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jalview/analysis/AAFrequency.js
jalview/analysis/AlignSeq.js
jalview/analysis/AlignmentAnnotationUtils.js
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jalview/analysis/AlignmentUtils.js
jalview/analysis/AnnotationSorter.js
jalview/analysis/Conservation.js
jalview/analysis/CrossRef.js
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jalview/analysis/SeqsetUtils.js
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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
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jalview/analysis/scoremodels/SimilarityScoreModel.js
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jalview/api/AlignCalcWorkerI.js
jalview/api/AlignViewControllerGuiI.js
jalview/api/AlignViewControllerI.js
jalview/api/AlignViewportI.js
jalview/api/AlignmentViewPanel.js
jalview/api/BuildDetailsI.js
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jalview/api/FeatureColourI.js
jalview/api/FeatureRenderer.js
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jalview/api/FeaturesDisplayedI.js
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jalview/api/OOMHandlerI.js
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jalview/api/StructureSelectionManagerProvider.js
jalview/api/ViewStyleI.js
jalview/api/analysis/PairwiseScoreModelI.js
jalview/api/analysis/ScoreModelI.js
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jalview/bin/ArgsParser.js
jalview/bin/BuildDetails.js
jalview/bin/Cache.js
jalview/bin/Jalview.js
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jalview/controller/AlignViewController.js
jalview/datamodel/ASequence.js
jalview/datamodel/ASequenceI.js
jalview/datamodel/Alignment.js
jalview/datamodel/AlignmentAnnotation.js
jalview/datamodel/AlignmentI.js
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jalview/datamodel/AlignmentView.js
jalview/datamodel/AnnotatedCollectionI.js
jalview/datamodel/Annotation.js
jalview/datamodel/CigarSimple.js
jalview/datamodel/ColumnSelection.js
jalview/datamodel/ContiguousI.js
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jalview/datamodel/DBRefSource.js
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jalview/datamodel/HiddenColumns.js
jalview/datamodel/HiddenColumnsCursor.js
jalview/datamodel/HiddenCursorPosition.js
jalview/datamodel/HiddenSequences.js
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jalview/datamodel/PDBEntry.js
jalview/datamodel/Profile.js
jalview/datamodel/ProfileI.js
jalview/datamodel/Range.js
jalview/datamodel/RangeIterator.js
jalview/datamodel/ResidueCount.js
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jalview/datamodel/SearchResults.js
jalview/datamodel/SearchResultsI.js
jalview/datamodel/SeqCigar.js
jalview/datamodel/SequenceGroup.js
jalview/datamodel/SequenceI.js
jalview/datamodel/SequenceNode.js
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jalview/datamodel/features/FeatureLocationI.js
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jalview/datamodel/features/FeatureStore.js
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jalview/datamodel/features/SequenceFeatures.js
jalview/datamodel/features/SequenceFeaturesI.js
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jalview/gui/AlignFrame.js
jalview/gui/AlignViewport.js
jalview/gui/AlignmentPanel.js
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jalview/gui/AnnotationLabels.js
jalview/gui/AnnotationPanel.js
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jalview/gui/ColourMenuHelper.js
jalview/gui/ComboBoxTooltipRenderer.js
jalview/gui/Desktop.js
jalview/gui/FeatureRenderer.js
jalview/gui/IProgressIndicator.js
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jalview/gui/IdCanvas.js
jalview/gui/IdPanel.js
jalview/gui/IdwidthAdjuster.js
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jalview/gui/JalviewChangeSupport.js
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jalview/gui/JvSwingUtils.js
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jalview/gui/PaintRefresher.js
jalview/gui/PopupMenu.js
jalview/gui/Preferences.js
jalview/gui/ScalePanel.js
jalview/gui/SeqCanvas.js
jalview/gui/SeqPanel.js
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jalview/gui/SequenceRenderer.js
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jalview/gui/TreeCanvas.js
jalview/gui/TreePanel.js
jalview/gui/ViewSelectionMenu.js
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jalview/io/AlignFile.js
jalview/io/AlignmentFileReaderI.js
jalview/io/AlignmentFileWriterI.js
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jalview/io/AppletFormatAdapter.js
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jalview/io/DataSourceType.js
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jalview/io/FileFormat.js
jalview/io/FileFormatI.js
jalview/io/FileFormats.js
jalview/io/FileLoader.js
jalview/io/FileParse.js
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jalview/io/IdentifyFile.js
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jalview/io/PIRFile.js
jalview/io/ScoreMatrixFile.js
jalview/io/SequenceAnnotationReport.js
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jalview/javascript/log4j/ConsoleAppender.js
jalview/javascript/log4j/Layout.js
jalview/javascript/log4j/Level.js
jalview/javascript/log4j/Priority.js
jalview/javascript/log4j/SimpleLayout.js
jalview/javascript/log4j/spi/OptionHandler.js
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jalview/jbgui/GAlignFrame.js
jalview/jbgui/GAlignmentPanel.js
jalview/jbgui/GDesktop.js
jalview/jbgui/GPreferences.js
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jalview/jbgui/GTreePanel.js
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jalview/project/Jalview2XML.js
jalview/renderer/AnnotationRenderer.js
jalview/renderer/AwtRenderPanelI.js
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jalview/renderer/ResidueColourFinder.js
jalview/renderer/ResidueShader.js
jalview/renderer/ResidueShaderI.js
jalview/schemes/ColourSchemes.js
jalview/schemes/Consensus.js
jalview/schemes/FeatureColour.js
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jalview/schemes/HelixColourScheme.js
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jalview/schemes/HydrophobicColourScheme.js
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jalview/schemes/JalviewColourScheme.js
jalview/schemes/NucleotideColourScheme.js
jalview/schemes/PIDColourScheme.js
jalview/schemes/TaylorColourScheme.js
jalview/schemes/TurnColourScheme.js
jalview/schemes/ZappoColourScheme.js
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jalview/structure/CommandListener.js
jalview/structure/SelectionListener.js
jalview/structure/SelectionSource.js
jalview/urls/api/UrlProviderFactoryI.js
jalview/urls/api/UrlProviderI.js
jalview/urls/desktop/DesktopUrlProviderFactory.js
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jalview/util/ColorUtils.js
jalview/util/Comparison.js
jalview/util/DBRefUtils.js
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jalview/util/Format.js
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jalview/util/MessageManager.js
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jalview/util/Platform.js
jalview/util/QuickSort.js
jalview/util/StringUtils.js
jalview/util/UrlLink.js
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jalview/util/jarInputStreamProvider.js
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jalview/viewmodel/AlignmentViewport.js
jalview/viewmodel/ViewportListenerI.js
jalview/viewmodel/ViewportProperties.js
jalview/viewmodel/ViewportRanges.js
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jalview/viewmodel/seqfeatures/FeatureRendererModel.js
jalview/viewmodel/seqfeatures/FeatureRendererSettings.js
jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
jalview/viewmodel/styles/ViewStyle.js
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jalview/workers/AlignCalcWorker.js
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jalview/workers/ConsensusThread.js
jalview/workers/ConservationThread.js
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jalview/ws/sifts/SiftsSettings.js
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jalview/xml/binding/jalview/Annotation.js
jalview/xml/binding/jalview/AnnotationElement.js
jalview/xml/binding/jalview/Feature.js
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jalview/xml/binding/jalview/JalviewModel.js
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jalview/xml/binding/jalview/Pdbentry.js
jalview/xml/binding/jalview/Sequence.js
jalview/xml/binding/jalview/SequenceSet.js
java/awt/AlphaComposite.js
java/awt/BasicStroke.js
java/awt/BorderLayout.js
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java/awt/Color.js
java/awt/Component.js
java/awt/ComponentOrientation.js
java/awt/Cursor.js
java/awt/DefaultFocusTraversalPolicy.js
java/awt/DefaultKeyboardFocusManager.js
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java/awt/Dialog.js
java/awt/Dimension.js
java/awt/EventDispatchThread.js
java/awt/GraphicsConfiguration.js
java/awt/GraphicsDevice.js
java/awt/GraphicsEnvironment.js
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java/awt/GridLayout.js
java/awt/Image.js
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java/awt/Insets.js
java/awt/ItemSelectable.js
java/awt/JSComponent.js
java/awt/LayoutManager.js
java/awt/LayoutManager2.js
java/awt/LightweightDispatcher.js
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java/awt/Paint.js
java/awt/Point.js
java/awt/Queue.js
java/awt/SentEvent.js
java/awt/Shape.js
java/awt/Stroke.js
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java/awt/Toolkit.js
java/awt/Transparency.js
java/awt/VKCollection.js
java/awt/event/FocusEvent.js
java/awt/event/FocusListener.js
java/awt/event/HierarchyBoundsListener.js
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java/awt/event/HierarchyListener.js
java/awt/event/InputEvent.js
java/awt/event/InputMethodListener.js
java/awt/event/MouseListener.js
java/awt/event/MouseMotionAdapter.js
java/awt/event/MouseMotionListener.js
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java/awt/event/MouseWheelListener.js
java/awt/event/TextListener.js
java/awt/event/WindowAdapter.js
java/awt/event/WindowListener.js
java/awt/event/WindowStateListener.js
java/awt/font/FontRenderContext.js
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java/awt/geom/AffineTransform.js
java/awt/geom/Dimension2D.js
java/awt/geom/Path2D.js
java/awt/image/DataBuffer.js
java/awt/image/DataBufferInt.js
java/awt/image/DirectColorModel.js
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java/awt/image/ImageObserver.js
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java/awt/image/PackedColorModel.js
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java/awt/image/Raster.js
java/awt/image/RenderedImage.js
java/awt/image/SampleModel.js
java/awt/image/WritableRaster.js
java/awt/peer/ComponentPeer.js
java/awt/peer/ContainerPeer.js
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java/awt/peer/FramePeer.js
java/awt/peer/KeyboardFocusManagerPeer.js
java/awt/peer/LightweightPeer.js
java/beans/PropertyChangeSupport.js
java/io/BufferedInputStream.js
java/io/BufferedReader.js
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java/io/ByteArrayInputStream.js
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java/io/Closeable.js
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java/io/File.js
java/io/FileDescriptor.js
java/io/FileInputStream.js
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java/io/FileReader.js
java/io/FileSystem.js
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java/io/FilterInputStream.js
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java/io/InputStream.js
java/io/InputStreamReader.js
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java/io/Reader.js
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java/lang/AbstractStringBuilder.js
java/lang/AutoCloseable.js
java/lang/Class.js
java/lang/Iterable.js
java/lang/Readable.js
java/lang/Runtime.js
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java/lang/StringBuffer.js
java/lang/StringBuilder.js
java/lang/Thread.js
java/lang/ThreadGroup.js
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java/lang/reflect/Constructor.js
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java/lang/reflect/Method.js
java/math/BigDecimal.js
java/math/BigInteger.js
java/math/MathContext.js
java/math/RoundingMode.js
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java/net/HttpURLConnection.js
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java/net/URL.js
java/net/URLConnection.js
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java/net/URLStreamHandler.js
java/net/URLStreamHandlerFactory.js
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-java/nio/HeapByteBuffer.js
-java/nio/HeapCharBuffer.js
-java/nio/charset/Charset.js
-java/nio/charset/CharsetDecoder.js
-java/nio/charset/CoderResult.js
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java/security/AccessController.js
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java/security/PrivilegedAction.js
java/security/PrivilegedExceptionAction.js
java/text/AttributedCharacterIterator.js
java/text/Format.js
java/text/MessageFormat.js
java/text/NumberFormat.js
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java/text/SimpleDateFormat.js
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java/util/AbstractCollection.js
java/util/AbstractList.js
java/util/AbstractMap.js
java/util/Calendar.js
java/util/Collection.js
java/util/Collections.js
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java/util/Comparator.js
java/util/Deque.js
java/util/Dictionary.js
java/util/DualPivotQuicksort.js
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java/util/Enumeration.js
java/util/EventListener.js
java/util/EventObject.js
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java/util/GregorianCalendar.js
java/util/HashMap.js
java/util/HashSet.js
java/util/Hashtable.js
java/util/IdentityHashMap.js
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java/util/Iterator.js
java/util/LinkedHashMap.js
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java/util/LinkedList.js
java/util/List.js
java/util/ListIterator.js
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java/util/Locale.js
java/util/Map.js
java/util/NavigableMap.js
java/util/NavigableSet.js
java/util/Objects.js
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java/util/Properties.js
java/util/PropertyResourceBundle.js
java/util/Queue.js
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java/util/RandomAccess.js
java/util/ResourceBundle.js
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java/util/Set.js
java/util/SortedMap.js
java/util/SortedSet.js
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java/util/StringTokenizer.js
java/util/TimSort.js
java/util/TimeZone.js
java/util/TreeMap.js
java/util/TreeSet.js
java/util/Vector.js
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java/util/concurrent/AbstractExecutorService.js
java/util/concurrent/BlockingQueue.js
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git://source.jalview.org / jalview.git / blobdiff