From: BobHanson <hansonr@stolaf.edu>
Date: Wed, 30 Oct 2019 19:53:56 +0000 (-0500)
Subject: JAL-3210 new transpiler fixes problem that it could have a null-pointer
X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~83^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9fc58cdcb5f7c768aabc2c73b754cf3c444bd7d7

JAL-3210 new transpiler fixes problem that it could have a null-pointer
exception for comparison to history, where, apparently,
IProject.getProject().getLocation() is null.
---

diff --git a/swingjs/DEV_NOTES.txt b/swingjs/DEV_NOTES.txt
new file mode 100644
index 0000000..751d81c
--- /dev/null
+++ b/swingjs/DEV_NOTES.txt
@@ -0,0 +1,10 @@
+This is sources/net.sf.j2s.java.core/dist/DEV_NOTES.txt
+
+_j2sclasslist.txt 
+
+the list of .js files concatenated into coreswingjs.js and minified to coreswingjs.z.js
+
+
+SwingJS-site.zip
+
+the full site directory for SwingJS including all files not in the test/ directory.
diff --git a/swingjs/README.txt b/swingjs/README.txt
new file mode 100644
index 0000000..f45850b
--- /dev/null
+++ b/swingjs/README.txt
@@ -0,0 +1,8 @@
+The swingjs directory contains the current transpiler (net.sf.j2s.core.jar) 
+and the run-time core site files (SwingJS-site.zip)
+
+In addition are version directories -- for example, ver/3.1.1 and ver/3.2.1
+
+The second of these, ver/3.2.1, adds Java 8 functionality.
+
+
diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index 07753fb..b5efc84 100644
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ
diff --git a/swingjs/_j2sclasslist.txt b/swingjs/_j2sclasslist.txt
index 9a790a0..e35111e 100644
--- a/swingjs/_j2sclasslist.txt
+++ b/swingjs/_j2sclasslist.txt
@@ -1,313 +1,35 @@
-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/Applet.js
 java/applet/AppletContext.js
 java/applet/AppletStub.js
 java/applet/JSApplet.js
+java/awt/ActiveEvent.js
+java/awt/Adjustable.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/Button.js
 java/awt/Color.js
+java/awt/color/ColorSpace.js
 java/awt/Component.js
 java/awt/ComponentOrientation.js
-java/awt/Composite.js
-java/awt/Container.js
 java/awt/ContainerOrderFocusTraversalPolicy.js
+java/awt/Container.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/AWTEventListener.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
@@ -317,13 +39,9 @@ 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
@@ -332,124 +50,103 @@ java/awt/event/WindowEvent.js
 java/awt/event/WindowFocusListener.js
 java/awt/event/WindowListener.js
 java/awt/event/WindowStateListener.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/font/FontRenderContext.js
+java/awt/FontMetrics.js
+java/awt/Frame.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/geom/RectIterator.js
+java/awt/GraphicsCallback.js
+java/awt/GraphicsConfiguration.js
+java/awt/GraphicsDevice.js
+java/awt/GraphicsEnvironment.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/Insets.js
+java/awt/ItemSelectable.js
+java/awt/JSComponent.js
+java/awt/JSDialog.js
+java/awt/JSFrame.js
+java/awt/JSPanel.js
+java/awt/KeyboardFocusManager.js
+java/awt/KeyEventDispatcher.js
+java/awt/KeyEventPostProcessor.js
+java/awt/Label.js
+java/awt/LayoutManager.js
+java/awt/LayoutManager2.js
+java/awt/LightweightDispatcher.js
+java/awt/Paint.js
+java/awt/Panel.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/awt/Point.js
+java/awt/Queue.js
+java/awt/Rectangle.js
+java/awt/RenderingHints.js
+java/awt/Scrollbar.js
+java/awt/ScrollPane.js
+java/awt/Shape.js
+java/awt/Stroke.js
+java/awt/TextArea.js
+java/awt/TextComponent.js
+java/awt/TextField.js
+java/awt/Toolkit.js
+java/awt/Transparency.js
+java/awt/Window.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/reflect/Constructor.js
+java/lang/reflect/Method.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
@@ -458,75 +155,26 @@ 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/Random.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/AU.js
 javajs/util/JSThread.js
 javajs/util/Lst.js
 javajs/util/PT.js
-javajs/util/Rdr.js
 javajs/util/SB.js
+javax/net/ssl/HttpsUrlConnection.js
 javax/swing/AbstractAction.js
 javax/swing/AbstractButton.js
 javax/swing/AbstractListModel.js
@@ -534,6 +182,13 @@ javax/swing/Action.js
 javax/swing/ActionMap.js
 javax/swing/AncestorNotifier.js
 javax/swing/ArrayTable.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/BorderFactory.js
 javax/swing/BoundedRangeModel.js
 javax/swing/BoxLayout.js
@@ -541,14 +196,31 @@ 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/DropMode.js
+javax/swing/event/AncestorEvent.js
+javax/swing/event/AncestorListener.js
+javax/swing/event/CaretEvent.js
+javax/swing/event/CaretListener.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/ListDataEvent.js
+javax/swing/event/ListDataListener.js
+javax/swing/event/UndoableEditEvent.js
+javax/swing/event/UndoableEditListener.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
@@ -556,10 +228,7 @@ 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
@@ -567,179 +236,124 @@ 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/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/ListCellRenderer.js
+javax/swing/KeyStroke.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/plaf/ActionMapUIResource.js
+javax/swing/plaf/basic/BasicBorders.js
+javax/swing/plaf/BorderUIResource.js
+javax/swing/plaf/ColorUIResource.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/RepaintManager.js
 javax/swing/RootPaneContainer.js
+javax/swing/Scrollable.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/text/AbstractDocument.js
+javax/swing/text/AttributeSet.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/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/tree/TreeNode.js
 javax/swing/UIDefaults.js
 javax/swing/UIManager.js
+javax/swing/undo/AbstractUndoableEdit.js
+javax/swing/undo/CompoundEdit.js
+javax/swing/undo/UndoableEdit.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/AWTAutoShutdown.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/a2s/A2SContainer.js
+swingjs/a2s/A2SEvent.js
+swingjs/a2s/A2SListener.js
+swingjs/a2s/Applet.js
+swingjs/a2s/Button.js
+swingjs/a2s/Label.js
+swingjs/a2s/Panel.js
+swingjs/a2s/Scrollbar.js
+swingjs/a2s/ScrollPane.js
+swingjs/a2s/TextArea.js
+swingjs/a2s/TextField.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/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/JSNullComponentPeer.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
@@ -749,12 +363,9 @@ 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
@@ -764,8 +375,6 @@ 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
@@ -773,187 +382,14 @@ 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/JSTextAreaUI.js
+swingjs/plaf/JSTextFieldUI.js
+swingjs/plaf/JSTextUI.js
+swingjs/plaf/JSTextViewUI.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
-intervalstore/api/IntervalI.js
-intervalstore/api/IntervalStoreI.js
-intervalstore/impl/BinarySearcher.js
-intervalstore/impl/IntervalStore.js
-jalview/analysis/GeneticCodeI.js
-jalview/analysis/GeneticCodes.js
-jalview/api/FeaturesSourceI.js
-jalview/io/FastaFile.js
-jalview/io/FeaturesFile.js
-jalview/io/FormatAdapter.js
-jalview/schemes/IdColourScheme.js
-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/HttpsURLConnection.js
-java/net/URI.js
-java/util/ComparableTimSort.js
-java/util/LinkedHashSet.js
-java/util/WeakHashMap.js
-javajs/util/Base64.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
diff --git a/swingjs/net.sf.j2s.core.jar b/swingjs/net.sf.j2s.core.jar
index 341a2b3..e2efdd4 100644
Binary files a/swingjs/net.sf.j2s.core.jar and b/swingjs/net.sf.j2s.core.jar differ
diff --git a/swingjs/timestamp b/swingjs/timestamp
index 35434c5..d4e34e1 100644
--- a/swingjs/timestamp
+++ b/swingjs/timestamp
@@ -1 +1 @@
-20191029103701 
+20191030143851 
diff --git a/swingjs/ver/3.2.4/DEV_NOTES.txt b/swingjs/ver/3.2.4/DEV_NOTES.txt
new file mode 100644
index 0000000..751d81c
--- /dev/null
+++ b/swingjs/ver/3.2.4/DEV_NOTES.txt
@@ -0,0 +1,10 @@
+This is sources/net.sf.j2s.java.core/dist/DEV_NOTES.txt
+
+_j2sclasslist.txt 
+
+the list of .js files concatenated into coreswingjs.js and minified to coreswingjs.z.js
+
+
+SwingJS-site.zip
+
+the full site directory for SwingJS including all files not in the test/ directory.
diff --git a/swingjs/ver/3.2.4/SwingJS-site.zip b/swingjs/ver/3.2.4/SwingJS-site.zip
index 07753fb..b5efc84 100644
Binary files a/swingjs/ver/3.2.4/SwingJS-site.zip and b/swingjs/ver/3.2.4/SwingJS-site.zip differ
diff --git a/swingjs/ver/3.2.4/_j2sclasslist.txt b/swingjs/ver/3.2.4/_j2sclasslist.txt
new file mode 100644
index 0000000..e35111e
--- /dev/null
+++ b/swingjs/ver/3.2.4/_j2sclasslist.txt
@@ -0,0 +1,395 @@
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+
+
diff --git a/swingjs/ver/3.2.4/net.sf.j2s.core.jar b/swingjs/ver/3.2.4/net.sf.j2s.core.jar
index 341a2b3..e2efdd4 100644
Binary files a/swingjs/ver/3.2.4/net.sf.j2s.core.jar and b/swingjs/ver/3.2.4/net.sf.j2s.core.jar differ
diff --git a/swingjs/ver/3.2.4/timestamp b/swingjs/ver/3.2.4/timestamp
index 35434c5..d4e34e1 100644
--- a/swingjs/ver/3.2.4/timestamp
+++ b/swingjs/ver/3.2.4/timestamp
@@ -1 +1 @@
-20191029103701 
+20191030143851