coreclasses

   1 jalview/analysis/AAFrequency.js
   2 jalview/analysis/AlignSeq.js
   3 jalview/analysis/AnnotationSorter.js
   4 jalview/analysis/Conservation.js
   5 jalview/analysis/CrossRef.js
   6 jalview/analysis/scoremodels/DistanceScoreModel.js
   7 jalview/analysis/scoremodels/FeatureDistanceModel.js
   8 jalview/analysis/scoremodels/PIDModel.js
   9 jalview/analysis/scoremodels/ScoreMatrix.js
  10 jalview/analysis/scoremodels/ScoreModels.js
  11 jalview/analysis/scoremodels/SimilarityScoreModel.js
  12 jalview/api/AlignCalcManagerI.js
  13 jalview/api/AlignCalcWorkerI.js
  14 jalview/api/AlignViewControllerGuiI.js
  15 jalview/api/AlignViewControllerI.js
  16 jalview/api/AlignViewportI.js
  17 jalview/api/AlignmentViewPanel.js
  18 jalview/api/BuildDetailsI.js
  19 jalview/api/FeatureColourI.js
  20 jalview/api/FeatureRenderer.js
  21 jalview/api/FeaturesDisplayedI.js
  22 jalview/api/FeaturesSourceI.js
  23 jalview/api/OOMHandlerI.js
  24 jalview/api/SequenceRenderer.js
  25 jalview/api/StructureSelectionManagerProvider.js
  26 jalview/api/ViewStyleI.js
  27 jalview/api/analysis/PairwiseScoreModelI.js
  28 jalview/api/analysis/ScoreModelI.js
  29 jalview/bin/ArgsParser.js
  30 jalview/bin/BuildDetails.js
  31 jalview/bin/Cache.js
  32 jalview/bin/Jalview.js
  33 jalview/bin/JalviewJS.js
  34 jalview/controller/AlignViewController.js
  35 jalview/datamodel/ASequence.js
  36 jalview/datamodel/ASequenceI.js
  37 jalview/datamodel/Alignment.js
  38 jalview/datamodel/AlignmentAnnotation.js
  39 jalview/datamodel/AlignmentI.js
  40 jalview/datamodel/AnnotatedCollectionI.js
  41 jalview/datamodel/Annotation.js
  42 jalview/datamodel/ColumnSelection.js
  43 jalview/datamodel/ContiguousI.js
  44 jalview/datamodel/DBRefSource.js
  45 jalview/datamodel/HiddenColumns.js
  46 jalview/datamodel/HiddenColumnsCursor.js
  47 jalview/datamodel/HiddenCursorPosition.js
  48 jalview/datamodel/HiddenSequences.js
  49 jalview/datamodel/PDBEntry.js
  50 jalview/datamodel/Profile.js
  51 jalview/datamodel/ProfileI.js
  52 jalview/datamodel/Profiles.js
  53 jalview/datamodel/ProfilesI.js
  54 jalview/datamodel/Range.js
  55 jalview/datamodel/ResidueCount.js
  56 jalview/datamodel/SearchResults.js
  57 jalview/datamodel/SearchResultsI.js
  58 jalview/datamodel/Sequence.js
  59 jalview/datamodel/SequenceCollectionI.js
  60 jalview/datamodel/SequenceCursor.js
  61 jalview/datamodel/SequenceFeature.js
  62 jalview/datamodel/SequenceGroup.js
  63 jalview/datamodel/SequenceI.js
  64 jalview/datamodel/features/FeatureLocationI.js
  65 jalview/datamodel/features/FeatureStore.js
  66 jalview/datamodel/features/RangeComparator.js
  67 jalview/datamodel/features/SequenceFeatures.js
  68 jalview/datamodel/features/SequenceFeaturesI.js
  69 jalview/gui/AlignFrame.js
  70 jalview/gui/AlignViewport.js
  71 jalview/gui/AlignmentPanel.js
  72 jalview/gui/AnnotationLabels.js
  73 jalview/gui/AnnotationPanel.js
  74 jalview/gui/ColourMenuHelper.js
  75 jalview/gui/Desktop.js
  76 jalview/gui/FeatureRenderer.js
  77 jalview/gui/IProgressIndicator.js
  78 jalview/gui/IdCanvas.js
  79 jalview/gui/IdPanel.js
  80 jalview/gui/IdwidthAdjuster.js
  81 jalview/gui/JvSwingUtils.js
  82 jalview/gui/PaintRefresher.js
  83 jalview/gui/ProgressBar.js
  84 jalview/gui/ScalePanel.js
  85 jalview/gui/SeqCanvas.js
  86 jalview/gui/SeqPanel.js
  87 jalview/gui/SequenceRenderer.js
  88 jalview/gui/ViewSelectionMenu.js
  89 jalview/io/AlignFile.js
  90 jalview/io/AlignmentFileReaderI.js
  91 jalview/io/AlignmentFileWriterI.js
  92 jalview/io/AppletFormatAdapter.js
  93 jalview/io/DataSourceType.js
  94 jalview/io/FastaFile.js
  95 jalview/io/FeaturesFile.js
  96 jalview/io/FileFormat.js
  97 jalview/io/FileFormatI.js
  98 jalview/io/FileFormats.js
  99 jalview/io/FileLoader.js
 100 jalview/io/FileParse.js
 101 jalview/io/FormatAdapter.js
 102 jalview/io/IdentifyFile.js
 103 jalview/io/PIRFile.js
 104 jalview/io/ScoreMatrixFile.js
 105 jalview/io/SequenceAnnotationReport.js
 106 jalview/javascript/log4j/Level.js
 107 jalview/javascript/log4j/Logger.js
 108 jalview/javascript/log4j/Priority.js
 109 jalview/jbgui/GAlignFrame.js
 110 jalview/jbgui/GAlignmentPanel.js
 111 jalview/jbgui/GDesktop.js
 112 jalview/renderer/AnnotationRenderer.js
 113 jalview/renderer/AwtRenderPanelI.js
 114 jalview/renderer/ResidueColourFinder.js
 115 jalview/renderer/ResidueShader.js
 116 jalview/renderer/ResidueShaderI.js
 117 jalview/renderer/ScaleRenderer.js
 118 jalview/renderer/seqfeatures/FeatureRenderer.js
 119 jalview/schemes/Blosum62ColourScheme.js
 120 jalview/schemes/BuriedColourScheme.js
 121 jalview/schemes/ClustalxColourScheme.js
 122 jalview/schemes/ColourSchemeI.js
 123 jalview/schemes/ColourSchemeProperty.js
 124 jalview/schemes/ColourSchemes.js
 125 jalview/schemes/Consensus.js
 126 jalview/schemes/FeatureColour.js
 127 jalview/schemes/HelixColourScheme.js
 128 jalview/schemes/HydrophobicColourScheme.js
 129 jalview/schemes/JalviewColourScheme.js
 130 jalview/schemes/NucleotideColourScheme.js
 131 jalview/schemes/PIDColourScheme.js
 132 jalview/schemes/PurinePyrimidineColourScheme.js
 133 jalview/schemes/RNAHelicesColour.js
 134 jalview/schemes/ResidueColourScheme.js
 135 jalview/schemes/ResidueProperties.js
 136 jalview/schemes/ScoreColourScheme.js
 137 jalview/schemes/StrandColourScheme.js
 138 jalview/schemes/TCoffeeColourScheme.js
 139 jalview/schemes/TaylorColourScheme.js
 140 jalview/schemes/TurnColourScheme.js
 141 jalview/schemes/ZappoColourScheme.js
 142 jalview/structure/CommandListener.js
 143 jalview/structure/SelectionListener.js
 144 jalview/structure/SelectionSource.js
 145 jalview/structure/SequenceListener.js
 146 jalview/structure/StructureImportSettings.js
 147 jalview/structure/StructureSelectionManager.js
 148 jalview/structure/VamsasSource.js
 149 jalview/urls/IdOrgSettings.js
 150 jalview/util/ColorUtils.js
 151 jalview/util/Comparison.js
 152 jalview/util/DBRefUtils.js
 153 jalview/util/Format.js
 154 jalview/util/LinkedIdentityHashSet.js
 155 jalview/util/MessageManager.js
 156 jalview/util/ParseHtmlBodyAndLinks.js
 157 jalview/util/Platform.js
 158 jalview/util/StringUtils.js
 159 jalview/viewmodel/AlignmentViewport.js
 160 jalview/viewmodel/ViewportListenerI.js
 161 jalview/viewmodel/ViewportProperties.js
 162 jalview/viewmodel/ViewportRanges.js
 163 jalview/viewmodel/seqfeatures/FeatureRendererModel.js
 164 jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
 165 jalview/viewmodel/styles/ViewStyle.js
 166 jalview/workers/AlignCalcManager.js
 167 jalview/workers/AlignCalcWorker.js
 168 jalview/workers/ConsensusThread.js
 169 jalview/workers/ConservationThread.js
 170 jalview/ws/sifts/SiftsSettings.js
 171 java/awt/AWTKeyStroke.js
 172 java/awt/AlphaComposite.js
 173 java/awt/Composite.js
 174 java/awt/GridLayout.js
 175 java/awt/IllegalComponentStateException.js
 176 java/awt/Image.js
 177 java/awt/datatransfer/ClipboardOwner.js
 178 java/awt/dnd/DropTargetListener.js
 179 java/awt/event/ActionEvent.js
 180 java/awt/event/ComponentAdapter.js
 181 java/awt/event/FocusAdapter.js
 182 java/awt/event/KeyAdapter.js
 183 java/awt/event/MouseAdapter.js
 184 java/awt/event/MouseMotionAdapter.js
 185 java/awt/image/BufferedImage.js
 186 java/awt/image/ColorModel.js
 187 java/awt/image/DataBuffer.js
 188 java/awt/image/DataBufferInt.js
 189 java/awt/image/DirectColorModel.js
 190 java/awt/image/PackedColorModel.js
 191 java/awt/image/Raster.js
 192 java/awt/image/RenderedImage.js
 193 java/awt/image/SampleModel.js
 194 java/awt/image/SinglePixelPackedSampleModel.js
 195 java/awt/image/WritableRaster.js
 196 java/awt/print/Printable.js
 197 java/io/BufferedInputStream.js
 198 java/io/BufferedReader.js
 199 java/io/ByteArrayInputStream.js
 200 java/io/File.js
 201 java/io/FileDescriptor.js
 202 java/io/FileInputStream.js
 203 java/io/FileSystem.js
 204 java/io/FilterInputStream.js
 205 java/io/InputStream.js
 206 java/io/InputStreamReader.js
 207 java/io/Reader.js
 208 java/lang/Readable.js
 209 java/lang/Runtime.js
 210 java/lang/StringBuilder.js
 211 java/math/RoundingMode.js
 212 java/net/MalformedURLException.js
 213 java/net/URLConnection.js
 214 java/net/URLStreamHandler.js
 215 java/text/AttributedCharacterIterator.js
 216 java/text/CharacterIterator.js
 217 java/text/DateFormat.js
 218 java/text/DateFormatSymbols.js
 219 java/text/DecimalFormat.js
 220 java/text/DecimalFormatSymbols.js
 221 java/text/DigitList.js
 222 java/text/FieldPosition.js
 223 java/text/Format.js
 224 java/text/MessageFormat.js
 225 java/text/NumberFormat.js
 226 java/text/SimpleDateFormat.js
 227 java/util/ArrayDeque.js
 228 java/util/BitSet.js
 229 java/util/Calendar.js
 230 java/util/Deque.js
 231 java/util/GregorianCalendar.js
 232 java/util/LinkedHashMap.js
 233 java/util/ListResourceBundle.js
 234 java/util/NavigableMap.js
 235 java/util/NavigableSet.js
 236 java/util/Objects.js
 237 java/util/Properties.js
 238 java/util/PropertyResourceBundle.js
 239 java/util/ResourceBundle.js
 240 java/util/SortedMap.js
 241 java/util/SortedSet.js
 242 java/util/StringTokenizer.js
 243 java/util/TimeZone.js
 244 java/util/TreeMap.js
 245 java/util/concurrent/ConcurrentHashMap.js
 246 java/util/concurrent/ConcurrentMap.js
 247 java/util/concurrent/atomic/AtomicBoolean.js
 248 java/util/concurrent/atomic/AtomicInteger.js
 249 java/util/concurrent/locks/Lock.js
 250 java/util/concurrent/locks/ReadWriteLock.js
 251 java/util/concurrent/locks/ReentrantReadWriteLock.js
 252 java/util/regex/Pattern.js
 253 javajs/api/GenericLineReader.js
 254 javajs/api/JSONEncodable.js
 255 javajs/util/AjaxURLStreamHandler.js
 256 javajs/util/BS.js
 257 javajs/util/Rdr.js
 258 javajs/util/SB.js
 259 javax/swing/ComponentInputMap.js
 260 javax/swing/InputMap.js
 261 javax/swing/JInternalFrame.js
 262 javax/swing/JScrollPane.js
 263 javax/swing/JTabbedPane.js
 264 javax/swing/JToolTip.js
 265 javax/swing/JViewport.js
 266 javax/swing/JWindow.js
 267 javax/swing/KeyStroke.js
 268 javax/swing/Popup.js
 269 javax/swing/PopupFactory.js
 270 javax/swing/ScrollPaneConstants.js
 271 javax/swing/ScrollPaneLayout.js
 272 javax/swing/Scrollable.js
 273 javax/swing/Timer.js
 274 javax/swing/ToolTipManager.js
 275 javax/swing/ViewportLayout.js
 276 javax/swing/border/LineBorder.js
 277 javax/swing/event/MenuListener.js
 278 javax/swing/plaf/ComponentInputMapUIResource.js
 279 sun/awt/SunGraphicsCallback.js
 280 sun/awt/image/DataStealer.js
 281 sun/awt/image/IntegerComponentRaster.js
 282 sun/awt/image/IntegerInterleavedRaster.js
 283 sun/awt/image/SunWritableRaster.js
 284 sun/font/FontDesignMetrics.js
 285 sun/java2d/StateTrackable.js
 286 sun/java2d/StateTrackableDelegate.js
 287 sun/swing/DefaultLookup.js
 288 sun/text/resources/FormatData.js
 289 sun/text/resources/FormatData_en.js
 290 sun/util/calendar/AbstractCalendar.js
 291 sun/util/calendar/BaseCalendar.js
 292 sun/util/calendar/CalendarDate.js
 293 sun/util/calendar/CalendarSystem.js
 294 sun/util/calendar/CalendarUtils.js
 295 sun/util/calendar/Gregorian.js
 296 sun/util/calendar/ZoneInfo.js
 297 sun/util/resources/LocaleData.js
 298 swingjs/plaf/JSAppletUI.js
 299 swingjs/plaf/JSDesktopIconUI.js
 300 swingjs/plaf/JSInternalFrameUI.js
 301 swingjs/plaf/JSScrollPaneUI.js
 302 swingjs/plaf/JSTabbedPaneUI.js
 303 swingjs/plaf/JSToolTipUI.js
 304 swingjs/plaf/JSViewportUI.js