X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=_j2sclasslist.txt;h=425e51f540d27bfa204294a7257a8ec1a049e442;hb=b2761facaf7c85bf37dc48b4485fd733a7d3e989;hp=9a790a0835b444186fa69b21527864af056069bc;hpb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;p=jalview.git

diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt
index 9a790a0..425e51f 100644
--- 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
@@ -649,10 +672,12 @@ 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/DatatypeFactory.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/DatatypeFactoryImpl.js
 org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js
 org/json/simple/parser/JSONParser.js
 org/json/simple/parser/ParseException.js
@@ -664,7 +689,6 @@ 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
@@ -707,14 +731,15 @@ 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/JSDummyApplet.js
 swingjs/JSFocusPeer.js
 swingjs/JSFontMetrics.js
 swingjs/JSFrameViewer.js
 swingjs/JSGraphics2D.js
+swingjs/JSGraphicsCompositor.js
 swingjs/JSGraphicsConfiguration.js
 swingjs/JSGraphicsEnvironment.js
 swingjs/JSKeyEvent.js
@@ -791,8 +816,7 @@ 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
@@ -826,12 +850,12 @@ java/awt/CardLayout.js
 java/awt/TextComponent.js
 java/awt/image/ImageConsumer.js
 java/io/ObjectStreamField.js
-java/net/HttpsURLConnection.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
@@ -897,11 +921,8 @@ 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
@@ -957,3 +978,21 @@ jalview/api/structures/JalviewStructureDisplayI.js
 jalview/datamodel/DBRefEntry.js
 jalview/datamodel/Mapping.js
 jalview/datamodel/features/FeatureAttributes.js
+
+intervalstore/impl/BinarySearcher.js
+intervalstore/impl/IntervalStore.js
+jalview/api/AlignmentColsCollectionI.js
+jalview/api/AlignmentRowsCollectionI.js
+jalview/api/RendererListenerI.js
+jalview/bin/JalviewJSApi.js
+jalview/datamodel/VisibleColsCollection.js
+jalview/datamodel/VisibleRowsCollection.js
+jalview/datamodel/VisibleRowsIterator.js
+jalview/gui/OverviewCanvas.js
+jalview/gui/OverviewPanel.js
+jalview/gui/ProgressPanel.js
+jalview/renderer/OverviewRenderer.js
+jalview/renderer/OverviewResColourFinder.js
+jalview/renderer/seqfeatures/FeatureColourFinder.js
+jalview/viewmodel/OverviewDimensions.js
+jalview/viewmodel/OverviewDimensionsHideHidden.js