JAL-3210 Fixed jalviewjs dependencies. Changed linkCheck to tee output to .out file...

diff --git a/.gitignore b/.gitignore
index f313551..543fe0f 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -20,7 +20,7 @@ TESTNG
 /.gradle
 /build
 /local.properties
-/utils/HelpLinksChecker.touch
+/utils/HelpLinksChecker.out
 /getdown/website
 /getdown/full_app
 /getdown/files

diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt
deleted file mode 100644 (file)
index 9a790a0..0000000
--- a/_j2sclasslist.txt
+++ /dev/null
@@ -1,959 +0,0 @@
-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/AppletContext.js
-java/applet/AppletStub.js
-java/applet/JSApplet.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/Color.js
-java/awt/Component.js
-java/awt/ComponentOrientation.js
-java/awt/Composite.js
-java/awt/Container.js
-java/awt/ContainerOrderFocusTraversalPolicy.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/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
-java/awt/event/HierarchyListener.js
-java/awt/event/InputEvent.js
-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
-java/awt/event/WindowAdapter.js
-java/awt/event/WindowEvent.js
-java/awt/event/WindowFocusListener.js
-java/awt/event/WindowListener.js
-java/awt/event/WindowStateListener.js
-java/awt/font/FontRenderContext.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/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/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/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/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
-java/util/IdentityHashMap.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/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/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/JSThread.js
-javajs/util/Lst.js
-javajs/util/PT.js
-javajs/util/Rdr.js
-javajs/util/SB.js
-javax/swing/AbstractAction.js
-javax/swing/AbstractButton.js
-javax/swing/AbstractListModel.js
-javax/swing/Action.js
-javax/swing/ActionMap.js
-javax/swing/AncestorNotifier.js
-javax/swing/ArrayTable.js
-javax/swing/BorderFactory.js
-javax/swing/BoundedRangeModel.js
-javax/swing/BoxLayout.js
-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/InputMap.js
-javax/swing/JApplet.js
-javax/swing/JButton.js
-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
-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/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/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/RepaintManager.js
-javax/swing/RootPaneContainer.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/UIDefaults.js
-javax/swing/UIManager.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/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/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/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
-swingjs/plaf/JSAppletUI.js
-swingjs/plaf/JSButtonUI.js
-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
-swingjs/plaf/JSMenuBarUI.js
-swingjs/plaf/JSMenuItemUI.js
-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
-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/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/build.gradle b/build.gradle
index b7f2162..d45afa4 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -642,9 +642,9 @@ task copyHelp(type: Copy) {
   def outputDir = "${classes}/${helpDir}"
   from(inputDir) {
     exclude '**/*.gif'
-      exclude '**/*.jpg'
-      exclude '**/*.png'
-      filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+    exclude '**/*.jpg'
+    exclude '**/*.png'
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
   }
   from(inputDir) {
     include '**/*.gif'
@@ -737,21 +737,27 @@ task compileLinkCheck(type: JavaCompile) {
   outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
 }
 
-def helplinkscheckertouchfile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.touch")
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
+
+  def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
   classpath = files("${jalviewDir}/${utilsDir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
   def help = "${classes}/${helpDir}"
   args = [ "${classes}/${helpDir}", "-nointernet" ]
 
-  doLast {
-    helplinkscheckertouchfile.createNewFile()
-  }
+  def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
+  def errFOS = outFOS
+  standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+    outFOS,
+    standardOutput)
+  errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+    outFOS,
+    errorOutput)
 
   inputs.dir("${classes}/${helpDir}")
-  outputs.file(helplinkscheckertouchfile)
+  outputs.file(helpLinksCheckerOutFile)
 }
 
 // import the pubhtmlhelp target
@@ -1265,11 +1271,7 @@ def jalviewjsTransferSiteDir
 task jalviewjsSitePath {
   def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
   jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
-  if (jalviewjs_site_dir.startsWith('/')) {
-    jalviewjsSiteDir = jalviewjs_site_dir
-  } else {
-    jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
-  }
+  jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
   jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site"
 }
 
@@ -1283,12 +1285,13 @@ task jalviewjsSetEclipseWorkspace {
       propVal = System.getProperty("user.home") + propVal.substring(1)
     }
   }
-  def propsFileName = "${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+  def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+  def propsFile = file(propsFileName)
   def eclipseWsDir = propVal
   def props = new Properties()
 
-  if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && file(propsFileName).exists()) {
-    def ins = new FileInputStream("${jalviewDirAbsolutePath}/${propsFileName}")
+  if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
+    def ins = new FileInputStream(propsFileName)
     props.load(ins)
     ins.close()
     if (props.getProperty(propKey, null) != null) {
@@ -1296,30 +1299,32 @@ task jalviewjsSetEclipseWorkspace {
     }
   }
 
+  def writeProps = false
   if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
     def tempDir = File.createTempDir()
     eclipseWsDir = tempDir.getAbsolutePath()
-    props.setProperty(propKey, eclipseWsDir)
-    def propsFile = file(propsFileName)
-    propsFile.parentFile.mkdirs()
-    propsFile.createNewFile() // doesn't affect existing file
-    def outs = new FileOutputStream(propsFile, false)
-    props.store(outs, null)
-    outs.close()
+    writeProps = true
   }
-
   eclipseWorkspace = file(eclipseWsDir)
 
   doFirst {
+    if (writeProps) {
+      props.setProperty(propKey, eclipseWsDir)
+      propsFile.parentFile.mkdirs()
+      def bytes = new ByteArrayOutputStream()
+      props.store(bytes, null)
+      def propertiesString = bytes.toString()
+      propsFile.text = propertiesString
+    }
+
     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
   }
+
   inputs.property(propKey, eclipseWsDir)
   outputs.file(propsFileName)
 }
 
 
-def eclipseDropinsDir
-def utilsDropinsDir
 def eclipseBinary
 def eclipseVersion
 def eclipseDebug = false
@@ -1333,21 +1338,18 @@ task jalviewjsEclipsePaths {
   }
   if (OperatingSystem.current().isMacOsX()) {
     eclipseRoot += "/Eclipse.app"
-    eclipseDropinsDir = "${eclipseRoot}/Contents/Eclipse/dropins"
     eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
     eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
   } else if (OperatingSystem.current().isWindows()) { // check these paths!!
     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
       eclipseRoot += "/eclipse"
     }
-    eclipseDropinsDir = "${eclipseRoot}/dropins"
     eclipseBinary = "${eclipseRoot}/eclipse"
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
   } else { // linux or unix
     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
       eclipseRoot += "/eclipse"
     }
-    eclipseDropinsDir = "${eclipseRoot}/dropins"
     eclipseBinary = "${eclipseRoot}/eclipse"
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
   }
@@ -1371,16 +1373,15 @@ task jalviewjsEclipsePaths {
   } else {
     eclipseVersionSuffix = "_4.13"
   }
-  utilsDropinsDir = "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}${eclipseVersionSuffix}"
   */
 
-  utilsDropinsDir = "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}"
+  
   def propKey = "eclipse_debug"
   eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
 
   doFirst {
     if (!assumedVersion) {
-      println("ECLIPSE_VERSION=${eclipseVersion}")
+      println("ECLIPSE VERSION=${eclipseVersion}")
     }
   }
 }
@@ -1395,9 +1396,9 @@ task eclipseSetup {
 task OLDjalviewjsEclipseCopyDropins {
   dependsOn jalviewjsEclipsePaths
   dependsOn jalviewjsCleanEclipse
-  def inputFiles = fileTree(dir: utilsDropinsDir, include: "*.jar")
+  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
   inputFiles += file(jalviewjs_j2s_plugin)
-  def outputDir = eclipseDropinsDir
+  def outputDir = "${buildDir}/jalviewjs
 
   inputs.files inputFiles
   inputFiles.each { file ->
@@ -1419,15 +1420,12 @@ task OLDjalviewjsEclipseCopyDropins {
 task jalviewjsEclipseCopyDropins(type: Copy) {
   dependsOn jalviewjsEclipsePaths
 
-  from utilsDropinsDir
-  into eclipseDropinsDir
+  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+  inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}")
+  def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
 
-  doLast {
-    copy {
-      from jalviewjs_j2s_plugin
-      into eclipseDropinsDir
-    }
-  }
+  from inputFiles
+  into outputDir
 }
 
 // this eclipse -clean doesn't actually work
@@ -1448,10 +1446,6 @@ y
 """
   def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
   standardInput = inputByteStream
-
-  doFirst {
-    println("CLEAN ECLIPSE_DEBUG=${eclipseDebug}")
-  }
 }
 /* not really working yet
 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
@@ -1486,14 +1480,14 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
     if (val != null) {
       if (prop == siteDirProperty) {
         if (!(val.startsWith('/') || val.startsWith("file://") )) {
-          val = "${jalviewjsTransferSiteDir}/${val}"
+          val = "${jalviewDir}/${jalviewjsTransferSiteDir}/${val}"
         }
         setSiteDir = true
       }
       property(prop,val)
     }
     if (!setSiteDir) { // default site location, don't override specifically set property
-      property(siteDirProperty,jalviewjsTransferSiteDir)
+      property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteDir}")
     }
   }
   inputs.properties(j2s_props)
@@ -1555,14 +1549,9 @@ task jalviewjsProjectImport(type: Exec) {
   if (eclipseDebug) {
     args += "-debug"
   }
-  // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=utils/jalviewjs/eclipse/dropins"] here? (instead of copying plugins to eclipse dropins dir)
-
-  doFirst {
-    println("IMPORT ECLIPSE_DEBUG=${eclipseDebug}")
-  }
+  args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
 
   inputs.file("${jalviewDir}/.project")
-  outputs.dir(projdir)
   outputs.upToDateWhen { file(projdir).exists() }
 }
 
@@ -1576,67 +1565,63 @@ task jalviewjsTranspile(type: Exec) {
   if (eclipseDebug) {
     args += "-debug"
   }
-  // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=swingjs"] here? (instead of copying plugins to eclipse dropins dir)
+  args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
 
   def stdout
   def stderr
-  stdout = new ByteArrayOutputStream()
-  stderr = new ByteArrayOutputStream()
+  doFirst {
+    stdout = new ByteArrayOutputStream()
+    stderr = new ByteArrayOutputStream()
 
-  def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
-  def logOutFile = file(logOutFileName)
-  logOutFile.createNewFile()
-  logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
+    def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
+    def logOutFile = file(logOutFileName)
+    logOutFile.createNewFile()
+    logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
 BINARY: ${eclipseBinary}
 VERSION: ${eclipseVersion}
 WORKSPACE: ${eclipseWorkspace}
 DEBUG: ${eclipseDebug}
 ----
 """
-  def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
-  //def logErrFileName = "${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
-  //def logErrFile = file(logFileName)
-  //logErrFile.createNewFile()
-  //def logErrFOS = new FileErrputStream(logErrFile, false)
-  // combine stdout and stderr
-  def logErrFOS = logOutFOS
-
-  if (jalviewjs_j2s_to_console.equals("true")) {
-    standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
-      new org.apache.tools.ant.util.TeeOutputStream(
-        logOutFOS,
-        stdout),
-      standardOutput)
+    def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+    //def logErrFileName = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
+    //def logErrFile = file(logFileName)
+    //logErrFile.createNewFile()
+    //def logErrFOS = new FileErrputStream(logErrFile, false)
+    // combine stdout and stderr
+    def logErrFOS = logOutFOS
+
+    if (jalviewjs_j2s_to_console.equals("true")) {
+      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+        new org.apache.tools.ant.util.TeeOutputStream(
+          logOutFOS,
+          stdout),
+        standardOutput)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
         errorOutput)
-  } else {
-    standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
-      logOutFOS,
-      stdout)
+    } else {
+      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+        logOutFOS,
+        stdout)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logErrFOS,
         stderr)
+    }
   }
 
   doLast {
     if (stdout.toString().contains("Error processing ")) {
       // j2s did not complete transpile
-      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
+      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
     }
   }
 
-  doFirst {
-    println("TRANSPILE ECLIPSE_DEBUG=${eclipseDebug}")
-  }
-
   inputs.dir("${jalviewDir}/${sourceDir}")
-  outputs.dir("${jalviewDir}/${eclipse_bin_dir}/main")
   outputs.dir("${jalviewDir}/${jalviewjsTransferSiteDir}")
-  outputs.upToDateWhen { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() }
-
+  outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() } )
 }
 
 task jalviewjsCopyTransferSite(type: Copy) {
@@ -1667,8 +1652,8 @@ task jalviewjsBuildSite {
 
 task cleanJalviewjsSite {
   doFirst {
-    delete jalviewjsTransferSiteDir
-    delete jalviewjsSiteDir
+    delete "${jalviewDir}/${jalviewjsTransferSiteDir}"
+    delete "${jalviewDir}/${jalviewjsSiteDir}"
   }
 }
 
@@ -1685,10 +1670,10 @@ task jalviewjsSiteTar(type: Tar) {
 
   compression Compression.GZIP
 
-  from jalviewjsSiteDir
+  from "${jalviewDir}/${jalviewjsSiteDir}"
   into jalviewjs_site_dir // this is inside the tar file
 
-  inputs.dir(jalviewjsSiteDir)
+  inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
 }
 
 task jalviewjsServer {
@@ -1736,13 +1721,15 @@ task cleanJalviewjsAll {
   dependsOn jalviewjsEclipsePaths
   
   doFirst {
-    delete jalviewjsBuildDir
+    delete "${jalviewDir}/${jalviewjsBuildDir}"
     delete "${jalviewDir}/${eclipse_bin_dir}"
     if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
       delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
     }
     delete "${jalviewDir}/${jalviewjs_j2s_settings}"
   }
+
+  outputs.upToDateWhen( { false } )
 }
 
 task jalviewjs {
@@ -1753,8 +1740,8 @@ task jalviewjs {
 
 
 task jalviewjsIDECopyTransferSite(type: Copy) {
-  from jalviewjsTransferSiteDir
-  into jalviewjsSiteDir
+  from "${jalviewDir}/${jalviewjsTransferSiteDir}"
+  into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
 task jalviewjsIDEj2s {

diff --git a/gradle.properties b/gradle.properties
index 3cadc78..7569d00 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -150,7 +150,6 @@ eclipse_debug = false
 
 jalviewjs_eclipse_root = ~/buildtools/eclipse/jee-2019-09
 
-jalviewjs_utils_dir = utils/jalviewjs
 jalviewjs_eclipse_dropins_dir = utils/jalviewjs/eclipse/dropins
 jalviewjs_swingjs_zip = swingjs/SwingJS-site.zip
 jalviewjs_j2s_plugin = swingjs/net.sf.j2s.core.jar
@@ -159,6 +158,7 @@ jalviewjs_site_resource_dir = utils/jalviewjs/site-resources
 jalviewjs_j2s_settings = .j2s
 #jalviewjs_eclipse_workspace = ~/tmp/eclipse-workspace
 # these 3 files/dirs found in build/jalviewjs
+jalviewjs_eclipse_tmp_dropins_dir = eclipse_dropins
 jalviewjs_eclipse_workspace_location_file = eclipse_workspace_location
 jalviewjs_site_dir = site
 jalviewjs_j2s_subdir = swingjs/j2s