SwingJS transpiler to 3.2.5.v1 (fixed java.util.stream)

[jalview.git] / _j2sclasslist.txt

diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt
index 8fd8415..f51640c 100644 (file)
--- a/_j2sclasslist.txt
+++ b/_j2sclasslist.txt
@@ -2,11 +2,13 @@ jalview/analysis/AAFrequency.js
 jalview/analysis/AlignSeq.js
 jalview/analysis/AlignmentAnnotationUtils.js
 jalview/analysis/AlignmentUtils.js
+jalview/analysis/AlignmentSorter.js
 jalview/analysis/AnnotationSorter.js
 jalview/analysis/Conservation.js
 jalview/analysis/CrossRef.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
@@ -20,12 +22,14 @@ jalview/api/AlignCalcManagerI.js
 jalview/api/AlignCalcWorkerI.js
 jalview/api/AlignViewControllerGuiI.js
 jalview/api/AlignViewControllerI.js
+jalview/api/AlignFrameI.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/JalviewApp.js
 jalview/api/OOMHandlerI.js
 jalview/api/SequenceRenderer.js
 jalview/api/StructureSelectionManagerProvider.js
@@ -33,11 +37,15 @@ jalview/api/ViewStyleI.js
 jalview/api/analysis/PairwiseScoreModelI.js
 jalview/api/analysis/ScoreModelI.js
 jalview/api/analysis/SimilarityParamsI.js
+jalview/bin/AppletParams.js
+jalview/bin/ApplicationSingletonProvider.js
 jalview/bin/ArgsParser.js
 jalview/bin/BuildDetails.js
 jalview/bin/Cache.js
 jalview/bin/Jalview.js
-jalview/bin/JalviewJS2.js
+jalview/bin/JalviewAppLoader.js
+jalview/commands/CommandI.js
+jalview/commands/OrderCommand.js
 jalview/controller/AlignViewController.js
 jalview/datamodel/ASequence.js
 jalview/datamodel/ASequenceI.js
@@ -82,7 +90,9 @@ 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/FeatureStoreI.js
+jalview/datamodel/features/FeatureStoreJS.js
+
 jalview/datamodel/features/SequenceFeatures.js
 jalview/datamodel/features/SequenceFeaturesI.js
 jalview/gui/AlignFrame.js
@@ -123,9 +133,11 @@ jalview/io/FileFormats.js
 jalview/io/FileLoader.js
 jalview/io/FileParse.js
 jalview/io/IdentifyFile.js
+jalview/io/NewickFile.js
 jalview/io/PIRFile.js
 jalview/io/ScoreMatrixFile.js
 jalview/io/SequenceAnnotationReport.js
+jalview/javascript/JalviewLiteJSApi.js
 jalview/javascript/log4j/ConsoleAppender.js
 jalview/javascript/log4j/Layout.js
 jalview/javascript/log4j/Level.js
@@ -154,6 +166,8 @@ jalview/schemes/ClustalxColourScheme.js
 jalview/schemes/ColourSchemeI.js
 jalview/schemes/ColourSchemeProperty.js
 jalview/schemes/ColourSchemes.js
+jalview/schemes/ColourSchemeLoader.js
+jalview/schemes/UserColourScheme.js
 jalview/schemes/Consensus.js
 jalview/schemes/FeatureColour.js
 jalview/schemes/HelixColourScheme.js
@@ -170,6 +184,7 @@ jalview/schemes/StrandColourScheme.js
 jalview/schemes/TCoffeeColourScheme.js
 jalview/schemes/TaylorColourScheme.js
 jalview/schemes/TurnColourScheme.js
+jalview/schemes/UserColourScheme.js
 jalview/schemes/ZappoColourScheme.js
 jalview/structure/CommandListener.js
 jalview/structure/SelectionListener.js
@@ -549,6 +564,13 @@ javax/swing/DefaultDesktopManager.js
 javax/swing/DefaultListCellRenderer.js
 javax/swing/DefaultSingleSelectionModel.js
 javax/swing/DesktopManager.js
+javax/swing/FocusManager.js
+javax/swing/InternalFrameFocusTraversalPolicy.js
+javax/swing/LayoutComparator.js
+javax/swing/LayoutFocusTraversalPolicy.js
+javax/swing/SortingFocusTraversalPolicy.js
+javax/swing/SwingContainerOrderFocusTraversalPolicy.js
+javax/swing/SwingDefaultFocusTraversalPolicy.js
 javax/swing/InputMap.js
 javax/swing/JApplet.js
 javax/swing/JButton.js
@@ -608,6 +630,7 @@ 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
@@ -711,6 +734,7 @@ swingjs/JSApplet.js
 swingjs/JSAppletThread.js
 swingjs/JSAppletViewer.js
 swingjs/JSCharSet.js
+swingjs/JSDummyApplet.js
 swingjs/JSFocusPeer.js
 swingjs/JSFontMetrics.js
 swingjs/JSFrameViewer.js
@@ -791,8 +815,7 @@ swingjs/xml/JSXMLInputFactory.js
 swingjs/xml/JSXMLStreamReader.js
 intervalstore/api/IntervalI.js
 intervalstore/api/IntervalStoreI.js
-intervalstore/impl/BinarySearcher.js
-intervalstore/impl/IntervalStore.js
+intervalstore/nonc/IntervalStore.js
 jalview/analysis/GeneticCodeI.js
 jalview/analysis/GeneticCodes.js
 jalview/api/FeaturesSourceI.js
@@ -804,3 +827,156 @@ jalview/util/LinkedIdentityHashSet.js
 jalview/util/ParseHtmlBodyAndLinks.js
 java/util/function/Function.js
 swingjs/a2s/A2SContainer.js
+
+jalview/fts/api/FTSData.js
+jalview/fts/api/FTSDataColumnI.js
+jalview/fts/api/FTSRestClientI.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/service/pdb/PDBFTSRestClient.js
+jalview/gui/StructureChooser.js
+jalview/javascript/json/JSON.js
+jalview/javascript/web/Client.js
+jalview/javascript/web/ClientResponse.js
+jalview/javascript/web/WebResource.js
+jalview/jbgui/BackupFilesPresetEntry.js
+jalview/jbgui/GStructureChooser.js
+jalview/jbgui/IntKeyStringValueEntry.js
+java/awt/CardLayout.js
+java/awt/TextComponent.js
+java/awt/image/ImageConsumer.js
+java/io/ObjectStreamField.js
+java/net/URI.js
+java/util/ComparableTimSort.js
+java/util/LinkedHashSet.js
+java/util/WeakHashMap.js
+javajs/util/Base64.js
+javax/net/ssl/HttpsURLConnection.js
+javax/swing/CellRendererPane.js
+javax/swing/DefaultListSelectionModel.js
+javax/swing/DefaultRowSorter.js
+javax/swing/DropMode.js
+javax/swing/Icon.js
+javax/swing/ImageIcon.js
+javax/swing/JTable.js
+javax/swing/JTextField.js
+javax/swing/ListSelectionModel.js
+javax/swing/RowSorter.js
+javax/swing/SortOrder.js
+javax/swing/event/CaretEvent.js
+javax/swing/event/CaretListener.js
+javax/swing/event/CellEditorListener.js
+javax/swing/event/DocumentListener.js
+javax/swing/event/ListSelectionEvent.js
+javax/swing/event/ListSelectionListener.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/plaf/InputMapUIResource.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/TableRowSorter.js
+javax/swing/text/Caret.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/JTextComponent.js
+javax/swing/text/Position.js
+javax/swing/text/TextAction.js
+javax/swing/text/View.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
+sun/swing/StringUIClientPropertyKey.js
+sun/swing/SwingUtilities2.js
+sun/swing/UIClientPropertyKey.js
+sun/swing/table/DefaultTableCellHeaderRenderer.js
+swingjs/JSAbstractDocument.js
+swingjs/JSImage.js
+swingjs/JSImagekit.js
+swingjs/JSPlainDocument.js
+swingjs/api/JSMinimalAbstractDocument.js
+swingjs/json/JSON.js
+swingjs/plaf/BasicHTML.js
+swingjs/plaf/CellHolder.js
+swingjs/plaf/JSTableHeaderUI.js
+swingjs/plaf/JSTableUI.js
+swingjs/plaf/JSTextFieldUI.js
+swingjs/plaf/JSTextUI.js
+swingjs/plaf/TextListener.js
+
+com/stevesoft/pat/Bracket.js
+com/stevesoft/pat/CaseMgr.js
+com/stevesoft/pat/FastMulti.js
+com/stevesoft/pat/NUnicodeAlpha.js
+com/stevesoft/pat/NUnicodeCurrency.js
+com/stevesoft/pat/NUnicodeDigit.js
+com/stevesoft/pat/NUnicodeMath.js
+com/stevesoft/pat/NUnicodePunct.js
+com/stevesoft/pat/NUnicodeW.js
+com/stevesoft/pat/NUnicodeWhite.js
+com/stevesoft/pat/NoPattern.js
+com/stevesoft/pat/Or.js
+com/stevesoft/pat/OrMark.js
+com/stevesoft/pat/Pattern.js
+com/stevesoft/pat/PatternSub.js
+com/stevesoft/pat/Pthings.js
+com/stevesoft/pat/Range.js
+com/stevesoft/pat/RegOpt.js
+com/stevesoft/pat/RegRes.js
+com/stevesoft/pat/Regex.js
+com/stevesoft/pat/Rthings.js
+com/stevesoft/pat/StrPos.js
+com/stevesoft/pat/StringLike.js
+com/stevesoft/pat/SubMark.js
+com/stevesoft/pat/UniValidator.js
+com/stevesoft/pat/UnicodeAlpha.js
+com/stevesoft/pat/UnicodeCurrency.js
+com/stevesoft/pat/UnicodeDigit.js
+com/stevesoft/pat/UnicodeLower.js
+com/stevesoft/pat/UnicodeMath.js
+com/stevesoft/pat/UnicodePunct.js
+com/stevesoft/pat/UnicodeUpper.js
+com/stevesoft/pat/UnicodeW.js
+com/stevesoft/pat/UnicodeWhite.js
+com/stevesoft/pat/Validator.js
+com/stevesoft/pat/oneChar.js
+com/stevesoft/pat/parsePerl.js
+com/stevesoft/pat/patInt.js
+com/stevesoft/pat/wrap/StringWrap.js
+
+jalview/api/DBRefEntryI.js
+jalview/api/SequenceStructureBinding.js
+jalview/api/structures/JalviewStructureDisplayI.js
+jalview/datamodel/DBRefEntry.js
+jalview/datamodel/Mapping.js
+jalview/datamodel/features/FeatureAttributes.js