_j2sclasslist.txt

   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/OOMHandlerI.js
  23 jalview/api/SequenceRenderer.js
  24 jalview/api/StructureSelectionManagerProvider.js
  25 jalview/api/ViewStyleI.js
  26 jalview/api/analysis/PairwiseScoreModelI.js
  27 jalview/api/analysis/ScoreModelI.js
  28 jalview/bin/ArgsParser.js
  29 jalview/bin/BuildDetails.js
  30 jalview/bin/Cache.js
  31 jalview/bin/Jalview.js
  32 jalview/bin/JalviewJS2.js
  33 jalview/controller/AlignViewController.js
  34 jalview/datamodel/ASequence.js
  35 jalview/datamodel/ASequenceI.js
  36 jalview/datamodel/Alignment.js
  37 jalview/datamodel/AlignmentAnnotation.js
  38 jalview/datamodel/AlignmentI.js
  39 jalview/datamodel/AnnotatedCollectionI.js
  40 jalview/datamodel/Annotation.js
  41 jalview/datamodel/ColumnSelection.js
  42 jalview/datamodel/ContiguousI.js
  43 jalview/datamodel/DBRefSource.js
  44 jalview/datamodel/HiddenColumns.js
  45 jalview/datamodel/HiddenColumnsCursor.js
  46 jalview/datamodel/HiddenCursorPosition.js
  47 jalview/datamodel/HiddenSequences.js
  48 jalview/datamodel/PDBEntry.js
  49 jalview/datamodel/Profile.js
  50 jalview/datamodel/ProfileI.js
  51 jalview/datamodel/Profiles.js
  52 jalview/datamodel/ProfilesI.js
  53 jalview/datamodel/Range.js
  54 jalview/datamodel/ResidueCount.js
  55 jalview/datamodel/SearchResults.js
  56 jalview/datamodel/SearchResultsI.js
  57 jalview/datamodel/Sequence.js
  58 jalview/datamodel/SequenceCollectionI.js
  59 jalview/datamodel/SequenceCursor.js
  60 jalview/datamodel/SequenceFeature.js
  61 jalview/datamodel/SequenceGroup.js
  62 jalview/datamodel/SequenceI.js
  63 jalview/datamodel/features/FeatureLocationI.js
  64 jalview/datamodel/features/FeatureMatcher.js
  65 jalview/datamodel/features/FeatureMatcherI.js
  66 jalview/datamodel/features/FeatureMatcherSet.js
  67 jalview/datamodel/features/FeatureMatcherSetI.js
  68 jalview/datamodel/features/FeatureStore.js
  69 jalview/datamodel/features/RangeComparator.js
  70 jalview/datamodel/features/SequenceFeatures.js
  71 jalview/datamodel/features/SequenceFeaturesI.js
  72 jalview/gui/AlignFrame.js
  73 jalview/gui/AlignViewport.js
  74 jalview/gui/AlignmentPanel.js
  75 jalview/gui/AnnotationLabels.js
  76 jalview/gui/AnnotationPanel.js
  77 jalview/gui/ColourMenuHelper.js
  78 jalview/gui/Desktop.js
  79 jalview/gui/FeatureRenderer.js
  80 jalview/gui/IProgressIndicator.js
  81 jalview/gui/IdCanvas.js
  82 jalview/gui/IdPanel.js
  83 jalview/gui/IdwidthAdjuster.js
  84 jalview/gui/JalviewChangeSupport.js
  85 jalview/gui/JvSwingUtils.js
  86 jalview/gui/PaintRefresher.js
  87 jalview/gui/ProgressBar.js
  88 jalview/gui/ScalePanel.js
  89 jalview/gui/SeqCanvas.js
  90 jalview/gui/SeqPanel.js
  91 jalview/gui/SequenceRenderer.js
  92 jalview/gui/ViewSelectionMenu.js
  93 jalview/io/AlignFile.js
  94 jalview/io/AlignmentFileReaderI.js
  95 jalview/io/AlignmentFileWriterI.js
  96 jalview/io/AppletFormatAdapter.js
  97 jalview/io/DataSourceType.js
  98 jalview/io/FileFormat.js
  99 jalview/io/FileFormatI.js
 100 jalview/io/FileFormats.js
 101 jalview/io/FileLoader.js
 102 jalview/io/FileParse.js
 103 jalview/io/IdentifyFile.js
 104 jalview/io/PIRFile.js
 105 jalview/io/ScoreMatrixFile.js
 106 jalview/io/SequenceAnnotationReport.js
 107 jalview/javascript/log4j/ConsoleAppender.js
 108 jalview/javascript/log4j/Layout.js
 109 jalview/javascript/log4j/Level.js
 110 jalview/javascript/log4j/Logger.js
 111 jalview/javascript/log4j/Priority.js
 112 jalview/javascript/log4j/SimpleLayout.js
 113 jalview/javascript/log4j/spi/OptionHandler.js
 114 jalview/jbgui/GAlignFrame.js
 115 jalview/jbgui/GAlignmentPanel.js
 116 jalview/jbgui/GDesktop.js
 117 jalview/project/Jalview2XML.js
 118 jalview/renderer/AnnotationRenderer.js
 119 jalview/renderer/AwtRenderPanelI.js
 120 jalview/renderer/ResidueColourFinder.js
 121 jalview/renderer/ResidueShader.js
 122 jalview/renderer/ResidueShaderI.js
 123 jalview/renderer/ScaleRenderer.js
 124 jalview/renderer/seqfeatures/FeatureRenderer.js
 125 jalview/schemes/Blosum62ColourScheme.js
 126 jalview/schemes/BuriedColourScheme.js
 127 jalview/schemes/ClustalxColourScheme.js
 128 jalview/schemes/ColourSchemeI.js
 129 jalview/schemes/ColourSchemeProperty.js
 130 jalview/schemes/ColourSchemes.js
 131 jalview/schemes/Consensus.js
 132 jalview/schemes/FeatureColour.js
 133 jalview/schemes/HelixColourScheme.js
 134 jalview/schemes/HydrophobicColourScheme.js
 135 jalview/schemes/JalviewColourScheme.js
 136 jalview/schemes/NucleotideColourScheme.js
 137 jalview/schemes/PIDColourScheme.js
 138 jalview/schemes/PurinePyrimidineColourScheme.js
 139 jalview/schemes/RNAHelicesColour.js
 140 jalview/schemes/ResidueColourScheme.js
 141 jalview/schemes/ResidueProperties.js
 142 jalview/schemes/ScoreColourScheme.js
 143 jalview/schemes/StrandColourScheme.js
 144 jalview/schemes/TCoffeeColourScheme.js
 145 jalview/schemes/TaylorColourScheme.js
 146 jalview/schemes/TurnColourScheme.js
 147 jalview/schemes/ZappoColourScheme.js
 148 jalview/structure/CommandListener.js
 149 jalview/structure/SelectionListener.js
 150 jalview/structure/SelectionSource.js
 151 jalview/structure/SequenceListener.js
 152 jalview/structure/StructureImportSettings.js
 153 jalview/structure/StructureSelectionManager.js
 154 jalview/structure/VamsasSource.js
 155 jalview/urls/IdOrgSettings.js
 156 jalview/util/ColorUtils.js
 157 jalview/util/Comparison.js
 158 jalview/util/DBRefUtils.js
 159 jalview/util/Format.js
 160 jalview/util/MessageManager.js
 161 jalview/util/Platform.js
 162 jalview/util/QuickSort.js
 163 jalview/util/jarInputStreamProvider.js
 164 jalview/util/matcher/Condition.js
 165 jalview/util/matcher/Matcher.js
 166 jalview/util/matcher/MatcherI.js
 167 jalview/viewmodel/AlignmentViewport.js
 168 jalview/viewmodel/ViewportListenerI.js
 169 jalview/viewmodel/ViewportProperties.js
 170 jalview/viewmodel/ViewportRanges.js
 171 jalview/viewmodel/seqfeatures/FeatureRendererModel.js
 172 jalview/viewmodel/seqfeatures/FeatureRendererSettings.js
 173 jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
 174 jalview/viewmodel/styles/ViewStyle.js
 175 jalview/workers/AlignCalcManager.js
 176 jalview/workers/AlignCalcWorker.js
 177 jalview/workers/ConsensusThread.js
 178 jalview/workers/ConservationThread.js
 179 jalview/ws/sifts/SiftsSettings.js
 180 jalview/xml/binding/jalview/Annotation.js
 181 jalview/xml/binding/jalview/AnnotationElement.js
 182 jalview/xml/binding/jalview/Feature.js
 183 jalview/xml/binding/jalview/FeatureMatcher.js
 184 jalview/xml/binding/jalview/FeatureMatcherSet.js
 185 jalview/xml/binding/jalview/FilterBy.js
 186 jalview/xml/binding/jalview/JalviewModel.js
 187 jalview/xml/binding/jalview/NoValueColour.js
 188 jalview/xml/binding/jalview/Pdbentry.js
 189 jalview/xml/binding/jalview/Sequence.js
 190 jalview/xml/binding/jalview/SequenceSet.js
 191 jalview/xml/binding/jalview/SequenceType.js
 192 jalview/xml/binding/jalview/VAMSAS.js
 193 jalview/xml/binding/jalview/WebServiceParameterSet.js
 194 java/awt/AWTKeyStroke.js
 195 java/awt/AlphaComposite.js
 196 java/awt/Composite.js
 197 java/awt/ContainerOrderFocusTraversalPolicy.js
 198 java/awt/DefaultFocusTraversalPolicy.js
 199 java/awt/DefaultKeyboardFocusManager.js
 200 java/awt/FocusTraversalPolicy.js
 201 java/awt/GridLayout.js
 202 java/awt/Image.js
 203 java/awt/KeyEventDispatcher.js
 204 java/awt/KeyEventPostProcessor.js
 205 java/awt/KeyboardFocusManager.js
 206 java/awt/VKCollection.js
 207 java/awt/datatransfer/ClipboardOwner.js
 208 java/awt/datatransfer/FlavorMap.js
 209 java/awt/datatransfer/FlavorTable.js
 210 java/awt/datatransfer/SystemFlavorMap.js
 211 java/awt/dnd/DropTarget.js
 212 java/awt/dnd/DropTargetContext.js
 213 java/awt/dnd/DropTargetListener.js
 214 java/awt/dnd/peer/DropTargetPeer.js
 215 java/awt/event/ComponentAdapter.js
 216 java/awt/event/ContainerEvent.js
 217 java/awt/event/FocusAdapter.js
 218 java/awt/event/KeyAdapter.js
 219 java/awt/event/MouseAdapter.js
 220 java/awt/event/MouseMotionAdapter.js
 221 java/awt/geom/Path2D.js
 222 java/awt/geom/PathIterator.js
 223 java/awt/geom/RectIterator.js
 224 java/awt/image/BufferedImage.js
 225 java/awt/image/ColorModel.js
 226 java/awt/image/DataBuffer.js
 227 java/awt/image/DataBufferInt.js
 228 java/awt/image/DirectColorModel.js
 229 java/awt/image/PackedColorModel.js
 230 java/awt/image/Raster.js
 231 java/awt/image/RenderedImage.js
 232 java/awt/image/SampleModel.js
 233 java/awt/image/SinglePixelPackedSampleModel.js
 234 java/awt/image/WritableRaster.js
 235 java/awt/peer/KeyboardFocusManagerPeer.js
 236 java/awt/print/Printable.js
 237 java/io/BufferedInputStream.js
 238 java/io/BufferedReader.js
 239 java/io/ByteArrayInputStream.js
 240 java/io/Closeable.js
 241 java/io/File.js
 242 java/io/FileDescriptor.js
 243 java/io/FileInputStream.js
 244 java/io/FileSystem.js
 245 java/io/FilterInputStream.js
 246 java/io/InputStream.js
 247 java/io/InputStreamReader.js
 248 java/io/PushbackInputStream.js
 249 java/io/Reader.js
 250 java/lang/AutoCloseable.js
 251 java/lang/Iterable.js
 252 java/lang/Readable.js
 253 java/lang/Runtime.js
 254 java/lang/StringBuilder.js
 255 java/lang/reflect/Constructor.js
 256 java/lang/reflect/Method.js
 257 java/math/BigDecimal.js
 258 java/math/BigInteger.js
 259 java/math/MathContext.js
 260 java/math/RoundingMode.js
 261 java/net/HttpURLConnection.js
 262 java/net/MalformedURLException.js
 263 java/net/URLConnection.js
 264 java/net/URLDecoder.js
 265 java/net/URLStreamHandler.js
 266 java/security/AccessControlContext.js
 267 java/security/AccessController.js
 268 java/security/PrivilegedAction.js
 269 java/security/PrivilegedExceptionAction.js
 270 java/text/AttributedCharacterIterator.js
 271 java/text/CharacterIterator.js
 272 java/text/DateFormat.js
 273 java/text/DateFormatSymbols.js
 274 java/text/DecimalFormat.js
 275 java/text/DecimalFormatSymbols.js
 276 java/text/DigitList.js
 277 java/text/FieldPosition.js
 278 java/text/Format.js
 279 java/text/MessageFormat.js
 280 java/text/NumberFormat.js
 281 java/text/SimpleDateFormat.js
 282 java/util/AbstractQueue.js
 283 java/util/AbstractSequentialList.js
 284 java/util/ArrayDeque.js
 285 java/util/BitSet.js
 286 java/util/Calendar.js
 287 java/util/Collection.js
 288 java/util/Comparator.js
 289 java/util/Deque.js
 290 java/util/Enumeration.js
 291 java/util/GregorianCalendar.js
 292 java/util/Iterator.js
 293 java/util/LinkedHashMap.js
 294 java/util/LinkedList.js
 295 java/util/List.js
 296 java/util/ListIterator.js
 297 java/util/ListResourceBundle.js
 298 java/util/Map.js
 299 java/util/NavigableMap.js
 300 java/util/NavigableSet.js
 301 java/util/Objects.js
 302 java/util/Properties.js
 303 java/util/PropertyResourceBundle.js
 304 java/util/Queue.js
 305 java/util/RandomAccess.js
 306 java/util/ResourceBundle.js
 307 java/util/Set.js
 308 java/util/SortedMap.js
 309 java/util/SortedSet.js
 310 java/util/StringTokenizer.js
 311 java/util/TimSort.js
 312 java/util/TimeZone.js
 313 java/util/TreeMap.js
 314 java/util/concurrent/AbstractExecutorService.js
 315 java/util/concurrent/BlockingQueue.js
 316 java/util/concurrent/ConcurrentHashMap.js
 317 java/util/concurrent/ConcurrentMap.js
 318 java/util/concurrent/Executor.js
 319 java/util/concurrent/ExecutorService.js
 320 java/util/concurrent/Executors.js
 321 java/util/concurrent/LinkedBlockingQueue.js
 322 java/util/concurrent/RejectedExecutionHandler.js
 323 java/util/concurrent/Semaphore.js
 324 java/util/concurrent/ThreadFactory.js
 325 java/util/concurrent/ThreadPoolExecutor.js
 326 java/util/concurrent/TimeUnit.js
 327 java/util/concurrent/atomic/AtomicBoolean.js
 328 java/util/concurrent/atomic/AtomicInteger.js
 329 java/util/concurrent/locks/AbstractOwnableSynchronizer.js
 330 java/util/concurrent/locks/AbstractQueuedSynchronizer.js
 331 java/util/concurrent/locks/Condition.js
 332 java/util/concurrent/locks/Lock.js
 333 java/util/concurrent/locks/ReadWriteLock.js
 334 java/util/concurrent/locks/ReentrantLock.js
 335 java/util/concurrent/locks/ReentrantReadWriteLock.js
 336 java/util/jar/JarEntry.js
 337 java/util/jar/JarInputStream.js
 338 java/util/logging/Level.js
 339 java/util/logging/Logger.js
 340 java/util/regex/Pattern.js
 341 java/util/zip/CRC32.js
 342 java/util/zip/Inflater.js
 343 java/util/zip/InflaterInputStream.js
 344 java/util/zip/ZipConstants.js
 345 java/util/zip/ZipEntry.js
 346 java/util/zip/ZipInputStream.js
 347 javajs/api/GenericLineReader.js
 348 javajs/api/JSONEncodable.js
 349 javajs/util/AjaxURLStreamHandler.js
 350 javajs/util/Encoding.js
 351 javajs/util/Rdr.js
 352 javajs/util/SB.js
 353 javax/swing/AbstractAction.js
 354 javax/swing/Action.js
 355 javax/swing/ComponentInputMap.js
 356 javax/swing/DefaultDesktopManager.js
 357 javax/swing/DesktopManager.js
 358 javax/swing/InputMap.js
 359 javax/swing/JDesktopPane.js
 360 javax/swing/JDialog.js
 361 javax/swing/JInternalFrame.js
 362 javax/swing/JProgressBar.js
 363 javax/swing/JScrollPane.js
 364 javax/swing/JTabbedPane.js
 365 javax/swing/JToolTip.js
 366 javax/swing/JViewport.js
 367 javax/swing/KeyStroke.js
 368 javax/swing/ScrollPaneConstants.js
 369 javax/swing/ScrollPaneLayout.js
 370 javax/swing/Scrollable.js
 371 javax/swing/Timer.js
 372 javax/swing/ToolTipManager.js
 373 javax/swing/ViewportLayout.js
 374 javax/swing/border/LineBorder.js
 375 javax/swing/event/InternalFrameAdapter.js
 376 javax/swing/event/InternalFrameEvent.js
 377 javax/swing/event/InternalFrameListener.js
 378 javax/swing/event/MenuListener.js
 379 javax/swing/plaf/ComponentInputMapUIResource.js
 380 javax/xml/bind/ContextFinder.js
 381 javax/xml/bind/GetPropertyAction.js
 382 javax/xml/bind/JAXBContext.js
 383 javax/xml/bind/JAXBContextFactory.js
 384 javax/xml/bind/JAXBElement.js
 385 javax/xml/bind/ModuleUtil.js
 386 javax/xml/bind/ServiceLoaderUtil.js
 387 javax/xml/bind/Unmarshaller.js
 388 javax/xml/bind/ValidationEventHandler.js
 389 javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js
 390 javax/xml/bind/annotation/adapters/XmlAdapter.js
 391 javax/xml/bind/helpers/AbstractUnmarshallerImpl.js
 392 javax/xml/bind/helpers/DefaultValidationEventHandler.js
 393 javax/xml/datatype/XMLGregorianCalendar.js
 394 javax/xml/namespace/QName.js
 395 javax/xml/stream/XMLInputFactory.js
 396 javax/xml/stream/XMLStreamReader.js
 397 org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js
 398 org/xml/sax/AttributeList.js
 399 org/xml/sax/Attributes.js
 400 org/xml/sax/ContentHandler.js
 401 org/xml/sax/InputSource.js
 402 org/xml/sax/Parser.js
 403 org/xml/sax/XMLReader.js
 404 org/xml/sax/ext/Attributes2.js
 405 sun/awt/AWTAccessor.js
 406 sun/awt/CausedFocusEvent.js
 407 sun/awt/KeyboardFocusManagerPeerProvider.js
 408 sun/awt/SunGraphicsCallback.js
 409 sun/awt/image/DataStealer.js
 410 sun/awt/image/IntegerComponentRaster.js
 411 sun/awt/image/IntegerInterleavedRaster.js
 412 sun/awt/image/SunWritableRaster.js
 413 sun/font/FontDesignMetrics.js
 414 sun/java2d/StateTrackable.js
 415 sun/java2d/StateTrackableDelegate.js
 416 sun/swing/DefaultLookup.js
 417 sun/text/resources/FormatData.js
 418 sun/text/resources/FormatData_en.js
 419 sun/util/calendar/AbstractCalendar.js
 420 sun/util/calendar/BaseCalendar.js
 421 sun/util/calendar/CalendarDate.js
 422 sun/util/calendar/CalendarSystem.js
 423 sun/util/calendar/CalendarUtils.js
 424 sun/util/calendar/Gregorian.js
 425 sun/util/calendar/ZoneInfo.js
 426 sun/util/resources/LocaleData.js
 427 swingjs/JSFocusManager.js
 428 swingjs/a2s/Dialog.js
 429 swingjs/jzlib/Adler32.js
 430 swingjs/jzlib/CRC32.js
 431 swingjs/jzlib/Checksum.js
 432 swingjs/jzlib/InfBlocks.js
 433 swingjs/jzlib/InfCodes.js
 434 swingjs/jzlib/InfTree.js
 435 swingjs/jzlib/Inflate.js
 436 swingjs/jzlib/Inflater.js
 437 swingjs/jzlib/InflaterInputStream.js
 438 swingjs/jzlib/ZStream.js
 439 swingjs/plaf/JSAppletUI.js
 440 swingjs/plaf/JSDesktopIconUI.js
 441 swingjs/plaf/JSDesktopPaneUI.js
 442 swingjs/plaf/JSGraphicsUtils.js
 443 swingjs/plaf/JSInternalFrameUI.js
 444 swingjs/plaf/JSProgressBarUI.js
 445 swingjs/plaf/JSScrollPaneUI.js
 446 swingjs/plaf/JSTabbedPaneUI.js
 447 swingjs/plaf/JSToolTipUI.js
 448 swingjs/plaf/JSViewportUI.js
 449 swingjs/xml/JSJAXBClass.js
 450 swingjs/xml/JSJAXBContext.js
 451 swingjs/xml/JSJAXBContextFactory.js
 452 swingjs/xml/JSJAXBField.js
 453 swingjs/xml/JSJAXBUnmarshaller.js
 454 swingjs/xml/JSSAXAttributes.js
 455 swingjs/xml/JSSAXParser.js
 456 swingjs/xml/JSXMLGregorianCalendarImpl.js
 457 swingjs/xml/JSXMLInputFactory.js
 458 swingjs/xml/JSXMLStreamReader.js