSRestClientI.js
+jalview/fts/api/GFTSPanelI.js
+jalview/fts/api/StructureFTSRestClientI.js
+jalview/fts/core/DecimalFormatTableCellRenderer.js
+jalview/fts/core/FTSDataColumnPreferences.js
+jalview/fts/core/FTSRestClient.js
+jalview/fts/core/FTSRestRequest.js
+jalview/fts/core/FTSRestResponse.js
+jalview/fts/core/GFTSPanel.js
+jalview/fts/service/alphafold/AlphafoldRestClient.js
+jalview/fts/service/pdb/PDBFTSPanel.js
+jalview/fts/service/pdb/PDBFTSRestClient.js
+jalview/fts/service/threedbeacons/TDB_FTSData.js
+jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.js
+jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.js
+jalview/fts/service/uniprot/UniProtFTSRestClient.js
+jalview/fts/service/uniprot/UniprotFTSPanel.js
 jalview/gui/APQHandlers.js
+jalview/gui/AlignExportOptions.js
 jalview/gui/AlignFrame.js
 jalview/gui/AlignViewport.js
 jalview/gui/AlignmentPanel.js
+jalview/gui/AnnotationChooser.js
+jalview/gui/AnnotationColourChooser.js
+jalview/gui/AnnotationColumnChooser.js
+jalview/gui/AnnotationExporter.js
 jalview/gui/AnnotationLabels.js
 jalview/gui/AnnotationPanel.js
+jalview/gui/AnnotationRowFilter.js
+jalview/gui/AppJmol.js
+jalview/gui/AppJmolBinding.js
+jalview/gui/AppVarna.js
+jalview/gui/AppVarnaBinding.js
+jalview/gui/AssociatePdbFileWithSeq.js
+jalview/gui/BlogReader.js
+jalview/gui/CalculationChooser.js
+jalview/gui/ChimeraViewFrame.js
+jalview/gui/ChimeraXViewFrame.js
 jalview/gui/ColourMenuHelper.js
+jalview/gui/ComboBoxTooltipRenderer.js
+jalview/gui/Console.js
+jalview/gui/CrossRefAction.js
+jalview/gui/CutAndPasteHtmlTransfer.js
+jalview/gui/CutAndPasteTransfer.js
 jalview/gui/Desktop.js
+jalview/gui/EditNameDialog.js
+jalview/gui/FeatureEditor.js
 jalview/gui/FeatureRenderer.js
+jalview/gui/FeatureSettings.js
+jalview/gui/FeatureTypeSettings.js
+jalview/gui/Finder.js
+jalview/gui/FontChooser.js
+jalview/gui/Help.js
 jalview/gui/IProgressIndicator.js
+jalview/gui/IProgressIndicatorHandler.js
 jalview/gui/IdCanvas.js
 jalview/gui/IdPanel.js
 jalview/gui/IdwidthAdjuster.js
+jalview/gui/ImageExporter.js
+jalview/gui/JDatabaseTree.js
+jalview/gui/JalviewBooleanRadioButtons.js
 jalview/gui/JalviewChangeSupport.js
+jalview/gui/JalviewChimeraBindingModel.js
+jalview/gui/JalviewChimeraXBindingModel.js
+jalview/gui/JalviewColourChooser.js
+jalview/gui/JalviewDialog.js
+jalview/gui/JvOptionPane.js
 jalview/gui/JvSwingUtils.js
+jalview/gui/LineartOptions.js
+jalview/gui/MenuChooser.js
+jalview/gui/OOMWarning.js
+jalview/gui/OptsAndParamsPage.js
+jalview/gui/OptsParametersContainerI.js
+jalview/gui/OverviewCanvas.js
+jalview/gui/OverviewPanel.js
+jalview/gui/PCAPanel.js
 jalview/gui/PaintRefresher.js
+jalview/gui/PairwiseAlignPanel.js
+jalview/gui/PopupMenu.js
+jalview/gui/Preferences.js
 jalview/gui/ProgressBar.js
+jalview/gui/ProgressPanel.js
+jalview/gui/PromptUserConfig.js
+jalview/gui/PymolBindingModel.js
+jalview/gui/PymolViewer.js
 jalview/gui/QuitHandler.js
+jalview/gui/RedundancyPanel.js
+jalview/gui/RestInputParamEditDialog.js
+jalview/gui/RestServiceEditorPane.js
+jalview/gui/RotatableCanvas.js
 jalview/gui/ScalePanel.js
 jalview/gui/SeqCanvas.js
 jalview/gui/SeqPanel.js
 jalview/gui/SequenceFetcher.js
 jalview/gui/SequenceRenderer.js
+jalview/gui/Slider.js
+jalview/gui/SliderPanel.js
 jalview/gui/SplashScreen.js
+jalview/gui/SplitFrame.js
+jalview/gui/StructureChooser.js
+jalview/gui/StructureViewer.js
+jalview/gui/StructureViewerBase.js
+jalview/gui/TextColourChooser.js
 jalview/gui/TreeCanvas.js
 jalview/gui/TreePanel.js
+jalview/gui/UserDefinedColours.js
+jalview/gui/UserQuestionnaireCheck.js
+jalview/gui/VamsasApplication.js
 jalview/gui/ViewSelectionMenu.js
+jalview/gui/WebserviceInfo.js
+jalview/gui/WsJobParameters.js
+jalview/gui/WsParamSetManager.js
+jalview/gui/WsPreferences.js
+jalview/gui/structurechooser/PDBStructureChooserQuerySource.js
+jalview/gui/structurechooser/StructureChooserQuerySource.js
+jalview/gui/structurechooser/TDBResultAnalyser.js
+jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.js
+jalview/httpserver/AbstractRequestHandler.js
+jalview/httpserver/HttpServer.js
+jalview/io/AMSAFile.js
 jalview/io/AlignFile.js
 jalview/io/AlignmentFileReaderI.js
 jalview/io/AlignmentFileWriterI.js
+jalview/io/AlignmentProperties.js
+jalview/io/AnnotationFile.js
 jalview/io/AppletFormatAdapter.js
+jalview/io/BLCFile.js
+jalview/io/BackupFilenameFilter.js
+jalview/io/BackupFilenameParts.js
 jalview/io/BackupFiles.js
 jalview/io/BackupFilesPresetEntry.js
+jalview/io/BioJsHTMLOutput.js
+jalview/io/ClustalFile.js
+jalview/io/DBRefFile.js
 jalview/io/DataSourceType.js
+jalview/io/EMBLLikeFlatFile.js
+jalview/io/EmblFlatFile.js
+jalview/io/FastaFile.js
+jalview/io/FeaturesFile.js
 jalview/io/FileFormat.js
+jalview/io/FileFormatException.js
 jalview/io/FileFormatI.js
 jalview/io/FileFormats.js
 jalview/io/FileLoader.js
 jalview/io/FileParse.js
+jalview/io/FormatAdapter.js
+jalview/io/GenBankFile.js
+jalview/io/HTMLOutput.js
+jalview/io/HtmlFile.js
+jalview/io/HtmlSvgOutput.js
 jalview/io/IdentifyFile.js
+jalview/io/InputStreamParser.js
 jalview/io/IntKeyStringValueEntry.js
+jalview/io/JPredFile.js
+jalview/io/JSONFile.js
 jalview/io/JalviewFileChooser.js
 jalview/io/JalviewFileFilter.js
 jalview/io/JalviewFileView.js
+jalview/io/JnetAnnotationMaker.js
+jalview/io/MSFfile.js
+jalview/io/ModellerDescription.js
 jalview/io/NewickFile.js
+jalview/io/PContactPredictionFile.js
+jalview/io/PDBFeatureSettings.js
 jalview/io/PIRFile.js
+jalview/io/PfamFile.js
+jalview/io/PhylipFile.js
+jalview/io/PileUpfile.js
+jalview/io/RnamlFile.js
 jalview/io/ScoreMatrixFile.js
 jalview/io/SequenceAnnotationReport.js
+jalview/io/SimpleBlastFile.js
+jalview/io/StockholmFile.js
+jalview/io/StructureFile.js
+jalview/io/TCoffeeScoreFile.js
+jalview/io/VamsasAppDatastore.js
+jalview/io/WSWUBlastClient.js
+jalview/io/cache/AppCache.js
+jalview/io/cache/JvCacheableInputBox.js
+jalview/io/exceptions/ImageOutputException.js
+jalview/io/gff/ExonerateHelper.js
+jalview/io/gff/Gff2Helper.js
+jalview/io/gff/Gff3Helper.js
+jalview/io/gff/GffConstants.js
+jalview/io/gff/GffHelperBase.js
+jalview/io/gff/GffHelperFactory.js
+jalview/io/gff/GffHelperI.js
+jalview/io/gff/InterProScanHelper.js
+jalview/io/gff/SequenceOntologyFactory.js
+jalview/io/gff/SequenceOntologyI.js
+jalview/io/gff/SequenceOntologyLite.js
+jalview/io/packed/DataProvider.js
+jalview/io/packed/JalviewDataset.js
+jalview/io/packed/ParsePackedSet.js
+jalview/io/packed/SimpleDataProvider.js
+jalview/io/vamsas/Datasetsequence.js
+jalview/io/vamsas/DatastoreItem.js
+jalview/io/vamsas/DatastoreRegistry.js
+jalview/io/vamsas/Dbref.js
+jalview/io/vamsas/LocalDocSyncObject.js
+jalview/io/vamsas/Rangetype.js
+jalview/io/vamsas/Sequencefeature.js
+jalview/io/vamsas/Sequencemapping.js
+jalview/io/vamsas/Tree.js
+jalview/io/vcf/VCFLoader.js
+jalview/javascript/JSFunctionExec.js
+jalview/javascript/JalviewLiteJsApi.js
+jalview/javascript/JsCallBack.js
+jalview/javascript/JsSelectionSender.js
+jalview/javascript/MouseOverListener.js
+jalview/javascript/MouseOverStructureListener.js
+jalview/javascript/json/JSON.js
+jalview/javascript/web/Client.js
+jalview/javascript/web/ClientResponse.js
+jalview/javascript/web/WebResource.js
+jalview/jbgui/FilterOption.js
 jalview/jbgui/GAlignFrame.js
 jalview/jbgui/GAlignmentPanel.js
+jalview/jbgui/GCutAndPasteHtmlTransfer.js
+jalview/jbgui/GCutAndPasteTransfer.js
 jalview/jbgui/GDesktop.js
+jalview/jbgui/GFinder.js
+jalview/jbgui/GFontChooser.js
+jalview/jbgui/GPCAPanel.js
+jalview/jbgui/GPairwiseAlignPanel.js
+jalview/jbgui/GPreferences.js
+jalview/jbgui/GRestInputParamEditDialog.js
+jalview/jbgui/GRestServiceEditorPane.js
+jalview/jbgui/GRnaStructureViewer.js
+jalview/jbgui/GSequenceLink.js
+jalview/jbgui/GSliderPanel.js
+jalview/jbgui/GSplitFrame.js
+jalview/jbgui/GStructureChooser.js
+jalview/jbgui/GStructureViewer.js
 jalview/jbgui/GTreePanel.js
+jalview/jbgui/GUserDefinedColours.js
+jalview/jbgui/GWebserviceInfo.js
+jalview/jbgui/GWsPreferences.js
+jalview/json/binding/biojs/BioJSReleasePojo.js
+jalview/json/binding/biojs/BioJSRepositoryPojo.js
+jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.js
+jalview/json/binding/biojson/v1/AlignmentPojo.js
+jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.js
+jalview/json/binding/biojson/v1/AnnotationPojo.js
+jalview/json/binding/biojson/v1/ColourSchemeMapper.js
+jalview/json/binding/biojson/v1/SequenceFeaturesPojo.js
+jalview/json/binding/biojson/v1/SequenceGrpPojo.js
+jalview/json/binding/biojson/v1/SequencePojo.js
 jalview/log/JLogger.js
 jalview/log/JLoggerI.js
 jalview/log/JLoggerLog4j.js
+jalview/log/JalviewAppender.js
+jalview/math/AlignmentDimension.js
+jalview/math/Matrix.js
+jalview/math/MatrixI.js
+jalview/math/RotatableMatrix.js
+jalview/math/SparseMatrix.js
 jalview/project/Jalview2XML.js
 jalview/renderer/AnnotationRenderer.js
 jalview/renderer/AnnotationRendererFactory.js
 jalview/renderer/AwtRenderPanelI.js
+jalview/renderer/ContactGeometry.js
+jalview/renderer/ContactMapRenderer.js
+jalview/renderer/OverviewRenderer.js
+jalview/renderer/OverviewResColourFinder.js
 jalview/renderer/ResidueColourFinder.js
 jalview/renderer/ResidueShader.js
 jalview/renderer/ResidueShaderI.js
 jalview/renderer/ScaleRenderer.js
 jalview/renderer/api/AnnotationRendererFactoryI.js
+jalview/renderer/api/AnnotationRowRendererI.js
+jalview/renderer/seqfeatures/FeatureColourFinder.js
 jalview/renderer/seqfeatures/FeatureRenderer.js
+jalview/rest/RestHandler.js
+jalview/schemes/AnnotationColourGradient.js
 jalview/schemes/BlossomColourScheme.js
 jalview/schemes/Blosum62ColourScheme.js
 jalview/schemes/BuriedColourScheme.js
 jalview/schemes/ClustalxColourScheme.js
 jalview/schemes/ColourSchemeI.js
+jalview/schemes/ColourSchemeLoader.js
 jalview/schemes/ColourSchemeProperty.js
 jalview/schemes/ColourSchemes.js
 jalview/schemes/Consensus.js
+jalview/schemes/CovariationColourScheme.js
+jalview/schemes/FeatureColour.js
+jalview/schemes/FeatureSettingsAdapter.js
 jalview/schemes/FlowerColourScheme.js
+jalview/schemes/FollowerColourScheme.js
 jalview/schemes/HelixColourScheme.js
 jalview/schemes/HydrophobicColourScheme.js
 jalview/schemes/IdColourScheme.js
@@ -217,6 +723,8 @@ jalview/schemes/OceanColourScheme.js
 jalview/schemes/PIDColourScheme.js
 jalview/schemes/PurinePyrimidineColourScheme.js
 jalview/schemes/RNAHelicesColour.js
+jalview/schemes/RNAHelicesColourChooser.js
+jalview/schemes/RNAInteractionColourScheme.js
 jalview/schemes/ResidueColourScheme.js
 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
 jalview/structure/StructureSelectionManager.js
+jalview/structure/VamsasListener.js
 jalview/structure/VamsasSource.js
+jalview/structures/models/AAStructureBindingModel.js
+jalview/structures/models/SequenceStructureBindingModel.js
+jalview/urls/CustomUrlProvider.js
 jalview/urls/IdOrgSettings.js
+jalview/urls/IdentifiersUrlProvider.js
+jalview/urls/UrlLinkDisplay.js
+jalview/urls/UrlLinkTableModel.js
+jalview/urls/UrlProvider.js
+jalview/urls/UrlProviderImpl.js
+jalview/urls/api/UrlProviderFactoryI.js
+jalview/urls/api/UrlProviderI.js
+jalview/urls/applet/AppletUrlProviderFactory.js
+jalview/urls/desktop/DesktopUrlProviderFactory.js
+jalview/util/AWTConsole.js
+jalview/util/ArrayUtils.js
+jalview/util/BrowserLauncher.js
+jalview/util/CaseInsensitiveString.js
 jalview/util/ChannelProperties.js
 jalview/util/ColorUtils.js
 jalview/util/Comparison.js
 jalview/util/DBRefUtils.js
+jalview/util/DnaUtils.js
 jalview/util/FileUtils.js
 jalview/util/Format.js
+jalview/util/GroupUrlLink.js
 jalview/util/HttpUtils.js
+jalview/util/IdUtils.js
+jalview/util/ImageMaker.js
+jalview/util/IntRangeComparator.js
+jalview/util/JSONUtils.js
+jalview/util/LaunchUtils.js
+jalview/util/LinkedIdentityHashSet.js
+jalview/util/Log4j.js
+jalview/util/MapList.js
+jalview/util/MapUtils.js
+jalview/util/MappingUtils.js
+jalview/util/MathUtils.js
 jalview/util/MessageManager.js
+jalview/util/ParseHtmlBodyAndLinks.js
 jalview/util/Platform.js
 jalview/util/QuickSort.js
+jalview/util/ReverseListIterator.js
+jalview/util/SetUtils.js
+jalview/util/ShiftList.js
 jalview/util/ShortcutKeyMaskExWrapper.js
+jalview/util/ShortcutKeyMaskExWrapper11.js
 jalview/util/ShortcutKeyMaskExWrapper8.js
 jalview/util/ShortcutKeyMaskExWrapperI.js
+jalview/util/SparseCount.js
 jalview/util/StringUtils.js
+jalview/util/TableSorter.js
+jalview/util/UrlConstants.js
+jalview/util/UrlLink.js
 jalview/util/dialogrunner/DialogRunnerI.js
+jalview/util/imagemaker/BitmapImageSizing.js
 jalview/util/jarInputStreamProvider.js
+jalview/util/matcher/Condition.js
+jalview/util/matcher/Matcher.js
+jalview/util/matcher/MatcherI.js
 jalview/viewmodel/AlignmentViewport.js
+jalview/viewmodel/OverviewDimensions.js
+jalview/viewmodel/OverviewDimensionsHideHidden.js
+jalview/viewmodel/OverviewDimensionsShowHidden.js
+jalview/viewmodel/PCAModel.js
 jalview/viewmodel/ViewportListenerI.js
 jalview/viewmodel/ViewportProperties.js
 jalview/viewmodel/ViewportRanges.js
+jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js
 jalview/viewmodel/seqfeatures/FeatureRendererModel.js
+jalview/viewmodel/seqfeatures/FeatureRendererSettings.js
+jalview/viewmodel/seqfeatures/FeatureSettingsModel.js
+jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
 jalview/viewmodel/styles/ViewStyle.js
 jalview/workers/AlignCalcManager.js
 jalview/workers/AlignCalcWorker.js
+jalview/workers/AlignmentAnnotationFactory.js
+jalview/workers/AnnotationProviderI.js
+jalview/workers/AnnotationWorker.js
+jalview/workers/ColumnCounterSetWorker.js
+jalview/workers/ComplementConsensusThread.js
 jalview/workers/ConsensusThread.js
 jalview/workers/ConservationThread.js
+jalview/workers/FeatureSetCounterI.js
+jalview/workers/StrucConsensusThread.js
+jalview/ws/AWSThread.js
+jalview/ws/AWsJob.js
+jalview/ws/DBRefFetcher.js
+jalview/ws/HttpClientUtils.js
+jalview/ws/JobStateSummary.js
 jalview/ws/SequenceFetcher.js
+jalview/ws/SequenceFetcherFactory.js
+jalview/ws/WSClient.js
+jalview/ws/WSClientI.js
+jalview/ws/WSMenuEntryProviderI.js
+jalview/ws/datamodel/MappableContactMatrixI.js
+jalview/ws/datamodel/alphafold/MappableContactMatrix.js
+jalview/ws/datamodel/alphafold/PAEContactMatrix.js
+jalview/ws/dbsources/EBIAlfaFold.js
 jalview/ws/dbsources/EbiFileRetrievedProxy.js
 jalview/ws/dbsources/EmblCdsSource.js
 jalview/ws/dbsources/EmblFlatfileSource.js
 jalview/ws/dbsources/EmblSource.js
+jalview/ws/dbsources/EmblXmlSource.js
+jalview/ws/dbsources/GeneDbSource.js
 jalview/ws/dbsources/Pdb.js
 jalview/ws/dbsources/Pfam.js
 jalview/ws/dbsources/PfamFull.js
 jalview/ws/dbsources/PfamSeed.js
 jalview/ws/dbsources/Rfam.js
+jalview/ws/dbsources/RfamFull.js
 jalview/ws/dbsources/RfamSeed.js
+jalview/ws/dbsources/TDBeacons.js
 jalview/ws/dbsources/Uniprot.js
+jalview/ws/dbsources/UniprotName.js
 jalview/ws/dbsources/Xfam.js
+jalview/ws/ebi/EBIFetchClient.js
+jalview/ws/io/mime/HttpContentHandler.js
+jalview/ws/io/mime/JalviewMimeContentHandler.js
+jalview/ws/io/mime/MimeTypes.js
+jalview/ws/jws1/Annotate3D.js
+jalview/ws/jws1/Discoverer.js
+jalview/ws/jws1/JPredClient.js
+jalview/ws/jws1/JPredThread.js
+jalview/ws/jws1/JWS1Thread.js
+jalview/ws/jws1/MsaWSClient.js
+jalview/ws/jws1/MsaWSThread.js
+jalview/ws/jws1/SeqSearchWSClient.js
+jalview/ws/jws1/SeqSearchWSThread.js
+jalview/ws/jws1/WS1Client.js
+jalview/ws/jws1/WSJob.js
+jalview/ws/jws2/AAConClient.js
+jalview/ws/jws2/AADisorderClient.js
+jalview/ws/jws2/AWS2Thread.js
+jalview/ws/jws2/AbstractJabaCalcWorker.js
+jalview/ws/jws2/JWs2Job.js
+jalview/ws/jws2/JabaParamStore.js
+jalview/ws/jws2/JabaPreset.js
+jalview/ws/jws2/JabaWsServerQuery.js
+jalview/ws/jws2/JabawsCalcWorker.js
+jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.js
+jalview/ws/jws2/Jws2Client.js
+jalview/ws/jws2/Jws2Discoverer.js
+jalview/ws/jws2/MsaWSClient.js
+jalview/ws/jws2/MsaWSThread.js
+jalview/ws/jws2/ParameterUtils.js
+jalview/ws/jws2/RNAalifoldClient.js
+jalview/ws/jws2/SequenceAnnotationWSClient.js
+jalview/ws/jws2/dm/AAConSettings.js
+jalview/ws/jws2/dm/JabaOption.js
+jalview/ws/jws2/dm/JabaParameter.js
+jalview/ws/jws2/dm/JabaValueConstrain.js
+jalview/ws/jws2/dm/JabaWsParamSet.js
+jalview/ws/jws2/jabaws2/Jws2Instance.js
+jalview/ws/jws2/jabaws2/Jws2InstanceFactory.js
+jalview/ws/params/ArgumentI.js
+jalview/ws/params/AutoCalcSetting.js
+jalview/ws/params/InvalidArgumentException.js
+jalview/ws/params/OptionI.js
+jalview/ws/params/ParamDatastoreI.js
+jalview/ws/params/ParamManager.js
+jalview/ws/params/ParameterI.js
+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
+org/jmol/modelset/AtomIteratorWithinModel.js
+org/jmol/modelset/Bond.js
+org/jmol/modelset/BondCollection.js
+org/jmol/modelset/BondIterator.js
+org/jmol/modelset/BondIteratorSelected.js
+org/jmol/modelset/Chain.js
+org/jmol/modelset/Group.js
+org/jmol/modelset/HBond.js
+org/jmol/modelset/LabelToken.js
+org/jmol/modelset/Measurement.js
+org/jmol/modelset/MeasurementData.js
+org/jmol/modelset/MeasurementPending.js
+org/jmol/modelset/Model.js
+org/jmol/modelset/ModelLoader.js
+org/jmol/modelset/ModelSet.js
+org/jmol/modelset/Orientation.js
+org/jmol/modelset/Structure.js
+org/jmol/modelset/Text.js
+org/jmol/modelset/TickInfo.js
+org/jmol/modelsetbio/AlphaMonomer.js
+org/jmol/modelsetbio/AlphaPolymer.js
+org/jmol/modelsetbio/AminoMonomer.js
+org/jmol/modelsetbio/AminoPolymer.js
+org/jmol/modelsetbio/BioModel.js
+org/jmol/modelsetbio/BioModelSet.js
+org/jmol/modelsetbio/BioPolymer.js
+org/jmol/modelsetbio/BioResolver.js
+org/jmol/modelsetbio/Helix.js
+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/JmolStateCreator.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/StateCreator.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/CDL.js
+org/json/Cookie.js
+org/json/CookieList.js
+org/json/HTTP.js
+org/json/HTTPTokener.js
+org/json/JSONArray.js
+org/json/JSONException.js
+org/json/JSONML.js
+org/json/JSONObject.js
+org/json/JSONPointer.js
+org/json/JSONPointerException.js
+org/json/JSONPropertyIgnore.js
+org/json/JSONPropertyName.js
+org/json/JSONString.js
+org/json/JSONStringer.js
+org/json/JSONTokener.js
+org/json/JSONWriter.js
+org/json/Property.js
+org/json/XML.js
+org/json/XMLTokener.js
+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 (file)
--- 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: ""
 }
 </script>
 </head>

diff --git a/utils/jalviewjs/classlists/jalview.txt b/utils/jalviewjs/classlists/jalview.txt
deleted file mode 100644 (file)
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
-jalview/analysis/scoremodels/SimilarityScoreModel.js
-jalview/api/AlignCalcManagerI.js
-jalview/api/AlignCalcWorkerI.js
-jalview/api/AlignViewControllerGuiI.js
-jalview/api/AlignViewControllerI.js
-jalview/api/AlignViewportI.js
-jalview/api/AlignmentViewPanel.js
-jalview/api/BuildDetailsI.js
-jalview/api/FeatureColourI.js
-jalview/api/FeatureRenderer.js
-jalview/api/FeaturesDisplayedI.js
-jalview/api/OOMHandlerI.js
-jalview/api/SequenceRenderer.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/bin/ArgsParser.js
-jalview/bin/BuildDetails.js
-jalview/bin/Cache.js
-jalview/bin/Jalview.js
-jalview/bin/JalviewJS2.js
-jalview/controller/AlignViewController.js
-jalview/datamodel/ASequence.js
-jalview/datamodel/ASequenceI.js
-jalview/datamodel/Alignment.js
-jalview/datamodel/AlignmentAnnotation.js
-jalview/datamodel/AlignmentI.js
-jalview/datamodel/AlignmentView.js
-jalview/datamodel/AnnotatedCollectionI.js
-jalview/datamodel/Annotation.js
-jalview/datamodel/BinaryNode.js
-jalview/datamodel/CigarArray.js
-jalview/datamodel/CigarBase.js
-jalview/datamodel/CigarSimple.js
-jalview/datamodel/ColumnSelection.js
-jalview/datamodel/ContiguousI.js
-jalview/datamodel/DBRefSource.js
-jalview/datamodel/HiddenColumns.js
-jalview/datamodel/HiddenColumnsCursor.js
-jalview/datamodel/HiddenCursorPosition.js
-jalview/datamodel/HiddenSequences.js
-jalview/datamodel/PDBEntry.js
-jalview/datamodel/Profile.js
-jalview/datamodel/ProfileI.js
-jalview/datamodel/Profiles.js
-jalview/datamodel/ProfilesI.js
-jalview/datamodel/Range.js
-jalview/datamodel/RangeIterator.js
-jalview/datamodel/ResidueCount.js
-jalview/datamodel/SearchResults.js
-jalview/datamodel/SearchResultsI.js
-jalview/datamodel/SeqCigar.js
-jalview/datamodel/Sequence.js
-jalview/datamodel/SequenceCollectionI.js
-jalview/datamodel/SequenceCursor.js
-jalview/datamodel/SequenceFeature.js
-jalview/datamodel/SequenceGroup.js
-jalview/datamodel/SequenceI.js
-jalview/datamodel/SequenceNode.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/FeatureStore.js
-jalview/datamodel/features/RangeComparator.js
-jalview/datamodel/features/SequenceFeatures.js
-jalview/datamodel/features/SequenceFeaturesI.js
-jalview/gui/AlignFrame.js
-jalview/gui/AlignViewport.js
-jalview/gui/AlignmentPanel.js
-jalview/gui/AnnotationLabels.js
-jalview/gui/AnnotationPanel.js
-jalview/gui/CalculationChooser.js
-jalview/gui/ColourMenuHelper.js
-jalview/gui/ComboBoxTooltipRenderer.js
-jalview/gui/Desktop.js
-jalview/gui/FeatureRenderer.js
-jalview/gui/IProgressIndicator.js
-jalview/gui/IdCanvas.js
-jalview/gui/IdPanel.js
-jalview/gui/IdwidthAdjuster.js
-jalview/gui/JalviewChangeSupport.js
-jalview/gui/JvSwingUtils.js
-jalview/gui/PaintRefresher.js
-jalview/gui/PopupMenu.js
-jalview/gui/Preferences.js
-jalview/gui/ProgressBar.js
-jalview/gui/ScalePanel.js
-jalview/gui/SeqCanvas.js
-jalview/gui/SeqPanel.js
-jalview/gui/SequenceRenderer.js
-jalview/gui/TreeCanvas.js
-jalview/gui/TreePanel.js
-jalview/gui/ViewSelectionMenu.js
-jalview/io/AlignFile.js
-jalview/io/AlignmentFileReaderI.js
-jalview/io/AlignmentFileWriterI.js
-jalview/io/AppletFormatAdapter.js
-jalview/io/DataSourceType.js
-jalview/io/FileFormat.js
-jalview/io/FileFormatI.js
-jalview/io/FileFormats.js
-jalview/io/FileLoader.js
-jalview/io/FileParse.js
-jalview/io/IdentifyFile.js
-jalview/io/PIRFile.js
-jalview/io/ScoreMatrixFile.js
-jalview/io/SequenceAnnotationReport.js
-jalview/javascript/log4j/ConsoleAppender.js
-jalview/javascript/log4j/Layout.js
-jalview/javascript/log4j/Level.js
-jalview/javascript/log4j/Logger.js
-jalview/javascript/log4j/Priority.js
-jalview/javascript/log4j/SimpleLayout.js
-jalview/javascript/log4j/spi/OptionHandler.js
-jalview/jbgui/GAlignFrame.js
-jalview/jbgui/GAlignmentPanel.js
-jalview/jbgui/GDesktop.js
-jalview/jbgui/GPreferences.js
-jalview/jbgui/GTreePanel.js
-jalview/math/Matrix.js
-jalview/math/MatrixI.js
-jalview/project/Jalview2XML.js
-jalview/renderer/AnnotationRenderer.js
-jalview/renderer/AwtRenderPanelI.js
-jalview/renderer/ResidueColourFinder.js
-jalview/renderer/ResidueShader.js
-jalview/renderer/ResidueShaderI.js
-jalview/renderer/ScaleRenderer.js
-jalview/renderer/seqfeatures/FeatureRenderer.js
-jalview/schemes/Blosum62ColourScheme.js
-jalview/schemes/BuriedColourScheme.js
-jalview/schemes/ClustalxColourScheme.js
-jalview/schemes/ColourSchemeI.js
-jalview/schemes/ColourSchemeProperty.js
-jalview/schemes/ColourSchemes.js
-jalview/schemes/Consensus.js
-jalview/schemes/FeatureColour.js
-jalview/schemes/HelixColourScheme.js
-jalview/schemes/HydrophobicColourScheme.js
-jalview/schemes/JalviewColourScheme.js
-jalview/schemes/NucleotideColourScheme.js
-jalview/schemes/PIDColourScheme.js
-jalview/schemes/PurinePyrimidineColourScheme.js
-jalview/schemes/RNAHelicesColour.js
-jalview/schemes/ResidueColourScheme.js
-jalview/schemes/ResidueProperties.js
-jalview/schemes/ScoreColourScheme.js
-jalview/schemes/StrandColourScheme.js
-jalview/schemes/TCoffeeColourScheme.js
-jalview/schemes/TaylorColourScheme.js
-jalview/schemes/TurnColourScheme.js
-jalview/schemes/ZappoColourScheme.js
-jalview/structure/CommandListener.js
-jalview/structure/SelectionListener.js
-jalview/structure/SelectionSource.js
-jalview/structure/SequenceListener.js
-jalview/structure/StructureImportSettings.js
-jalview/structure/StructureSelectionManager.js
-jalview/structure/VamsasSource.js
-jalview/urls/CustomUrlProvider.js
-jalview/urls/IdOrgSettings.js
-jalview/urls/IdentifiersUrlProvider.js
-jalview/urls/UrlLinkDisplay.js
-jalview/urls/UrlLinkTableModel.js
-jalview/urls/UrlProvider.js
-jalview/urls/UrlProviderImpl.js
-jalview/urls/api/UrlProviderFactoryI.js
-jalview/urls/api/UrlProviderI.js
-jalview/urls/desktop/DesktopUrlProviderFactory.js
-jalview/util/ColorUtils.js
-jalview/util/Comparison.js
-jalview/util/DBRefUtils.js
-jalview/util/Format.js
-jalview/util/MessageManager.js
-jalview/util/Platform.js
-jalview/util/QuickSort.js
-jalview/util/StringUtils.js
-jalview/util/UrlLink.js
-jalview/util/jarInputStreamProvider.js
-jalview/util/matcher/Condition.js
-jalview/util/matcher/Matcher.js
-jalview/util/matcher/MatcherI.js
-jalview/viewmodel/AlignmentViewport.js
-jalview/viewmodel/ViewportListenerI.js
-jalview/viewmodel/ViewportProperties.js
-jalview/viewmodel/ViewportRanges.js
-jalview/viewmodel/seqfeatures/FeatureRendererModel.js
-jalview/viewmodel/seqfeatures/FeatureRendererSettings.js
-jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
-jalview/viewmodel/styles/ViewStyle.js
-jalview/workers/AlignCalcManager.js
-jalview/workers/AlignCalcWorker.js
-jalview/workers/ConsensusThread.js
-jalview/workers/ConservationThread.js
-jalview/ws/sifts/SiftsSettings.js
-jalview/xml/binding/jalview/Annotation.js
-jalview/xml/binding/jalview/AnnotationElement.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/NoValueColour.js
-jalview/xml/binding/jalview/Pdbentry.js
-jalview/xml/binding/jalview/Sequence.js
-jalview/xml/binding/jalview/SequenceSet.js
-jalview/xml/binding/jalview/SequenceType.js
-jalview/xml/binding/jalview/VAMSAS.js
-jalview/xml/binding/jalview/WebServiceParameterSet.js
-java/applet/AppletContext.js
-java/applet/AppletStub.js
-java/applet/JSApplet.js
-java/awt/AWTEvent.js
-java/awt/AWTEventMulticaster.js
-java/awt/AWTKeyStroke.js
-java/awt/ActiveEvent.js
-java/awt/Adjustable.js
-java/awt/AlphaComposite.js
-java/awt/BasicStroke.js
-java/awt/BorderLayout.js
-java/awt/Color.js
-java/awt/Component.js
-java/awt/ComponentOrientation.js
-java/awt/Composite.js
-java/awt/Container.js
-java/awt/ContainerOrderFocusTraversalPolicy.js
-java/awt/Cursor.js
-java/awt/DefaultFocusTraversalPolicy.js
-java/awt/DefaultKeyboardFocusManager.js
-java/awt/Dialog.js
-java/awt/Dimension.js
-java/awt/EventDispatchThread.js
-java/awt/EventFilter.js
-java/awt/EventQueue.js
-java/awt/EventQueueItem.js
-java/awt/FlowLayout.js
-java/awt/FocusTraversalPolicy.js
-java/awt/Font.js
-java/awt/FontMetrics.js
-java/awt/GraphicsCallback.js
-java/awt/GraphicsConfiguration.js
-java/awt/GraphicsDevice.js
-java/awt/GraphicsEnvironment.js
-java/awt/GridLayout.js
-java/awt/Image.js
-java/awt/Insets.js
-java/awt/ItemSelectable.js
-java/awt/JSComponent.js
-java/awt/JSDialog.js
-java/awt/JSFrame.js
-java/awt/JSPanel.js
-java/awt/KeyEventDispatcher.js
-java/awt/KeyEventPostProcessor.js
-java/awt/KeyboardFocusManager.js
-java/awt/LayoutManager.js
-java/awt/LayoutManager2.js
-java/awt/LightweightDispatcher.js
-java/awt/Paint.js
-java/awt/Point.js
-java/awt/Queue.js
-java/awt/Rectangle.js
-java/awt/RenderingHints.js
-java/awt/SentEvent.js
-java/awt/Shape.js
-java/awt/Stroke.js
-java/awt/Toolkit.js
-java/awt/Transparency.js
-java/awt/VKCollection.js
-java/awt/Window.js
-java/awt/color/ColorSpace.js
-java/awt/datatransfer/ClipboardOwner.js
-java/awt/datatransfer/FlavorMap.js
-java/awt/datatransfer/FlavorTable.js
-java/awt/datatransfer/SystemFlavorMap.js
-java/awt/dnd/DropTarget.js
-java/awt/dnd/DropTargetContext.js
-java/awt/dnd/DropTargetListener.js
-java/awt/dnd/peer/DropTargetPeer.js
-java/awt/event/AWTEventListener.js
-java/awt/event/ActionEvent.js
-java/awt/event/ActionListener.js
-java/awt/event/AdjustmentEvent.js
-java/awt/event/AdjustmentListener.js
-java/awt/event/ComponentAdapter.js
-java/awt/event/ComponentEvent.js
-java/awt/event/ComponentListener.js
-java/awt/event/ContainerEvent.js
-java/awt/event/ContainerListener.js
-java/awt/event/FocusAdapter.js
-java/awt/event/FocusEvent.js
-java/awt/event/FocusListener.js
-java/awt/event/HierarchyBoundsListener.js
-java/awt/event/HierarchyListener.js
-java/awt/event/InputEvent.js
-java/awt/event/InputMethodListener.js
-java/awt/event/InvocationEvent.js
-java/awt/event/ItemEvent.js
-java/awt/event/ItemListener.js
-java/awt/event/KeyAdapter.js
-java/awt/event/KeyEvent.js
-java/awt/event/KeyListener.js
-java/awt/event/MouseAdapter.js
-java/awt/event/MouseEvent.js
-java/awt/event/MouseListener.js
-java/awt/event/MouseMotionAdapter.js
-java/awt/event/MouseMotionListener.js
-java/awt/event/MouseWheelListener.js
-java/awt/event/TextListener.js
-java/awt/event/WindowAdapter.js
-java/awt/event/WindowEvent.js
-java/awt/event/WindowFocusListener.js
-java/awt/event/WindowListener.js
-java/awt/event/WindowStateListener.js
-java/awt/font/FontRenderContext.js
-java/awt/geom/AffineTransform.js
-java/awt/geom/Dimension2D.js
-java/awt/geom/Path2D.js
-java/awt/geom/PathIterator.js
-java/awt/geom/Point2D.js
-java/awt/geom/RectIterator.js
-java/awt/geom/Rectangle2D.js
-java/awt/geom/RectangularShape.js
-java/awt/image/BufferedImage.js
-java/awt/image/ColorModel.js
-java/awt/image/DataBuffer.js
-java/awt/image/DataBufferInt.js
-java/awt/image/DirectColorModel.js
-java/awt/image/ImageObserver.js
-java/awt/image/PackedColorModel.js
-java/awt/image/Raster.js
-java/awt/image/RenderedImage.js
-java/awt/image/SampleModel.js
-java/awt/image/SinglePixelPackedSampleModel.js
-java/awt/image/WritableRaster.js
-java/awt/peer/ComponentPeer.js
-java/awt/peer/ContainerPeer.js
-java/awt/peer/FramePeer.js
-java/awt/peer/KeyboardFocusManagerPeer.js
-java/awt/peer/LightweightPeer.js
-java/awt/peer/WindowPeer.js
-java/awt/print/Printable.js
-java/beans/ChangeListenerMap.js
-java/beans/PropertyChangeEvent.js
-java/beans/PropertyChangeListener.js
-java/beans/PropertyChangeSupport.js
-java/io/BufferedInputStream.js
-java/io/BufferedReader.js
-java/io/ByteArrayInputStream.js
-java/io/Closeable.js
-java/io/File.js
-java/io/FileDescriptor.js
-java/io/FileInputStream.js
-java/io/FileReader.js
-java/io/FileSystem.js
-java/io/FilterInputStream.js
-java/io/InputStream.js
-java/io/InputStreamReader.js
-java/io/PushbackInputStream.js
-java/io/Reader.js
-java/lang/AbstractStringBuilder.js
-java/lang/AutoCloseable.js
-java/lang/Class.js
-java/lang/Enum.js
-java/lang/Iterable.js
-java/lang/Readable.js
-java/lang/Runtime.js
-java/lang/StringBuffer.js
-java/lang/StringBuilder.js
-java/lang/Thread.js
-java/lang/ThreadGroup.js
-java/lang/reflect/Constructor.js
-java/lang/reflect/Method.js
-java/math/BigDecimal.js
-java/math/BigInteger.js
-java/math/MathContext.js
-java/math/RoundingMode.js
-java/net/HttpURLConnection.js
-java/net/MalformedURLException.js
-java/net/URL.js
-java/net/URLConnection.js
-java/net/URLDecoder.js
-java/net/URLStreamHandler.js
-java/net/URLStreamHandlerFactory.js
-java/nio/Bits.js
-java/nio/Buffer.js
-java/nio/ByteBuffer.js
-java/nio/ByteOrder.js
-java/nio/CharBuffer.js
-java/nio/HeapByteBuffer.js
-java/nio/HeapCharBuffer.js
-java/nio/charset/Charset.js
-java/nio/charset/CharsetDecoder.js
-java/nio/charset/CoderResult.js
-java/nio/charset/CodingErrorAction.js
-java/security/AccessControlContext.js
-java/security/AccessController.js
-java/security/PrivilegedAction.js
-java/security/PrivilegedExceptionAction.js
-java/text/AttributedCharacterIterator.js
-java/text/CharacterIterator.js
-java/text/DateFormat.js
-java/text/DateFormatSymbols.js
-java/text/DecimalFormat.js
-java/text/DecimalFormatSymbols.js
-java/text/DigitList.js
-java/text/FieldPosition.js
-java/text/Format.js
-java/text/MessageFormat.js
-java/text/NumberFormat.js
-java/text/SimpleDateFormat.js
-java/util/AbstractCollection.js
-java/util/AbstractList.js
-java/util/AbstractMap.js
-java/util/AbstractQueue.js
-java/util/AbstractSequentialList.js
-java/util/AbstractSet.js
-java/util/ArrayDeque.js
-java/util/ArrayList.js
-java/util/Arrays.js
-java/util/BitSet.js
-java/util/Calendar.js
-java/util/Collection.js
-java/util/Collections.js
-java/util/Comparator.js
-java/util/Deque.js
-java/util/Dictionary.js
-java/util/DualPivotQuicksort.js
-java/util/Enumeration.js
-java/util/EventListener.js
-java/util/EventObject.js
-java/util/GregorianCalendar.js
-java/util/HashMap.js
-java/util/HashSet.js
-java/util/Hashtable.js
-java/util/IdentityHashMap.js
-java/util/Iterator.js
-java/util/LinkedHashMap.js
-java/util/LinkedList.js
-java/util/List.js
-java/util/ListIterator.js
-java/util/ListResourceBundle.js
-java/util/Locale.js
-java/util/Map.js
-java/util/NavigableMap.js
-java/util/NavigableSet.js
-java/util/Objects.js
-java/util/Properties.js
-java/util/PropertyResourceBundle.js
-java/util/Queue.js
-java/util/RandomAccess.js
-java/util/ResourceBundle.js
-java/util/Set.js
-java/util/SortedMap.js
-java/util/SortedSet.js
-java/util/StringTokenizer.js
-java/util/TimSort.js
-java/util/TimeZone.js
-java/util/TreeMap.js
-java/util/TreeSet.js
-java/util/Vector.js
-java/util/concurrent/AbstractExecutorService.js
-java/util/concurrent/BlockingQueue.js
-java/util/concurrent/ConcurrentHashMap.js
-java/util/concurrent/ConcurrentMap.js
-java/util/concurrent/Executor.js
-java/util/concurrent/ExecutorService.js
-java/util/concurrent/Executors.js
-java/util/concurrent/LinkedBlockingQueue.js
-java/util/concurrent/RejectedExecutionHandler.js
-java/util/concurrent/Semaphore.js
-java/util/concurrent/ThreadFactory.js
-java/util/concurrent/ThreadPoolExecutor.js
-java/util/concurrent/TimeUnit.js
-java/util/concurrent/atomic/AtomicBoolean.js
-java/util/concurrent/atomic/AtomicInteger.js
-java/util/concurrent/locks/AbstractOwnableSynchronizer.js
-java/util/concurrent/locks/AbstractQueuedSynchronizer.js
-java/util/concurrent/locks/Condition.js
-java/util/concurrent/locks/Lock.js
-java/util/concurrent/locks/ReadWriteLock.js
-java/util/concurrent/locks/ReentrantLock.js
-java/util/concurrent/locks/ReentrantReadWriteLock.js
-java/util/jar/JarEntry.js
-java/util/jar/JarInputStream.js
-java/util/logging/Level.js
-java/util/logging/Logger.js
-java/util/regex/MatchResult.js
-java/util/regex/Matcher.js
-java/util/regex/Pattern.js
-java/util/zip/CRC32.js
-java/util/zip/Inflater.js
-java/util/zip/InflaterInputStream.js
-java/util/zip/ZipConstants.js
-java/util/zip/ZipEntry.js
-java/util/zip/ZipInputStream.js
-javajs/api/GenericLineReader.js
-javajs/api/JSFunction.js
-javajs/api/JSONEncodable.js
-javajs/util/AU.js
-javajs/util/AjaxURLConnection.js
-javajs/util/AjaxURLStreamHandler.js
-javajs/util/AjaxURLStreamHandlerFactory.js
-javajs/util/Encoding.js
-javajs/util/JSThread.js
-javajs/util/Lst.js
-javajs/util/PT.js
-javajs/util/Rdr.js
-javajs/util/SB.js
-javax/swing/AbstractAction.js
-javax/swing/AbstractButton.js
-javax/swing/AbstractListModel.js
-javax/swing/Action.js
-javax/swing/ActionMap.js
-javax/swing/AncestorNotifier.js
-javax/swing/ArrayTable.js
-javax/swing/BorderFactory.js
-javax/swing/BoundedRangeModel.js
-javax/swing/BoxLayout.js
-javax/swing/ButtonGroup.js
-javax/swing/ButtonModel.js
-javax/swing/ClientPropertyKey.js
-javax/swing/ComboBoxModel.js
-javax/swing/ComponentInputMap.js
-javax/swing/DefaultBoundedRangeModel.js
-javax/swing/DefaultButtonModel.js
-javax/swing/DefaultComboBoxModel.js
-javax/swing/DefaultDesktopManager.js
-javax/swing/DefaultListCellRenderer.js
-javax/swing/DefaultSingleSelectionModel.js
-javax/swing/DesktopManager.js
-javax/swing/InputMap.js
-javax/swing/JApplet.js
-javax/swing/JButton.js
-javax/swing/JCheckBox.js
-javax/swing/JCheckBoxMenuItem.js
-javax/swing/JComboBox.js
-javax/swing/JComponent.js
-javax/swing/JDesktopPane.js
-javax/swing/JDialog.js
-javax/swing/JFrame.js
-javax/swing/JInternalFrame.js
-javax/swing/JLabel.js
-javax/swing/JLayeredPane.js
-javax/swing/JMenu.js
-javax/swing/JMenuBar.js
-javax/swing/JMenuItem.js
-javax/swing/JPanel.js
-javax/swing/JPopupMenu.js
-javax/swing/JProgressBar.js
-javax/swing/JRadioButton.js
-javax/swing/JRadioButtonMenuItem.js
-javax/swing/JRootPane.js
-javax/swing/JScrollBar.js
-javax/swing/JScrollPane.js
-javax/swing/JSeparator.js
-javax/swing/JTabbedPane.js
-javax/swing/JToggleButton.js
-javax/swing/JToolTip.js
-javax/swing/JViewport.js
-javax/swing/JWindow.js
-javax/swing/KeyStroke.js
-javax/swing/KeyboardManager.js
-javax/swing/ListCellRenderer.js
-javax/swing/ListModel.js
-javax/swing/LookAndFeel.js
-javax/swing/MenuElement.js
-javax/swing/MenuSelectionManager.js
-javax/swing/MutableComboBoxModel.js
-javax/swing/Popup.js
-javax/swing/PopupFactory.js
-javax/swing/RepaintManager.js
-javax/swing/RootPaneContainer.js
-javax/swing/ScrollPaneConstants.js
-javax/swing/ScrollPaneLayout.js
-javax/swing/Scrollable.js
-javax/swing/SingleSelectionModel.js
-javax/swing/SizeRequirements.js
-javax/swing/SwingConstants.js
-javax/swing/SwingPaintEventDispatcher.js
-javax/swing/SwingUtilities.js
-javax/swing/Timer.js
-javax/swing/ToolTipManager.js
-javax/swing/UIDefaults.js
-javax/swing/UIManager.js
-javax/swing/ViewportLayout.js
-javax/swing/WindowConstants.js
-javax/swing/border/AbstractBorder.js
-javax/swing/border/BevelBorder.js
-javax/swing/border/Border.js
-javax/swing/border/EmptyBorder.js
-javax/swing/border/EtchedBorder.js
-javax/swing/border/LineBorder.js
-javax/swing/border/TitledBorder.js
-javax/swing/event/AncestorEvent.js
-javax/swing/event/AncestorListener.js
-javax/swing/event/ChangeEvent.js
-javax/swing/event/ChangeListener.js
-javax/swing/event/EventListenerList.js
-javax/swing/event/InternalFrameAdapter.js
-javax/swing/event/InternalFrameEvent.js
-javax/swing/event/InternalFrameListener.js
-javax/swing/event/ListDataListener.js
-javax/swing/event/MenuKeyListener.js
-javax/swing/event/MenuListener.js
-javax/swing/event/TableModelListener.js
-javax/swing/plaf/ActionMapUIResource.js
-javax/swing/plaf/BorderUIResource.js
-javax/swing/plaf/ColorUIResource.js
-javax/swing/plaf/ComponentInputMapUIResource.js
-javax/swing/plaf/ComponentUI.js
-javax/swing/plaf/DimensionUIResource.js
-javax/swing/plaf/FontUIResource.js
-javax/swing/plaf/InsetsUIResource.js
-javax/swing/plaf/UIResource.js
-javax/swing/plaf/basic/BasicBorders.js
-javax/swing/table/AbstractTableModel.js
-javax/swing/table/TableModel.js
-javax/xml/bind/ContextFinder.js
-javax/xml/bind/GetPropertyAction.js
-javax/xml/bind/JAXBContext.js
-javax/xml/bind/JAXBContextFactory.js
-javax/xml/bind/JAXBElement.js
-javax/xml/bind/ModuleUtil.js
-javax/xml/bind/ServiceLoaderUtil.js
-javax/xml/bind/Unmarshaller.js
-javax/xml/bind/ValidationEventHandler.js
-javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js
-javax/xml/bind/annotation/adapters/XmlAdapter.js
-javax/xml/bind/helpers/AbstractUnmarshallerImpl.js
-javax/xml/bind/helpers/DefaultValidationEventHandler.js
-javax/xml/datatype/XMLGregorianCalendar.js
-javax/xml/namespace/QName.js
-javax/xml/stream/XMLInputFactory.js
-javax/xml/stream/XMLStreamReader.js
-org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js
-org/json/simple/parser/JSONParser.js
-org/json/simple/parser/ParseException.js
-org/json/simple/parser/Yylex.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/AWTAccessor.js
-sun/awt/AWTAutoShutdown.js
-sun/awt/AppContext.js
-sun/awt/CausedFocusEvent.js
-sun/awt/ComponentFactory.js
-sun/awt/EventQueueItem.js
-sun/awt/KeyboardFocusManagerPeerProvider.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/WindowClosingListener.js
-sun/awt/WindowClosingSupport.js
-sun/awt/image/DataStealer.js
-sun/awt/image/IntegerComponentRaster.js
-sun/awt/image/IntegerInterleavedRaster.js
-sun/awt/image/SunWritableRaster.js
-sun/font/FontDesignMetrics.js
-sun/java2d/StateTrackable.js
-sun/java2d/StateTrackableDelegate.js
-sun/nio/cs/ArrayDecoder.js
-sun/nio/cs/HistoricallyNamedCharset.js
-sun/nio/cs/StandardCharsets.js
-sun/nio/cs/ThreadLocalCoders.js
-sun/nio/cs/UTF_8.js
-sun/nio/cs/Unicode.js
-sun/swing/DefaultLookup.js
-sun/swing/SwingLazyValue.js
-sun/swing/UIAction.js
-sun/text/resources/FormatData.js
-sun/text/resources/FormatData_en.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/resources/LocaleData.js
-swingjs/JSApp.js
-swingjs/JSApplet.js
-swingjs/JSAppletThread.js
-swingjs/JSAppletViewer.js
-swingjs/JSCharSet.js
-swingjs/JSFocusPeer.js
-swingjs/JSFontMetrics.js
-swingjs/JSFrameViewer.js
-swingjs/JSGraphics2D.js
-swingjs/JSGraphicsConfiguration.js
-swingjs/JSGraphicsEnvironment.js
-swingjs/JSKeyEvent.js
-swingjs/JSMenuManager.js
-swingjs/JSMouse.js
-swingjs/JSScreenDevice.js
-swingjs/JSThreadGroup.js
-swingjs/JSToolkit.js
-swingjs/JSUtil.js
-swingjs/a2s/Dialog.js
-swingjs/api/Interface.js
-swingjs/api/js/DOMNode.js
-swingjs/api/js/HTML5CanvasContext2D.js
-swingjs/api/js/JSInterface.js
-swingjs/jquery/JQueryUI.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/ButtonListener.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/JSComponentUI.js
-swingjs/plaf/JSDesktopIconUI.js
-swingjs/plaf/JSDesktopPaneUI.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/JSMenuBarUI.js
-swingjs/plaf/JSMenuItemUI.js
-swingjs/plaf/JSMenuUI.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/JSToolTipUI.js
-swingjs/plaf/JSViewportUI.js
-swingjs/plaf/JSWindowUI.js
-swingjs/plaf/LazyActionMap.js
-swingjs/plaf/Resizer.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/classlists/jvexamplefile.txt b/utils/jalviewjs/classlists/jvexamplefile.txt
deleted file mode 100644 (file)
index fd38213..0000000
--- a/utils/jalviewjs/classlists/jvexamplefile.txt
+++ /dev/null
@@ -1,1031 +0,0 @@
-com/stevesoft/pat/Boundary.js
-com/stevesoft/pat/Start.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/bin/JalviewTaskbar.js
-jalview/datamodel/AlignedCodonFrame.js
-jalview/ext/ensembl/EnsemblFeatures.js
-jalview/ext/ensembl/EnsemblLookup.js
-jalview/ext/ensembl/EnsemblSymbol.js
-jalview/ext/ensembl/EnsemblXref.js
-jalview/ext/ensembl/Species.js
-jalview/fts/api/StructureFTSRestClientI.js
-jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.js
-jalview/gui/APQHandlers.js
-jalview/gui/CrossRefAction.js
-jalview/gui/CutAndPasteTransfer.js
-jalview/gui/JvOptionPane.js
-jalview/gui/SplashScreen.js
-jalview/gui/structurechooser/PDBStructureChooserQuerySource.js
-jalview/gui/structurechooser/StructureChooserQuerySource.js
-jalview/gui/structurechooser/TDBResultAnalyser.js
-jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.js
-jalview/io/gff/SequenceOntologyFactory.js
-jalview/io/gff/SequenceOntologyI.js
-jalview/io/gff/SequenceOntologyLite.js
-jalview/jbgui/FilterOption.js
-jalview/jbgui/GCutAndPasteTransfer.js
-jalview/structure/AtomSpecModel.js
-jalview/structure/StructureCommand.js
-jalview/structure/StructureCommandI.js
-jalview/structure/StructureCommandsBase.js
-jalview/structure/StructureCommandsI.js
-jalview/util/ChannelProperties.js
-jalview/util/HttpUtils.js
-jalview/util/IntRangeComparator.js
-jalview/util/JSONUtils.js
-jalview/util/ShortcutKeyMaskExWrapper.js
-jalview/util/ShortcutKeyMaskExWrapper8.js
-jalview/util/ShortcutKeyMaskExWrapperI.js
-jalview/ws/SequenceFetcherFactory.js
-jalview/ws/dbsources/EBIAlfaFold.js
-jalview/ws/dbsources/EmblFlatfileSource.js
-jalview/ws/utils/UrlDownloadClient.js
-jalview/xml/binding/uniprot/InteractantType.js
-jalview/xml/binding/uniprot/MoleculeType.js
-jalview/xml/binding/uniprot/ReactionType.js
-java/applet/AppletContext.js
-java/applet/AppletStub.js
-java/applet/JSApplet.js
-java/awt/AWTEvent.js
-java/awt/AWTEventMulticaster.js
-java/awt/AWTKeyStroke.js
-java/awt/ActiveEvent.js
-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
-java/awt/Composite.js
-java/awt/Container.js
-java/awt/ContainerOrderFocusTraversalPolicy.js
-java/awt/Cursor.js
-java/awt/DefaultFocusTraversalPolicy.js
-java/awt/DefaultKeyboardFocusManager.js
-java/awt/Desktop.js
-java/awt/Dialog.js
-java/awt/Dimension.js
-java/awt/EventDispatchThread.js
-java/awt/EventFilter.js
-java/awt/EventQueue.js
-java/awt/EventQueueItem.js
-java/awt/FlowLayout.js
-java/awt/FocusTraversalPolicy.js
-java/awt/Font.js
-java/awt/FontMetrics.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
-java/awt/ItemSelectable.js
-java/awt/JSComponent.js
-java/awt/JSDialog.js
-java/awt/JSFrame.js
-java/awt/JSPanel.js
-java/awt/KeyEventDispatcher.js
-java/awt/KeyEventPostProcessor.js
-java/awt/KeyboardFocusManager.js
-java/awt/LayoutManager.js
-java/awt/LayoutManager2.js
-java/awt/LightweightDispatcher.js
-java/awt/Paint.js
-java/awt/Point.js
-java/awt/Queue.js
-java/awt/Rectangle.js
-java/awt/RenderingHints.js
-java/awt/SentEvent.js
-java/awt/Shape.js
-java/awt/Stroke.js
-java/awt/Taskbar.js
-java/awt/TextComponent.js
-java/awt/Toolkit.js
-java/awt/Transparency.js
-java/awt/VKCollection.js
-java/awt/Window.js
-java/awt/color/ColorSpace.js
-java/awt/datatransfer/ClipboardOwner.js
-java/awt/datatransfer/FlavorMap.js
-java/awt/datatransfer/FlavorTable.js
-java/awt/datatransfer/SystemFlavorMap.js
-java/awt/dnd/DropTarget.js
-java/awt/dnd/DropTargetContext.js
-java/awt/dnd/DropTargetListener.js
-java/awt/dnd/peer/DropTargetPeer.js
-java/awt/event/AWTEventListener.js
-java/awt/event/ActionEvent.js
-java/awt/event/ActionListener.js
-java/awt/event/AdjustmentEvent.js
-java/awt/event/AdjustmentListener.js
-java/awt/event/ComponentAdapter.js
-java/awt/event/ComponentEvent.js
-java/awt/event/ComponentListener.js
-java/awt/event/ContainerEvent.js
-java/awt/event/ContainerListener.js
-java/awt/event/FocusAdapter.js
-java/awt/event/FocusEvent.js
-java/awt/event/FocusListener.js
-java/awt/event/HierarchyBoundsListener.js
-java/awt/event/HierarchyEvent.js
-java/awt/event/HierarchyListener.js
-java/awt/event/InputEvent.js
-java/awt/event/InputMethodListener.js
-java/awt/event/InvocationEvent.js
-java/awt/event/ItemEvent.js
-java/awt/event/ItemListener.js
-java/awt/event/KeyAdapter.js
-java/awt/event/KeyEvent.js
-java/awt/event/KeyListener.js
-java/awt/event/MouseAdapter.js
-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
-java/awt/event/WindowEvent.js
-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
-java/awt/geom/PathIterator.js
-java/awt/geom/Point2D.js
-java/awt/geom/RectIterator.js
-java/awt/geom/Rectangle2D.js
-java/awt/geom/RectangularShape.js
-java/awt/image/BufferedImage.js
-java/awt/image/ColorModel.js
-java/awt/image/DataBuffer.js
-java/awt/image/DataBufferInt.js
-java/awt/image/DirectColorModel.js
-java/awt/image/ImageConsumer.js
-java/awt/image/ImageObserver.js
-java/awt/image/ImageProducer.js
-java/awt/image/PackedColorModel.js
-java/awt/image/PixelGrabber.js
-java/awt/image/Raster.js
-java/awt/image/RenderedImage.js
-java/awt/image/SampleModel.js
-java/awt/image/SinglePixelPackedSampleModel.js
-java/awt/image/WritableRaster.js
-java/awt/peer/ComponentPeer.js
-java/awt/peer/ContainerPeer.js
-java/awt/peer/DialogPeer.js
-java/awt/peer/FramePeer.js
-java/awt/peer/KeyboardFocusManagerPeer.js
-java/awt/peer/LightweightPeer.js
-java/awt/peer/WindowPeer.js
-java/awt/print/Printable.js
-java/beans/ChangeListenerMap.js
-java/beans/PropertyChangeEvent.js
-java/beans/PropertyChangeListener.js
-java/beans/PropertyChangeSupport.js
-java/io/BufferedInputStream.js
-java/io/BufferedReader.js
-java/io/BufferedWriter.js
-java/io/ByteArrayInputStream.js
-java/io/ByteArrayOutputStream.js
-java/io/Closeable.js
-java/io/DataInput.js
-java/io/DataInputStream.js
-java/io/File.js
-java/io/FileDescriptor.js
-java/io/FileInputStream.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/OutputStream.js
-java/io/OutputStreamWriter.js
-java/io/PrintStream.js
-java/io/Reader.js
-java/io/StringReader.js
-java/io/StringWriter.js
-java/io/Writer.js
-java/lang/AbstractStringBuilder.js
-java/lang/AutoCloseable.js
-java/lang/Class.js
-java/lang/Enum.js
-java/lang/Iterable.js
-java/lang/Readable.js
-java/lang/Runtime.js
-java/lang/StringBuffer.js
-java/lang/StringBuilder.js
-java/lang/Thread.js
-java/lang/ThreadGroup.js
-java/lang/ThreadLocal.js
-java/lang/ref/ReferenceQueue.js
-java/lang/reflect/AccessibleObject.js
-java/lang/reflect/AnnotatedElement.js
-java/lang/reflect/Constructor.js
-java/lang/reflect/Method.js
-java/math/BigDecimal.js
-java/math/BigInteger.js
-java/math/MathContext.js
-java/math/RoundingMode.js
-java/net/ContentHandler.js
-java/net/HttpURLConnection.js
-java/net/URI.js
-java/net/URL.js
-java/net/URLConnection.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
-java/text/AttributedCharacterIterator.js
-java/text/CharacterIterator.js
-java/text/DateFormat.js
-java/text/DateFormatSymbols.js
-java/text/DecimalFormat.js
-java/text/DecimalFormatSymbols.js
-java/text/DigitList.js
-java/text/FieldPosition.js
-java/text/Format.js
-java/text/MessageFormat.js
-java/text/NumberFormat.js
-java/text/SimpleDateFormat.js
-java/text/spi/BreakIteratorProvider.js
-java/text/spi/CollatorProvider.js
-java/text/spi/DateFormatProvider.js
-java/text/spi/DateFormatSymbolsProvider.js
-java/text/spi/DecimalFormatSymbolsProvider.js
-java/text/spi/NumberFormatProvider.js
-java/util/AbstractCollection.js
-java/util/AbstractList.js
-java/util/AbstractMap.js
-java/util/AbstractQueue.js
-java/util/AbstractSequentialList.js
-java/util/AbstractSet.js
-java/util/ArrayDeque.js
-java/util/ArrayList.js
-java/util/Arrays.js
-java/util/BitSet.js
-java/util/Calendar.js
-java/util/Collection.js
-java/util/Collections.js
-java/util/ComparableTimSort.js
-java/util/Comparator.js
-java/util/Deque.js
-java/util/Dictionary.js
-java/util/DualPivotQuicksort.js
-java/util/Enumeration.js
-java/util/EventListener.js
-java/util/EventObject.js
-java/util/Formatter.js
-java/util/GregorianCalendar.js
-java/util/HashMap.js
-java/util/HashSet.js
-java/util/Hashtable.js
-java/util/IdentityHashMap.js
-java/util/Iterator.js
-java/util/LinkedHashMap.js
-java/util/LinkedHashSet.js
-java/util/LinkedList.js
-java/util/List.js
-java/util/ListIterator.js
-java/util/Locale.js
-java/util/Map.js
-java/util/NavigableMap.js
-java/util/NavigableSet.js
-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/RandomAccessSubList.js
-java/util/ResourceBundle.js
-java/util/ServiceLoader.js
-java/util/Set.js
-java/util/SortedMap.js
-java/util/SortedSet.js
-java/util/Stack.js
-java/util/StringTokenizer.js
-java/util/SubList.js
-java/util/TimSort.js
-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/ConcurrentHashMap.js
-java/util/concurrent/ConcurrentMap.js
-java/util/concurrent/Executor.js
-java/util/concurrent/ExecutorService.js
-java/util/concurrent/Executors.js
-java/util/concurrent/LinkedBlockingQueue.js
-java/util/concurrent/RejectedExecutionHandler.js
-java/util/concurrent/Semaphore.js
-java/util/concurrent/ThreadFactory.js
-java/util/concurrent/ThreadPoolExecutor.js
-java/util/concurrent/TimeUnit.js
-java/util/concurrent/atomic/AtomicInteger.js
-java/util/concurrent/locks/AbstractOwnableSynchronizer.js
-java/util/concurrent/locks/AbstractQueuedSynchronizer.js
-java/util/concurrent/locks/Condition.js
-java/util/concurrent/locks/Lock.js
-java/util/concurrent/locks/ReadWriteLock.js
-java/util/concurrent/locks/ReentrantLock.js
-java/util/concurrent/locks/ReentrantReadWriteLock.js
-java/util/jar/JarEntry.js
-java/util/jar/JarInputStream.js
-java/util/regex/MatchResult.js
-java/util/regex/Matcher.js
-java/util/regex/Pattern.js
-java/util/spi/CalendarDataProvider.js
-java/util/spi/CurrencyNameProvider.js
-java/util/spi/LocaleNameProvider.js
-java/util/spi/LocaleServiceProvider.js
-java/util/spi/TimeZoneNameProvider.js
-java/util/zip/CRC32.js
-java/util/zip/Inflater.js
-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/GenericCifDataParser.js
-javajs/api/GenericLineReader.js
-javajs/api/GenericOutputChannel.js
-javajs/api/JSONEncodable.js
-javajs/util/A4.js
-javajs/util/AU.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/CifDataParser.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/M4.js
-javajs/util/OC.js
-javajs/util/P3.js
-javajs/util/P3i.js
-javajs/util/P4.js
-javajs/util/PT.js
-javajs/util/Rdr.js
-javajs/util/SB.js
-javajs/util/T3.js
-javajs/util/T3i.js
-javajs/util/T4.js
-javajs/util/V3.js
-javax/net/ssl/HttpsURLConnection.js
-javax/swing/AbstractAction.js
-javax/swing/AbstractButton.js
-javax/swing/AbstractListModel.js
-javax/swing/Action.js
-javax/swing/ActionMap.js
-javax/swing/AncestorNotifier.js
-javax/swing/ArrayTable.js
-javax/swing/Autoscroller.js
-javax/swing/BorderFactory.js
-javax/swing/BoundedRangeModel.js
-javax/swing/BoxLayout.js
-javax/swing/ButtonGroup.js
-javax/swing/ButtonModel.js
-javax/swing/CellRendererPane.js
-javax/swing/ClientPropertyKey.js
-javax/swing/ComboBoxEditor.js
-javax/swing/ComboBoxModel.js
-javax/swing/ComponentInputMap.js
-javax/swing/DefaultBoundedRangeModel.js
-javax/swing/DefaultButtonModel.js
-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
-javax/swing/FocusManager.js
-javax/swing/Icon.js
-javax/swing/ImageIcon.js
-javax/swing/InputMap.js
-javax/swing/InternalFrameFocusTraversalPolicy.js
-javax/swing/JApplet.js
-javax/swing/JButton.js
-javax/swing/JCheckBox.js
-javax/swing/JCheckBoxMenuItem.js
-javax/swing/JComboBox.js
-javax/swing/JComponent.js
-javax/swing/JDesktopPane.js
-javax/swing/JDialog.js
-javax/swing/JFrame.js
-javax/swing/JInternalFrame.js
-javax/swing/JLabel.js
-javax/swing/JLayeredPane.js
-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
-javax/swing/JRadioButtonMenuItem.js
-javax/swing/JRootPane.js
-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
-javax/swing/JToolTip.js
-javax/swing/JViewport.js
-javax/swing/JWindow.js
-javax/swing/KeyStroke.js
-javax/swing/KeyboardManager.js
-javax/swing/LayoutComparator.js
-javax/swing/LayoutFocusTraversalPolicy.js
-javax/swing/ListCellRenderer.js
-javax/swing/ListModel.js
-javax/swing/ListSelectionModel.js
-javax/swing/LookAndFeel.js
-javax/swing/MenuElement.js
-javax/swing/MenuSelectionManager.js
-javax/swing/MutableComboBoxModel.js
-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/SwingConstants.js
-javax/swing/SwingContainerOrderFocusTraversalPolicy.js
-javax/swing/SwingDefaultFocusTraversalPolicy.js
-javax/swing/SwingPaintEventDispatcher.js
-javax/swing/SwingUtilities.js
-javax/swing/Timer.js
-javax/swing/ToolTipManager.js
-javax/swing/TransferHandler.js
-javax/swing/UIDefaults.js
-javax/swing/UIManager.js
-javax/swing/ViewportLayout.js
-javax/swing/WindowConstants.js
-javax/swing/border/AbstractBorder.js
-javax/swing/border/BevelBorder.js
-javax/swing/border/Border.js
-javax/swing/border/CompoundBorder.js
-javax/swing/border/EmptyBorder.js
-javax/swing/border/EtchedBorder.js
-javax/swing/border/LineBorder.js
-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
-javax/swing/event/InternalFrameAdapter.js
-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/plaf/ActionMapUIResource.js
-javax/swing/plaf/BorderUIResource.js
-javax/swing/plaf/ColorUIResource.js
-javax/swing/plaf/ComponentInputMapUIResource.js
-javax/swing/plaf/ComponentUI.js
-javax/swing/plaf/DimensionUIResource.js
-javax/swing/plaf/FontUIResource.js
-javax/swing/plaf/InputMapUIResource.js
-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
-javax/swing/text/Caret.js
-javax/swing/text/CompositeView.js
-javax/swing/text/DefaultCaret.js
-javax/swing/text/DefaultEditorKit.js
-javax/swing/text/Document.js
-javax/swing/text/EditorKit.js
-javax/swing/text/Element.js
-javax/swing/text/GapContent.js
-javax/swing/text/GapVector.js
-javax/swing/text/JTextComponent.js
-javax/swing/text/MutableAttributeSet.js
-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
-javax/xml/bind/JAXBContextFactory.js
-javax/xml/bind/JAXBElement.js
-javax/xml/bind/ModuleUtil.js
-javax/xml/bind/ServiceLoaderUtil.js
-javax/xml/bind/Unmarshaller.js
-javax/xml/bind/ValidationEventHandler.js
-javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js
-javax/xml/bind/annotation/adapters/XmlAdapter.js
-javax/xml/bind/helpers/AbstractUnmarshallerImpl.js
-javax/xml/bind/helpers/DefaultValidationEventHandler.js
-javax/xml/datatype/XMLGregorianCalendar.js
-javax/xml/namespace/QName.js
-javax/xml/stream/XMLInputFactory.js
-javax/xml/stream/XMLStreamConstants.js
-javax/xml/stream/XMLStreamReader.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/jmol/adapter/readers/cif/CifReader.js
-org/jmol/adapter/readers/cif/MMCifReader.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/BondIterator.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/JmolAdapterBondIterator.js
-org/jmol/api/JmolAdapterStructureIterator.js
-org/jmol/api/JmolCallbackListener.js
-org/jmol/api/JmolFilesReaderInterface.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/io/FilesReader.js
-org/jmol/modelset/Atom.js
-org/jmol/modelset/AtomCollection.js
-org/jmol/modelset/AtomIteratorWithinModel.js
-org/jmol/modelset/Bond.js
-org/jmol/modelset/BondCollection.js
-org/jmol/modelset/BondIterator.js
-org/jmol/modelset/BondIteratorSelected.js
-org/jmol/modelset/Chain.js
-org/jmol/modelset/Group.js
-org/jmol/modelset/HBond.js
-org/jmol/modelset/LabelToken.js
-org/jmol/modelset/Measurement.js
-org/jmol/modelset/MeasurementData.js
-org/jmol/modelset/MeasurementPending.js
-org/jmol/modelset/Model.js
-org/jmol/modelset/ModelLoader.js
-org/jmol/modelset/ModelSet.js
-org/jmol/modelset/Orientation.js
-org/jmol/modelset/Structure.js
-org/jmol/modelset/Text.js
-org/jmol/modelset/TickInfo.js
-org/jmol/modelsetbio/AlphaMonomer.js
-org/jmol/modelsetbio/AlphaPolymer.js
-org/jmol/modelsetbio/AminoMonomer.js
-org/jmol/modelsetbio/AminoPolymer.js
-org/jmol/modelsetbio/BioModel.js
-org/jmol/modelsetbio/BioModelSet.js
-org/jmol/modelsetbio/BioPolymer.js
-org/jmol/modelsetbio/BioResolver.js
-org/jmol/modelsetbio/Helix.js
-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 (file)
--- 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: ""
 }
 </script>
 </head>

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 (file)
--- 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: ""
 }
 </script>
 </head>

diff --git a/utils/jalviewjs/some_commands.txt b/utils/jalviewjs/some_commands.txt
new file mode 100644 (file)
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/)