JAL-3033 more classes for the kitchen sink

diff --git a/classlists/jvexamplefile.txt b/classlists/jvexamplefile.txt
index 444b0bf..ce2152b 100644 (file)
--- a/classlists/jvexamplefile.txt
+++ b/classlists/jvexamplefile.txt
@@ -1,4 +1,3 @@
-com/stevesoft/pat/Any.js
 com/stevesoft/pat/Bracket.js
 com/stevesoft/pat/Branch.js
 com/stevesoft/pat/CaseMgr.js
@@ -56,19 +55,26 @@ intervalstore/impl/NCList.js
 intervalstore/impl/NCNode.js
 jalview/analysis/AAFrequency.js
 jalview/analysis/AlignSeq.js
+jalview/analysis/AlignmentAnnotationUtils.js
 jalview/analysis/AlignmentUtils.js
 jalview/analysis/AnnotationSorter.js
+jalview/analysis/AverageDistanceTree.js
 jalview/analysis/Conservation.js
 jalview/analysis/CrossRef.js
 jalview/analysis/GeneticCodeI.js
 jalview/analysis/GeneticCodes.js
+jalview/analysis/Grouping.js
+jalview/analysis/NJTree.js
+jalview/analysis/SeqsetUtils.js
 jalview/analysis/SequenceIdMatcher.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
@@ -93,6 +99,7 @@ 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/bin/ArgsParser.js
 jalview/bin/BuildDetails.js
@@ -104,13 +111,18 @@ 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/DBRefEntry.js
 jalview/datamodel/DBRefSource.js
+jalview/datamodel/GraphLine.js
 jalview/datamodel/HiddenColumns.js
 jalview/datamodel/HiddenColumnsCursor.js
 jalview/datamodel/HiddenCursorPosition.js
@@ -128,6 +140,7 @@ jalview/datamodel/ResidueCount.js
 jalview/datamodel/SearchResultMatchI.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
@@ -135,6 +148,7 @@ jalview/datamodel/SequenceFeature.js
 jalview/datamodel/SequenceGroup.js
 jalview/datamodel/SequenceI.js
 jalview/datamodel/SequenceNode.js
+jalview/datamodel/StartRegionIterator.js
 jalview/datamodel/StructureViewerModel.js
 jalview/datamodel/VisibleColsCollection.js
 jalview/datamodel/VisibleContigsIterator.js
@@ -144,6 +158,7 @@ jalview/datamodel/features/FeatureAttributes.js
 jalview/datamodel/features/FeatureLocationI.js
 jalview/datamodel/features/FeatureMatcherSet.js
 jalview/datamodel/features/FeatureMatcherSetI.js
+jalview/datamodel/features/FeatureSources.js
 jalview/datamodel/features/FeatureStore.js
 jalview/datamodel/features/SequenceFeatures.js
 jalview/datamodel/features/SequenceFeaturesI.js
@@ -173,16 +188,20 @@ jalview/fts/service/uniprot/UniprotFTSPanel.js
 jalview/gui/AlignFrame.js
 jalview/gui/AlignViewport.js
 jalview/gui/AlignmentPanel.js
+jalview/gui/AnnotationColumnChooser.js
 jalview/gui/AnnotationLabels.js
 jalview/gui/AnnotationPanel.js
+jalview/gui/AnnotationRowFilter.js
 jalview/gui/AppJmol.js
 jalview/gui/AppJmolBinding.js
+jalview/gui/CalculationChooser.js
 jalview/gui/ColourMenuHelper.js
 jalview/gui/ComboBoxTooltipRenderer.js
 jalview/gui/Desktop.js
 jalview/gui/FeatureRenderer.js
 jalview/gui/FeatureSettings.js
 jalview/gui/FeatureTypeSettings.js
+jalview/gui/FontChooser.js
 jalview/gui/IProgressIndicator.js
 jalview/gui/IdCanvas.js
 jalview/gui/IdPanel.js
@@ -195,6 +214,7 @@ jalview/gui/JvSwingUtils.js
 jalview/gui/OverviewCanvas.js
 jalview/gui/OverviewPanel.js
 jalview/gui/PaintRefresher.js
+jalview/gui/PopupMenu.js
 jalview/gui/Preferences.js
 jalview/gui/ProgressBar.js
 jalview/gui/ProgressPanel.js
@@ -204,6 +224,7 @@ jalview/gui/SeqPanel.js
 jalview/gui/SequenceFetcher.js
 jalview/gui/SequenceRenderer.js
 jalview/gui/SliderPanel.js
+jalview/gui/StructureChooser.js
 jalview/gui/StructureViewer.js
 jalview/gui/StructureViewerBase.js
 jalview/gui/TreeCanvas.js
@@ -246,11 +267,15 @@ jalview/jbgui/BackupFilesPresetEntry.js
 jalview/jbgui/GAlignFrame.js
 jalview/jbgui/GAlignmentPanel.js
 jalview/jbgui/GDesktop.js
+jalview/jbgui/GFontChooser.js
 jalview/jbgui/GPreferences.js
 jalview/jbgui/GSliderPanel.js
+jalview/jbgui/GStructureChooser.js
 jalview/jbgui/GStructureViewer.js
 jalview/jbgui/GTreePanel.js
 jalview/jbgui/IntKeyStringValueEntry.js
+jalview/math/Matrix.js
+jalview/math/MatrixI.js
 jalview/project/Jalview2XML.js
 jalview/renderer/AnnotationRenderer.js
 jalview/renderer/AwtRenderPanelI.js
@@ -320,6 +345,7 @@ jalview/util/MapList.js
 jalview/util/MessageManager.js
 jalview/util/Platform.js
 jalview/util/QuickSort.js
+jalview/util/SetUtils.js
 jalview/util/StringUtils.js
 jalview/util/UrlLink.js
 jalview/util/dialogrunner/DialogRunnerI.js
@@ -330,6 +356,7 @@ jalview/viewmodel/OverviewDimensionsHideHidden.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/FeaturesDisplayed.js
@@ -368,6 +395,34 @@ jalview/xml/binding/jalview/SequenceSet.js
 jalview/xml/binding/jalview/SequenceType.js
 jalview/xml/binding/jalview/VAMSAS.js
 jalview/xml/binding/jalview/WebServiceParameterSet.js
+jalview/xml/binding/uniprot/CitationType.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/GeneNameType.js
+jalview/xml/binding/uniprot/GeneType.js
+jalview/xml/binding/uniprot/IsoformType.js
+jalview/xml/binding/uniprot/KeywordType.js
+jalview/xml/binding/uniprot/LocationType.js
+jalview/xml/binding/uniprot/NameListType.js
+jalview/xml/binding/uniprot/OrganismNameType.js
+jalview/xml/binding/uniprot/OrganismType.js
+jalview/xml/binding/uniprot/PersonType.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/ReferenceType.js
+jalview/xml/binding/uniprot/SequenceType.js
+jalview/xml/binding/uniprot/SourceDataType.js
+jalview/xml/binding/uniprot/SourceType.js
+jalview/xml/binding/uniprot/SubcellularLocationType.js
+jalview/xml/binding/uniprot/Uniprot.js
 java/awt/AWTKeyStroke.js
 java/awt/AlphaComposite.js
 java/awt/CardLayout.js
@@ -514,6 +569,7 @@ java/util/Comparator.js
 java/util/Deque.js
 java/util/DualPivotQuicksort.js
 java/util/Enumeration.js
+java/util/Formatter.js
 java/util/GregorianCalendar.js
 java/util/Iterator.js
 java/util/LinkedHashMap.js
@@ -539,6 +595,7 @@ java/util/TimSort.js
 java/util/TimeZone.js
 java/util/TreeMap.js
 java/util/TreeSet.js
+java/util/WeakHashMap.js
 java/util/concurrent/AbstractExecutorService.js
 java/util/concurrent/BlockingQueue.js
 java/util/concurrent/ConcurrentHashMap.js
@@ -772,6 +829,24 @@ mc_view/Atom.js
 mc_view/Bond.js
 mc_view/PDBChain.js
 mc_view/Residue.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
@@ -1091,4 +1166,5 @@ swingjs/xml/JSSAXAttributes.js
 swingjs/xml/JSSAXParser.js
 swingjs/xml/JSXMLGregorianCalendarImpl.js
 swingjs/xml/JSXMLInputFactory.js
+swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Any.js
 swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Boundary.js