jalview/analysis/AlignSeq.js
jalview/analysis/AlignmentAnnotationUtils.js
jalview/analysis/AlignmentUtils.js
+jalview/analysis/AlignmentSorter.js
jalview/analysis/AnnotationSorter.js
jalview/analysis/Conservation.js
jalview/analysis/CrossRef.js
jalview/analysis/NJTree.js
jalview/analysis/SeqsetUtils.js
+jalview/analysis/SequenceIdMatcher.js
jalview/analysis/TreeBuilder.js
jalview/analysis/TreeModel.js
jalview/analysis/scoremodels/DistanceScoreModel.js
jalview/api/AlignCalcWorkerI.js
jalview/api/AlignViewControllerGuiI.js
jalview/api/AlignViewControllerI.js
+jalview/api/AlignFrameI.js
jalview/api/AlignViewportI.js
jalview/api/AlignmentViewPanel.js
jalview/api/BuildDetailsI.js
jalview/api/FeatureColourI.js
jalview/api/FeatureRenderer.js
jalview/api/FeaturesDisplayedI.js
+jalview/api/JalviewApp.js
jalview/api/OOMHandlerI.js
jalview/api/SequenceRenderer.js
jalview/api/StructureSelectionManagerProvider.js
jalview/api/analysis/PairwiseScoreModelI.js
jalview/api/analysis/ScoreModelI.js
jalview/api/analysis/SimilarityParamsI.js
+jalview/bin/AppletParams.js
+jalview/bin/ApplicationSingletonProvider.js
jalview/bin/ArgsParser.js
jalview/bin/BuildDetails.js
jalview/bin/Cache.js
jalview/bin/Jalview.js
-jalview/bin/JalviewJS2.js
+jalview/bin/JalviewAppLoader.js
+jalview/commands/CommandI.js
+jalview/commands/OrderCommand.js
jalview/controller/AlignViewController.js
jalview/datamodel/ASequence.js
jalview/datamodel/ASequenceI.js
jalview/datamodel/features/FeatureMatcherSet.js
jalview/datamodel/features/FeatureMatcherSetI.js
jalview/datamodel/features/FeatureStore.js
-jalview/datamodel/features/RangeComparator.js
+jalview/datamodel/features/FeatureStoreI.js
+jalview/datamodel/features/FeatureStoreJS.js
+
jalview/datamodel/features/SequenceFeatures.js
jalview/datamodel/features/SequenceFeaturesI.js
jalview/gui/AlignFrame.js
jalview/io/FileLoader.js
jalview/io/FileParse.js
jalview/io/IdentifyFile.js
+jalview/io/NewickFile.js
jalview/io/PIRFile.js
jalview/io/ScoreMatrixFile.js
jalview/io/SequenceAnnotationReport.js
+jalview/javascript/JalviewLiteJSApi.js
jalview/javascript/log4j/ConsoleAppender.js
jalview/javascript/log4j/Layout.js
jalview/javascript/log4j/Level.js
jalview/schemes/ColourSchemeI.js
jalview/schemes/ColourSchemeProperty.js
jalview/schemes/ColourSchemes.js
+jalview/schemes/ColourSchemeLoader.js
+jalview/schemes/UserColourScheme.js
jalview/schemes/Consensus.js
jalview/schemes/FeatureColour.js
jalview/schemes/HelixColourScheme.js
jalview/schemes/TCoffeeColourScheme.js
jalview/schemes/TaylorColourScheme.js
jalview/schemes/TurnColourScheme.js
+jalview/schemes/UserColourScheme.js
jalview/schemes/ZappoColourScheme.js
jalview/structure/CommandListener.js
jalview/structure/SelectionListener.js
javax/swing/DefaultListCellRenderer.js
javax/swing/DefaultSingleSelectionModel.js
javax/swing/DesktopManager.js
+javax/swing/FocusManager.js
+javax/swing/InternalFrameFocusTraversalPolicy.js
+javax/swing/LayoutComparator.js
+javax/swing/LayoutFocusTraversalPolicy.js
+javax/swing/SortingFocusTraversalPolicy.js
+javax/swing/SwingContainerOrderFocusTraversalPolicy.js
+javax/swing/SwingDefaultFocusTraversalPolicy.js
javax/swing/InputMap.js
javax/swing/JApplet.js
javax/swing/JButton.js
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
swingjs/JSAppletThread.js
swingjs/JSAppletViewer.js
swingjs/JSCharSet.js
+swingjs/JSDummyApplet.js
swingjs/JSFocusPeer.js
swingjs/JSFontMetrics.js
swingjs/JSFrameViewer.js
swingjs/xml/JSXMLStreamReader.js
intervalstore/api/IntervalI.js
intervalstore/api/IntervalStoreI.js
-intervalstore/impl/BinarySearcher.js
-intervalstore/impl/IntervalStore.js
+intervalstore/nonc/IntervalStore.js
jalview/analysis/GeneticCodeI.js
jalview/analysis/GeneticCodes.js
jalview/api/FeaturesSourceI.js
java/awt/TextComponent.js
java/awt/image/ImageConsumer.js
java/io/ObjectStreamField.js
-java/net/HttpsURLConnection.js
java/net/URI.js
java/util/ComparableTimSort.js
java/util/LinkedHashSet.js
java/util/WeakHashMap.js
javajs/util/Base64.js
+javax/net/ssl/HttpsURLConnection.js
javax/swing/CellRendererPane.js
javax/swing/DefaultListSelectionModel.js
javax/swing/DefaultRowSorter.js