jalview/analysis/AAFrequency.js
jalview/analysis/AlignSeq.js
jalview/analysis/AnnotationSorter.js
jalview/analysis/Conservation.js
jalview/analysis/CrossRef.js
jalview/analysis/scoremodels/DistanceScoreModel.js
jalview/analysis/scoremodels/FeatureDistanceModel.js
jalview/analysis/scoremodels/PIDModel.js
jalview/analysis/scoremodels/ScoreMatrix.js
jalview/analysis/scoremodels/ScoreModels.js
jalview/analysis/scoremodels/SimilarityScoreModel.js
jalview/api/AlignCalcManagerI.js
jalview/api/AlignCalcWorkerI.js
jalview/api/AlignViewControllerGuiI.js
jalview/api/AlignViewControllerI.js
jalview/api/AlignViewportI.js
jalview/api/AlignmentViewPanel.js
jalview/api/BuildDetailsI.js
jalview/api/FeatureColourI.js
jalview/api/FeatureRenderer.js
jalview/api/FeaturesDisplayedI.js
jalview/api/OOMHandlerI.js
jalview/api/SequenceRenderer.js
jalview/api/StructureSelectionManagerProvider.js
jalview/api/ViewStyleI.js
jalview/api/analysis/PairwiseScoreModelI.js
jalview/api/analysis/ScoreModelI.js
jalview/bin/ArgsParser.js
jalview/bin/BuildDetails.js
jalview/bin/Cache.js
jalview/bin/Jalview.js
jalview/bin/JalviewJS2.js
jalview/controller/AlignViewController.js
jalview/datamodel/ASequence.js
jalview/datamodel/ASequenceI.js
jalview/datamodel/Alignment.js
jalview/datamodel/AlignmentAnnotation.js
jalview/datamodel/AlignmentI.js
jalview/datamodel/AnnotatedCollectionI.js
jalview/datamodel/Annotation.js
jalview/datamodel/ColumnSelection.js
jalview/datamodel/ContiguousI.js
jalview/datamodel/DBRefSource.js
jalview/datamodel/HiddenColumns.js
jalview/datamodel/HiddenColumnsCursor.js
jalview/datamodel/HiddenCursorPosition.js
jalview/datamodel/HiddenSequences.js
jalview/datamodel/PDBEntry.js
jalview/datamodel/Profile.js
jalview/datamodel/ProfileI.js
jalview/datamodel/Profiles.js
jalview/datamodel/ProfilesI.js
jalview/datamodel/Range.js
jalview/datamodel/ResidueCount.js
jalview/datamodel/SearchResults.js
jalview/datamodel/SearchResultsI.js
jalview/datamodel/Sequence.js
jalview/datamodel/SequenceCollectionI.js
jalview/datamodel/SequenceCursor.js
jalview/datamodel/SequenceFeature.js
jalview/datamodel/SequenceGroup.js
jalview/datamodel/SequenceI.js
jalview/datamodel/features/FeatureLocationI.js
jalview/datamodel/features/FeatureMatcher.js
jalview/datamodel/features/FeatureMatcherI.js
jalview/datamodel/features/FeatureMatcherSet.js
jalview/datamodel/features/FeatureMatcherSetI.js
jalview/datamodel/features/FeatureStore.js
jalview/datamodel/features/RangeComparator.js
jalview/datamodel/features/SequenceFeatures.js
jalview/datamodel/features/SequenceFeaturesI.js
jalview/gui/AlignFrame.js
jalview/gui/AlignViewport.js
jalview/gui/AlignmentPanel.js
jalview/gui/AnnotationLabels.js
jalview/gui/AnnotationPanel.js
jalview/gui/ColourMenuHelper.js
jalview/gui/Desktop.js
jalview/gui/FeatureRenderer.js
jalview/gui/IProgressIndicator.js
jalview/gui/IdCanvas.js
jalview/gui/IdPanel.js
jalview/gui/IdwidthAdjuster.js
jalview/gui/JalviewChangeSupport.js
jalview/gui/JvSwingUtils.js
jalview/gui/PaintRefresher.js
jalview/gui/ProgressBar.js
jalview/gui/ScalePanel.js
jalview/gui/SeqCanvas.js
jalview/gui/SeqPanel.js
jalview/gui/SequenceRenderer.js
jalview/gui/ViewSelectionMenu.js
jalview/io/AlignFile.js
jalview/io/AlignmentFileReaderI.js
jalview/io/AlignmentFileWriterI.js
jalview/io/AppletFormatAdapter.js
jalview/io/DataSourceType.js
jalview/io/FileFormat.js
jalview/io/FileFormatI.js
jalview/io/FileFormats.js
jalview/io/FileLoader.js
jalview/io/FileParse.js
jalview/io/IdentifyFile.js
jalview/io/PIRFile.js
jalview/io/ScoreMatrixFile.js
jalview/io/SequenceAnnotationReport.js
jalview/javascript/log4j/ConsoleAppender.js
jalview/javascript/log4j/Layout.js
jalview/javascript/log4j/Level.js
jalview/javascript/log4j/Logger.js
jalview/javascript/log4j/Priority.js
jalview/javascript/log4j/SimpleLayout.js
jalview/javascript/log4j/spi/OptionHandler.js
jalview/jbgui/GAlignFrame.js
jalview/jbgui/GAlignmentPanel.js
jalview/jbgui/GDesktop.js
jalview/project/Jalview2XML.js
jalview/renderer/AnnotationRenderer.js
jalview/renderer/AwtRenderPanelI.js
jalview/renderer/ResidueColourFinder.js
jalview/renderer/ResidueShader.js
jalview/renderer/ResidueShaderI.js
jalview/renderer/ScaleRenderer.js
jalview/renderer/seqfeatures/FeatureRenderer.js
jalview/schemes/Blosum62ColourScheme.js
jalview/schemes/BuriedColourScheme.js
jalview/schemes/ClustalxColourScheme.js
jalview/schemes/ColourSchemeI.js
jalview/schemes/ColourSchemeProperty.js
jalview/schemes/ColourSchemes.js
jalview/schemes/Consensus.js
jalview/schemes/FeatureColour.js
jalview/schemes/HelixColourScheme.js
jalview/schemes/HydrophobicColourScheme.js
jalview/schemes/JalviewColourScheme.js
jalview/schemes/NucleotideColourScheme.js
jalview/schemes/PIDColourScheme.js
jalview/schemes/PurinePyrimidineColourScheme.js
jalview/schemes/RNAHelicesColour.js
jalview/schemes/ResidueColourScheme.js
jalview/schemes/ResidueProperties.js
jalview/schemes/ScoreColourScheme.js
jalview/schemes/StrandColourScheme.js
jalview/schemes/TCoffeeColourScheme.js
jalview/schemes/TaylorColourScheme.js
jalview/schemes/TurnColourScheme.js
jalview/schemes/ZappoColourScheme.js
jalview/structure/CommandListener.js
jalview/structure/SelectionListener.js
jalview/structure/SelectionSource.js
jalview/structure/SequenceListener.js
jalview/structure/StructureImportSettings.js
jalview/structure/StructureSelectionManager.js
jalview/structure/VamsasSource.js
jalview/urls/IdOrgSettings.js
jalview/util/ColorUtils.js
jalview/util/Comparison.js
jalview/util/DBRefUtils.js
jalview/util/Format.js
jalview/util/MessageManager.js
jalview/util/Platform.js
jalview/util/QuickSort.js
jalview/util/jarInputStreamProvider.js
jalview/util/matcher/Condition.js
jalview/util/matcher/Matcher.js
jalview/util/matcher/MatcherI.js
jalview/viewmodel/AlignmentViewport.js
jalview/viewmodel/ViewportListenerI.js
jalview/viewmodel/ViewportProperties.js
jalview/viewmodel/ViewportRanges.js
jalview/viewmodel/seqfeatures/FeatureRendererModel.js
jalview/viewmodel/seqfeatures/FeatureRendererSettings.js
jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
jalview/viewmodel/styles/ViewStyle.js
jalview/workers/AlignCalcManager.js
jalview/workers/AlignCalcWorker.js
jalview/workers/ConsensusThread.js
jalview/workers/ConservationThread.js
jalview/ws/sifts/SiftsSettings.js
jalview/xml/binding/jalview/Annotation.js
jalview/xml/binding/jalview/AnnotationElement.js
jalview/xml/binding/jalview/Feature.js
jalview/xml/binding/jalview/FeatureMatcher.js
jalview/xml/binding/jalview/FeatureMatcherSet.js
jalview/xml/binding/jalview/FilterBy.js
jalview/xml/binding/jalview/JalviewModel.js
jalview/xml/binding/jalview/NoValueColour.js
jalview/xml/binding/jalview/Pdbentry.js
jalview/xml/binding/jalview/Sequence.js
jalview/xml/binding/jalview/SequenceSet.js
jalview/xml/binding/jalview/SequenceType.js
jalview/xml/binding/jalview/VAMSAS.js
jalview/xml/binding/jalview/WebServiceParameterSet.js
java/awt/AWTKeyStroke.js
java/awt/AlphaComposite.js
java/awt/Composite.js
java/awt/ContainerOrderFocusTraversalPolicy.js
java/awt/DefaultFocusTraversalPolicy.js
java/awt/DefaultKeyboardFocusManager.js
java/awt/FocusTraversalPolicy.js
java/awt/GridLayout.js
java/awt/Image.js
java/awt/KeyEventDispatcher.js
java/awt/KeyEventPostProcessor.js
java/awt/KeyboardFocusManager.js
java/awt/VKCollection.js
java/awt/datatransfer/ClipboardOwner.js
java/awt/datatransfer/FlavorMap.js
java/awt/datatransfer/FlavorTable.js
java/awt/datatransfer/SystemFlavorMap.js
java/awt/dnd/DropTarget.js
java/awt/dnd/DropTargetContext.js
java/awt/dnd/DropTargetListener.js
java/awt/dnd/peer/DropTargetPeer.js
java/awt/event/ComponentAdapter.js
java/awt/event/ContainerEvent.js
java/awt/event/FocusAdapter.js
java/awt/event/KeyAdapter.js
java/awt/event/MouseAdapter.js
java/awt/event/MouseMotionAdapter.js
java/awt/geom/Path2D.js
java/awt/geom/PathIterator.js
java/awt/geom/RectIterator.js
java/awt/image/BufferedImage.js
java/awt/image/ColorModel.js
java/awt/image/DataBuffer.js
java/awt/image/DataBufferInt.js
java/awt/image/DirectColorModel.js
java/awt/image/PackedColorModel.js
java/awt/image/Raster.js
java/awt/image/RenderedImage.js
java/awt/image/SampleModel.js
java/awt/image/SinglePixelPackedSampleModel.js
java/awt/image/WritableRaster.js
java/awt/peer/KeyboardFocusManagerPeer.js
java/awt/print/Printable.js
java/io/BufferedInputStream.js
java/io/BufferedReader.js
java/io/ByteArrayInputStream.js
java/io/Closeable.js
java/io/File.js
java/io/FileDescriptor.js
java/io/FileInputStream.js
java/io/FileSystem.js
java/io/FilterInputStream.js
java/io/InputStream.js
java/io/InputStreamReader.js
java/io/PushbackInputStream.js
java/io/Reader.js
java/lang/AutoCloseable.js
java/lang/Iterable.js
java/lang/Readable.js
java/lang/Runtime.js
java/lang/StringBuilder.js
java/lang/reflect/Constructor.js
java/lang/reflect/Method.js
java/math/BigDecimal.js
java/math/BigInteger.js
java/math/MathContext.js
java/math/RoundingMode.js
java/net/HttpURLConnection.js
java/net/MalformedURLException.js
java/net/URLConnection.js
java/net/URLDecoder.js
java/net/URLStreamHandler.js
java/security/AccessControlContext.js
java/security/AccessController.js
java/security/PrivilegedAction.js
java/security/PrivilegedExceptionAction.js
java/text/AttributedCharacterIterator.js
java/text/CharacterIterator.js
java/text/DateFormat.js
java/text/DateFormatSymbols.js
java/text/DecimalFormat.js
java/text/DecimalFormatSymbols.js
java/text/DigitList.js
java/text/FieldPosition.js
java/text/Format.js
java/text/MessageFormat.js
java/text/NumberFormat.js
java/text/SimpleDateFormat.js
java/util/AbstractQueue.js
java/util/AbstractSequentialList.js
java/util/ArrayDeque.js
java/util/BitSet.js
java/util/Calendar.js
java/util/Collection.js
java/util/Comparator.js
java/util/Deque.js
java/util/Enumeration.js
java/util/GregorianCalendar.js
java/util/Iterator.js
java/util/LinkedHashMap.js
java/util/LinkedList.js
java/util/List.js
java/util/ListIterator.js
java/util/ListResourceBundle.js
java/util/Map.js
java/util/NavigableMap.js
java/util/NavigableSet.js
java/util/Objects.js
java/util/Properties.js
java/util/PropertyResourceBundle.js
java/util/Queue.js
java/util/RandomAccess.js
java/util/ResourceBundle.js
java/util/Set.js
java/util/SortedMap.js
java/util/SortedSet.js
java/util/StringTokenizer.js
java/util/TimSort.js
java/util/TimeZone.js
java/util/TreeMap.js
java/util/concurrent/AbstractExecutorService.js
java/util/concurrent/BlockingQueue.js
java/util/concurrent/ConcurrentHashMap.js
java/util/concurrent/ConcurrentMap.js
java/util/concurrent/Executor.js
java/util/concurrent/ExecutorService.js
java/util/concurrent/Executors.js
java/util/concurrent/LinkedBlockingQueue.js
java/util/concurrent/RejectedExecutionHandler.js
java/util/concurrent/Semaphore.js
java/util/concurrent/ThreadFactory.js
java/util/concurrent/ThreadPoolExecutor.js
java/util/concurrent/TimeUnit.js
java/util/concurrent/atomic/AtomicBoolean.js
java/util/concurrent/atomic/AtomicInteger.js
java/util/concurrent/locks/AbstractOwnableSynchronizer.js
java/util/concurrent/locks/AbstractQueuedSynchronizer.js
java/util/concurrent/locks/Condition.js
java/util/concurrent/locks/Lock.js
java/util/concurrent/locks/ReadWriteLock.js
java/util/concurrent/locks/ReentrantLock.js
java/util/concurrent/locks/ReentrantReadWriteLock.js
java/util/jar/JarEntry.js
java/util/jar/JarInputStream.js
java/util/logging/Level.js
java/util/logging/Logger.js
java/util/regex/Pattern.js
java/util/zip/CRC32.js
java/util/zip/Inflater.js
java/util/zip/InflaterInputStream.js
java/util/zip/ZipConstants.js
java/util/zip/ZipEntry.js
java/util/zip/ZipInputStream.js
javajs/api/GenericLineReader.js
javajs/api/JSONEncodable.js
javajs/util/AjaxURLStreamHandler.js
javajs/util/Encoding.js
javajs/util/Rdr.js
javajs/util/SB.js
javax/swing/AbstractAction.js
javax/swing/Action.js
javax/swing/ComponentInputMap.js
javax/swing/DefaultDesktopManager.js
javax/swing/DesktopManager.js
javax/swing/InputMap.js
javax/swing/JDesktopPane.js
javax/swing/JDialog.js
javax/swing/JInternalFrame.js
javax/swing/JProgressBar.js
javax/swing/JScrollPane.js
javax/swing/JTabbedPane.js
javax/swing/JToolTip.js
javax/swing/JViewport.js
javax/swing/KeyStroke.js
javax/swing/ScrollPaneConstants.js
javax/swing/ScrollPaneLayout.js
javax/swing/Scrollable.js
javax/swing/Timer.js
javax/swing/ToolTipManager.js
javax/swing/ViewportLayout.js
javax/swing/border/LineBorder.js
javax/swing/event/InternalFrameAdapter.js
javax/swing/event/InternalFrameEvent.js
javax/swing/event/InternalFrameListener.js
javax/swing/event/MenuListener.js
javax/swing/plaf/ComponentInputMapUIResource.js
javax/xml/bind/ContextFinder.js
javax/xml/bind/GetPropertyAction.js
javax/xml/bind/JAXBContext.js
javax/xml/bind/JAXBContextFactory.js
javax/xml/bind/JAXBElement.js
javax/xml/bind/ModuleUtil.js
javax/xml/bind/ServiceLoaderUtil.js
javax/xml/bind/Unmarshaller.js
javax/xml/bind/ValidationEventHandler.js
javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js
javax/xml/bind/annotation/adapters/XmlAdapter.js
javax/xml/bind/helpers/AbstractUnmarshallerImpl.js
javax/xml/bind/helpers/DefaultValidationEventHandler.js
javax/xml/datatype/XMLGregorianCalendar.js
javax/xml/namespace/QName.js
javax/xml/stream/XMLInputFactory.js
javax/xml/stream/XMLStreamReader.js
org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js
org/xml/sax/AttributeList.js
org/xml/sax/Attributes.js
org/xml/sax/ContentHandler.js
org/xml/sax/InputSource.js
org/xml/sax/Parser.js
org/xml/sax/XMLReader.js
org/xml/sax/ext/Attributes2.js
sun/awt/AWTAccessor.js
sun/awt/CausedFocusEvent.js
sun/awt/KeyboardFocusManagerPeerProvider.js
sun/awt/SunGraphicsCallback.js
sun/awt/image/DataStealer.js
sun/awt/image/IntegerComponentRaster.js
sun/awt/image/IntegerInterleavedRaster.js
sun/awt/image/SunWritableRaster.js
sun/font/FontDesignMetrics.js
sun/java2d/StateTrackable.js
sun/java2d/StateTrackableDelegate.js
sun/swing/DefaultLookup.js
sun/text/resources/FormatData.js
sun/text/resources/FormatData_en.js
sun/util/calendar/AbstractCalendar.js
sun/util/calendar/BaseCalendar.js
sun/util/calendar/CalendarDate.js
sun/util/calendar/CalendarSystem.js
sun/util/calendar/CalendarUtils.js
sun/util/calendar/Gregorian.js
sun/util/calendar/ZoneInfo.js
sun/util/resources/LocaleData.js
swingjs/JSFocusManager.js
swingjs/a2s/Dialog.js
swingjs/jzlib/Adler32.js
swingjs/jzlib/CRC32.js
swingjs/jzlib/Checksum.js
swingjs/jzlib/InfBlocks.js
swingjs/jzlib/InfCodes.js
swingjs/jzlib/InfTree.js
swingjs/jzlib/Inflate.js
swingjs/jzlib/Inflater.js
swingjs/jzlib/InflaterInputStream.js
swingjs/jzlib/ZStream.js
swingjs/plaf/JSAppletUI.js
swingjs/plaf/JSDesktopIconUI.js
swingjs/plaf/JSDesktopPaneUI.js
swingjs/plaf/JSGraphicsUtils.js
swingjs/plaf/JSInternalFrameUI.js
swingjs/plaf/JSProgressBarUI.js
swingjs/plaf/JSScrollPaneUI.js
swingjs/plaf/JSTabbedPaneUI.js
swingjs/plaf/JSToolTipUI.js
swingjs/plaf/JSViewportUI.js
swingjs/xml/JSJAXBClass.js
swingjs/xml/JSJAXBContext.js
swingjs/xml/JSJAXBContextFactory.js
swingjs/xml/JSJAXBField.js
swingjs/xml/JSJAXBUnmarshaller.js
swingjs/xml/JSSAXAttributes.js
swingjs/xml/JSSAXParser.js
swingjs/xml/JSXMLGregorianCalendarImpl.js
swingjs/xml/JSXMLInputFactory.js
swingjs/xml/JSXMLStreamReader.js