label work; adds preliminary _j2sclasslist.txt

[jalview.git] / _j2sclasslist.txt

diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt
new file mode 100644 (file)
index 0000000..27ab6a6
--- /dev/null
+++ b/_j2sclasslist.txt
@@ -0,0 +1,458 @@
+jalview/analysis/AAFrequency.js
+jalview/analysis/AlignSeq.js
+jalview/analysis/AnnotationSorter.js
+jalview/analysis/Conservation.js
+jalview/analysis/CrossRef.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/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/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/AnnotatedCollectionI.js
+jalview/datamodel/Annotation.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/ResidueCount.js
+jalview/datamodel/SearchResults.js
+jalview/datamodel/SearchResultsI.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/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/ColourMenuHelper.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/ProgressBar.js
+jalview/gui/ScalePanel.js
+jalview/gui/SeqCanvas.js
+jalview/gui/SeqPanel.js
+jalview/gui/SequenceRenderer.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/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/IdOrgSettings.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/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/awt/AWTKeyStroke.js
+java/awt/AlphaComposite.js
+java/awt/Composite.js
+java/awt/ContainerOrderFocusTraversalPolicy.js
+java/awt/DefaultFocusTraversalPolicy.js
+java/awt/DefaultKeyboardFocusManager.js
+java/awt/FocusTraversalPolicy.js
+java/awt/GridLayout.js
+java/awt/Image.js
+java/awt/KeyEventDispatcher.js
+java/awt/KeyEventPostProcessor.js
+java/awt/KeyboardFocusManager.js
+java/awt/VKCollection.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/ComponentAdapter.js
+java/awt/event/ContainerEvent.js
+java/awt/event/FocusAdapter.js
+java/awt/event/KeyAdapter.js
+java/awt/event/MouseAdapter.js
+java/awt/event/MouseMotionAdapter.js
+java/awt/geom/Path2D.js
+java/awt/geom/PathIterator.js
+java/awt/geom/RectIterator.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/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/KeyboardFocusManagerPeer.js
+java/awt/print/Printable.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/FileSystem.js
+java/io/FilterInputStream.js
+java/io/InputStream.js
+java/io/InputStreamReader.js
+java/io/PushbackInputStream.js
+java/io/Reader.js
+java/lang/AutoCloseable.js
+java/lang/Iterable.js
+java/lang/Readable.js
+java/lang/Runtime.js
+java/lang/StringBuilder.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/URLConnection.js
+java/net/URLDecoder.js
+java/net/URLStreamHandler.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/AbstractQueue.js
+java/util/AbstractSequentialList.js
+java/util/ArrayDeque.js
+java/util/BitSet.js
+java/util/Calendar.js
+java/util/Collection.js
+java/util/Comparator.js
+java/util/Deque.js
+java/util/Enumeration.js
+java/util/GregorianCalendar.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/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/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/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/JSONEncodable.js
+javajs/util/AjaxURLStreamHandler.js
+javajs/util/Encoding.js
+javajs/util/Rdr.js
+javajs/util/SB.js
+javax/swing/AbstractAction.js
+javax/swing/Action.js
+javax/swing/ComponentInputMap.js
+javax/swing/DefaultDesktopManager.js
+javax/swing/DesktopManager.js
+javax/swing/InputMap.js
+javax/swing/JDesktopPane.js
+javax/swing/JDialog.js
+javax/swing/JInternalFrame.js
+javax/swing/JProgressBar.js
+javax/swing/JScrollPane.js
+javax/swing/JTabbedPane.js
+javax/swing/JToolTip.js
+javax/swing/JViewport.js
+javax/swing/KeyStroke.js
+javax/swing/ScrollPaneConstants.js
+javax/swing/ScrollPaneLayout.js
+javax/swing/Scrollable.js
+javax/swing/Timer.js
+javax/swing/ToolTipManager.js
+javax/swing/ViewportLayout.js
+javax/swing/border/LineBorder.js
+javax/swing/event/InternalFrameAdapter.js
+javax/swing/event/InternalFrameEvent.js
+javax/swing/event/InternalFrameListener.js
+javax/swing/event/MenuListener.js
+javax/swing/plaf/ComponentInputMapUIResource.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/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/CausedFocusEvent.js
+sun/awt/KeyboardFocusManagerPeerProvider.js
+sun/awt/SunGraphicsCallback.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/swing/DefaultLookup.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/JSFocusManager.js
+swingjs/a2s/Dialog.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/JSAppletUI.js
+swingjs/plaf/JSDesktopIconUI.js
+swingjs/plaf/JSDesktopPaneUI.js
+swingjs/plaf/JSGraphicsUtils.js
+swingjs/plaf/JSInternalFrameUI.js
+swingjs/plaf/JSProgressBarUI.js
+swingjs/plaf/JSScrollPaneUI.js
+swingjs/plaf/JSTabbedPaneUI.js
+swingjs/plaf/JSToolTipUI.js
+swingjs/plaf/JSViewportUI.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
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