JAL-3658 Now only making cores from utils/jalviewjs/classlists/*.txt

diff --git a/build.gradle b/build.gradle
index 0be087f..86e984c 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -457,7 +457,6 @@ ext {
   jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
   jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
   jalviewjsJalviewCoreHtmlFile = string("")
-  jalviewjsJalviewCoreName = string(jalviewjs_core_name)
   jalviewjsCoreClasslists = []
   jalviewjsJalviewTemplateName = string(jalviewjs_name)
   jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
@@ -2523,10 +2522,6 @@ task jalviewjsBuildAllCores {
     ]
   }
 
-  // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
-  //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
-  classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
-
   jalviewjsCoreClasslists = []
 
   classlistFiles.each {
@@ -2549,8 +2544,8 @@ task jalviewjsBuildAllCores {
     }
     def list = fileTree(dir: j2sDir, includes: filelist)
 
-    def jsfile = "${outputDir}/core${name}.js"
-    def zjsfile = "${outputDir}/core${name}.z.js"
+    def jsfile = "${outputDir}/core_${name}.js"
+    def zjsfile = "${outputDir}/core_${name}.z.js"
 
     jalviewjsCoreClasslists += [
       'jsfile': jsfile,
@@ -2565,21 +2560,8 @@ task jalviewjsBuildAllCores {
     outputs.file(zjsfile)
   }
   
-  // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
-  def stevesoftClasslistName = "_stevesoft"
-  def stevesoftClasslist = [
-    'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
-    'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
-    'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
-    'name': stevesoftClasslistName
-  ]
-  jalviewjsCoreClasslists += stevesoftClasslist
-  inputs.files(stevesoftClasslist['list'])
-  outputs.file(stevesoftClasslist['jsfile'])
-  outputs.file(stevesoftClasslist['zjsfile'])
-
   // _all core
-  def allClasslistName = "_all"
+  def allClasslistName = "all"
   def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
   allJsFiles += fileTree(
     dir: libJ2sDir,
@@ -2602,8 +2584,8 @@ task jalviewjsBuildAllCores {
     ]
   )
   def allClasslist = [
-    'jsfile': "${outputDir}/core${allClasslistName}.js",
-    'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+    'jsfile': "${outputDir}/core_${allClasslistName}.js",
+    'zjsfile': "${outputDir}/core_${allClasslistName}.z.js",
     'list': allJsFiles,
     'name': allClasslistName
   ]

diff --git a/gradle.properties b/gradle.properties
index b99cdca..e700114 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -161,7 +161,6 @@ jalviewjs_j2s_plugin = swingjs/net.sf.j2s.core-j11.jar
 jalviewjs_libjs_dir = utils/jalviewjs/libjs
 jalviewjs_site_resource_dir = utils/jalviewjs/site-resources
 jalviewjs_classlists_dir = utils/jalviewjs/classlists
-jalviewjs_classlist_jalview = utils/jalviewjs/_j2sclasslist.txt
 jalviewjs_j2s_settings = .j2s
 #jalviewjs_eclipse_workspace = ~/tmp/eclipse-workspace
 # these 3 files/dirs found in build/jalviewjs
@@ -177,7 +176,6 @@ jalviewjs_eclipse_build_arg = cleanBuild
 jalviewjs_server_port = 9001
 jalviewjs_server_wait = 30
 jalviewjs_server_resource = /jalview_bin_Jalview.html
-jalviewjs_core_name = _jalview
 jalviewjs_name = JalviewJS
 jalviewjs_core_key = core
 #jalviewjs_core_key = preloadCore

diff --git a/utils/jalviewjs/_j2sclasslist.txt b/utils/jalviewjs/_j2sclasslist.txt
deleted file mode 100644 (file)
index e60fe60..0000000
--- a/utils/jalviewjs/_j2sclasslist.txt
+++ /dev/null
@@ -1,395 +0,0 @@
-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/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/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/dnd/peer/DropTargetPeer.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/ContainerListener.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/KeyListener.js
-java/awt/event/MouseEvent.js
-java/awt/event/MouseListener.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/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/Rectangle2D.js
-java/awt/geom/RectangularShape.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/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/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/lang/AbstractStringBuilder.js
-java/lang/Class.js
-java/lang/Enum.js
-java/lang/Iterable.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/math/RoundingMode.js
-java/net/URL.js
-java/net/URLStreamHandlerFactory.js
-java/text/CharacterIterator.js
-java/text/DecimalFormat.js
-java/text/DecimalFormatSymbols.js
-java/text/DigitList.js
-java/text/FieldPosition.js
-java/text/Format.js
-java/text/NumberFormat.js
-java/util/AbstractCollection.js
-java/util/AbstractList.js
-java/util/AbstractMap.js
-java/util/AbstractSequentialList.js
-java/util/AbstractSet.js
-java/util/ArrayList.js
-java/util/Arrays.js
-java/util/Collection.js
-java/util/Collections.js
-java/util/Comparator.js
-java/util/Deque.js
-java/util/Dictionary.js
-java/util/Enumeration.js
-java/util/EventListener.js
-java/util/EventObject.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/ListResourceBundle.js
-java/util/Locale.js
-java/util/Map.js
-java/util/Objects.js
-java/util/Queue.js
-java/util/Random.js
-java/util/RandomAccess.js
-java/util/ResourceBundle.js
-java/util/Set.js
-java/util/TimSort.js
-java/util/Vector.js
-javajs/api/JSFunction.js
-javajs/util/AjaxURLConnection.js
-javajs/util/AjaxURLStreamHandlerFactory.js
-javajs/util/AU.js
-javajs/util/JSThread.js
-javajs/util/Lst.js
-javajs/util/PT.js
-javajs/util/SB.js
-javax/net/ssl/HttpsUrlConnection.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/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
-javax/swing/ButtonGroup.js
-javax/swing/ButtonModel.js
-javax/swing/ClientPropertyKey.js
-javax/swing/ComboBoxModel.js
-javax/swing/DefaultBoundedRangeModel.js
-javax/swing/DefaultButtonModel.js
-javax/swing/DefaultComboBoxModel.js
-javax/swing/DefaultSingleSelectionModel.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
-javax/swing/JCheckBox.js
-javax/swing/JCheckBoxMenuItem.js
-javax/swing/JComboBox.js
-javax/swing/JComponent.js
-javax/swing/JFrame.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/JRadioButtonMenuItem.js
-javax/swing/JRootPane.js
-javax/swing/JScrollBar.js
-javax/swing/JScrollPane.js
-javax/swing/JSeparator.js
-javax/swing/JTextArea.js
-javax/swing/JTextField.js
-javax/swing/JToggleButton.js
-javax/swing/JViewport.js
-javax/swing/KeyboardManager.js
-javax/swing/KeyStroke.js
-javax/swing/ListModel.js
-javax/swing/LookAndFeel.js
-javax/swing/MenuElement.js
-javax/swing/MutableComboBoxModel.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/SingleSelectionModel.js
-javax/swing/SizeRequirements.js
-javax/swing/SwingConstants.js
-javax/swing/SwingPaintEventDispatcher.js
-javax/swing/SwingUtilities.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
-sun/awt/AppContext.js
-sun/awt/AWTAutoShutdown.js
-sun/awt/CausedFocusEvent.js
-sun/awt/ComponentFactory.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/SunToolkit.js
-sun/awt/WindowClosingListener.js
-sun/awt/WindowClosingSupport.js
-sun/font/FontDesignMetrics.js
-sun/swing/DefaultLookup.js
-sun/swing/SwingLazyValue.js
-sun/text/resources/FormatData.js
-sun/text/resources/en/FormatData_en.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/JSAppletThread.js
-swingjs/JSAppletViewer.js
-swingjs/JSFocusPeer.js
-swingjs/JSFontMetrics.js
-swingjs/JSFrameViewer.js
-swingjs/JSGraphics2D.js
-swingjs/JSGraphicsConfiguration.js
-swingjs/JSGraphicsEnvironment.js
-swingjs/JSMouse.js
-swingjs/JSNullComponentPeer.js
-swingjs/JSScreenDevice.js
-swingjs/JSThreadGroup.js
-swingjs/JSToolkit.js
-swingjs/JSUtil.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/JSEventHandler.js
-swingjs/plaf/JSFrameUI.js
-swingjs/plaf/JSGraphicsUtils.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/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/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/plaf/TextListener.js
-
-

diff --git a/utils/jalviewjs/classlists/jalview.txt b/utils/jalviewjs/classlists/jalview.txt
index 5d60006..e60fe60 100644 (file)
--- a/utils/jalviewjs/classlists/jalview.txt
+++ b/utils/jalviewjs/classlists/jalview.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/text/resources/en/FormatData_en.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
@@ -773,19 +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
+swingjs/plaf/TextListener.js
+
+

diff --git a/utils/jalviewjs/classlists/jvexamplefile.txt b/utils/jalviewjs/classlists/jvexamplefile.txt
deleted file mode 100644 (file)
index ae01fe1..0000000
--- a/utils/jalviewjs/classlists/jvexamplefile.txt
+++ /dev/null
@@ -1,1183 +0,0 @@
-
-com/stevesoft/pat/Any.js
-com/stevesoft/pat/Bracket.js
-com/stevesoft/pat/Branch.js
-com/stevesoft/pat/CaseMgr.js
-com/stevesoft/pat/DotMulti.js
-com/stevesoft/pat/End.js
-com/stevesoft/pat/FastBracket.js
-com/stevesoft/pat/FastChar.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/NullPattern.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/RegHolder.js
-com/stevesoft/pat/RegOpt.js
-com/stevesoft/pat/RegRes.js
-com/stevesoft/pat/Regex.js
-com/stevesoft/pat/ReplaceRule.js
-com/stevesoft/pat/Replacer.js
-com/stevesoft/pat/Rthings.js
-com/stevesoft/pat/Skip.js
-com/stevesoft/pat/StrPos.js
-com/stevesoft/pat/StringLike.js
-com/stevesoft/pat/StringRule.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/patInf.js
-com/stevesoft/pat/patInt.js
-com/stevesoft/pat/wrap/StringWrap.js
-intervalstore/api/IntervalI.js
-intervalstore/api/IntervalStoreI.js
-intervalstore/impl/BinarySearcher.js
-intervalstore/impl/IntervalStore.js
-intervalstore/impl/NCList.js
-intervalstore/impl/NCNode.js
-jalview/analysis/AAFrequency.js
-jalview/analysis/AlignSeq.js
-jalview/analysis/AlignmentAnnotationUtils.js
-jalview/analysis/AlignmentUtils.js
-jalview/analysis/AnnotationSorter.js
-jalview/analysis/AverageDistanceTree.js
-jalview/analysis/Conservation.js
-jalview/analysis/CrossRef.js
-jalview/analysis/GeneticCodeI.js
-jalview/analysis/GeneticCodes.js
-jalview/analysis/Grouping.js
-jalview/analysis/NJTree.js
-jalview/analysis/SeqsetUtils.js
-jalview/analysis/SequenceIdMatcher.js
-jalview/analysis/TreeBuilder.js
-jalview/analysis/TreeModel.js
-jalview/analysis/scoremodels/DistanceScoreModel.js
-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/AlignmentColsCollectionI.js
-jalview/api/AlignmentRowsCollectionI.js
-jalview/api/AlignmentViewPanel.js
-jalview/api/BuildDetailsI.js
-jalview/api/DBRefEntryI.js
-jalview/api/FeatureColourI.js
-jalview/api/FeatureRenderer.js
-jalview/api/FeatureSettingsControllerI.js
-jalview/api/FeatureSettingsModelI.js
-jalview/api/FeaturesDisplayedI.js
-jalview/api/OOMHandlerI.js
-jalview/api/RendererListenerI.js
-jalview/api/SequenceRenderer.js
-jalview/api/SequenceStructureBinding.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/api/structures/JalviewStructureDisplayI.js
-jalview/bin/ArgsParser.js
-jalview/bin/BuildDetails.js
-jalview/bin/Cache.js
-jalview/bin/Jalview.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/DBRefEntry.js
-jalview/datamodel/DBRefSource.js
-jalview/datamodel/GraphLine.js
-jalview/datamodel/HiddenColumns.js
-jalview/datamodel/HiddenColumnsCursor.js
-jalview/datamodel/HiddenCursorPosition.js
-jalview/datamodel/HiddenSequences.js
-jalview/datamodel/Mapping.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/RangeElementsIterator.js
-jalview/datamodel/RangeIterator.js
-jalview/datamodel/ResidueCount.js
-jalview/datamodel/SearchResultMatchI.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/StartRegionIterator.js
-jalview/datamodel/StructureViewerModel.js
-jalview/datamodel/VisibleColsCollection.js
-jalview/datamodel/VisibleContigsIterator.js
-jalview/datamodel/VisibleRowsCollection.js
-jalview/datamodel/VisibleRowsIterator.js
-jalview/datamodel/features/FeatureAttributes.js
-jalview/datamodel/features/FeatureLocationI.js
-jalview/datamodel/features/FeatureMatcherSet.js
-jalview/datamodel/features/FeatureMatcherSetI.js
-jalview/datamodel/features/FeatureSources.js
-jalview/datamodel/features/FeatureStore.js
-jalview/datamodel/features/SequenceFeatures.js
-jalview/datamodel/features/SequenceFeaturesI.js
-jalview/ext/ensembl/EnsemblData.js
-jalview/ext/ensembl/EnsemblGene.js
-jalview/ext/ensembl/EnsemblGenomes.js
-jalview/ext/ensembl/EnsemblRestClient.js
-jalview/ext/ensembl/EnsemblSeqProxy.js
-jalview/ext/ensembl/EnsemblSequenceFetcher.js
-jalview/ext/jmol/JalviewJmolBinding.js
-jalview/ext/jmol/JmolCommands.js
-jalview/ext/jmol/JmolParser.js
-jalview/fts/api/FTSData.js
-jalview/fts/api/FTSDataColumnI.js
-jalview/fts/api/FTSRestClientI.js
-jalview/fts/api/GFTSPanelI.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/core/GFTSPanel.js
-jalview/fts/service/pdb/PDBFTSPanel.js
-jalview/fts/service/pdb/PDBFTSRestClient.js
-jalview/fts/service/uniprot/UniProtFTSRestClient.js
-jalview/fts/service/uniprot/UniprotFTSPanel.js
-jalview/gui/AlignFrame.js
-jalview/gui/AlignViewport.js
-jalview/gui/AlignmentPanel.js
-jalview/gui/AnnotationColumnChooser.js
-jalview/gui/AnnotationLabels.js
-jalview/gui/AnnotationPanel.js
-jalview/gui/AnnotationRowFilter.js
-jalview/gui/AppJmol.js
-jalview/gui/AppJmolBinding.js
-jalview/gui/CalculationChooser.js
-jalview/gui/ColourMenuHelper.js
-jalview/gui/ComboBoxTooltipRenderer.js
-jalview/gui/Desktop.js
-jalview/gui/FeatureRenderer.js
-jalview/gui/FeatureSettings.js
-jalview/gui/FeatureTypeSettings.js
-jalview/gui/FontChooser.js
-jalview/gui/IProgressIndicator.js
-jalview/gui/IdCanvas.js
-jalview/gui/IdPanel.js
-jalview/gui/IdwidthAdjuster.js
-jalview/gui/JalviewBooleanRadioButtons.js
-jalview/gui/JalviewChangeSupport.js
-jalview/gui/JalviewColourChooser.js
-jalview/gui/JalviewDialog.js
-jalview/gui/JvSwingUtils.js
-jalview/gui/OverviewCanvas.js
-jalview/gui/OverviewPanel.js
-jalview/gui/PaintRefresher.js
-jalview/gui/PopupMenu.js
-jalview/gui/Preferences.js
-jalview/gui/ProgressBar.js
-jalview/gui/ProgressPanel.js
-jalview/gui/ScalePanel.js
-jalview/gui/SeqCanvas.js
-jalview/gui/SeqPanel.js
-jalview/gui/SequenceFetcher.js
-jalview/gui/SequenceRenderer.js
-jalview/gui/SliderPanel.js
-jalview/gui/StructureChooser.js
-jalview/gui/StructureViewer.js
-jalview/gui/StructureViewerBase.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/AnnotationFile.js
-jalview/io/AppletFormatAdapter.js
-jalview/io/DataSourceType.js
-jalview/io/FastaFile.js
-jalview/io/FileFormat.js
-jalview/io/FileFormatI.js
-jalview/io/FileFormats.js
-jalview/io/FileLoader.js
-jalview/io/FileParse.js
-jalview/io/FormatAdapter.js
-jalview/io/IdentifyFile.js
-jalview/io/JPredFile.js
-jalview/io/JalviewFileChooser.js
-jalview/io/JalviewFileFilter.js
-jalview/io/JalviewFileView.js
-jalview/io/JnetAnnotationMaker.js
-jalview/io/NewickFile.js
-jalview/io/PDBFeatureSettings.js
-jalview/io/PIRFile.js
-jalview/io/ScoreMatrixFile.js
-jalview/io/SequenceAnnotationReport.js
-jalview/io/StructureFile.js
-jalview/io/TCoffeeScoreFile.js
-jalview/io/cache/JvCacheableInputBox.js
-jalview/javascript/json/JSON.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/javascript/web/Client.js
-jalview/javascript/web/ClientResponse.js
-jalview/javascript/web/WebResource.js
-jalview/jbgui/BackupFilesPresetEntry.js
-jalview/jbgui/GAlignFrame.js
-jalview/jbgui/GAlignmentPanel.js
-jalview/jbgui/GDesktop.js
-jalview/jbgui/GFontChooser.js
-jalview/jbgui/GPreferences.js
-jalview/jbgui/GSliderPanel.js
-jalview/jbgui/GStructureChooser.js
-jalview/jbgui/GStructureViewer.js
-jalview/jbgui/GTreePanel.js
-jalview/jbgui/IntKeyStringValueEntry.js
-jalview/math/Matrix.js
-jalview/math/MatrixI.js
-jalview/project/Jalview2XML.js
-jalview/renderer/AnnotationRenderer.js
-jalview/renderer/AwtRenderPanelI.js
-jalview/renderer/OverviewRenderer.js
-jalview/renderer/OverviewResColourFinder.js
-jalview/renderer/ResidueColourFinder.js
-jalview/renderer/ResidueShader.js
-jalview/renderer/ResidueShaderI.js
-jalview/renderer/ScaleRenderer.js
-jalview/renderer/seqfeatures/FeatureColourFinder.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/FeatureSettingsAdapter.js
-jalview/schemes/HelixColourScheme.js
-jalview/schemes/HydrophobicColourScheme.js
-jalview/schemes/IdColourScheme.js
-jalview/schemes/JalviewColourScheme.js
-jalview/schemes/NucleotideColourScheme.js
-jalview/schemes/PIDColourScheme.js
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diff --git a/utils/jalviewjs/classlists/_jvjmol.txt b/utils/jalviewjs/classlists/jvjmol.txt
similarity index 100%
rename from utils/jalviewjs/classlists/_jvjmol.txt
rename to utils/jalviewjs/classlists/jvjmol.txt

diff --git a/utils/jalviewjs/classlists/stevesoft.txt b/utils/jalviewjs/classlists/stevesoft.txt
new file mode 100644 (file)
index 0000000..e8f1747
--- /dev/null
+++ b/utils/jalviewjs/classlists/stevesoft.txt
@@ -0,0 +1,105 @@
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