buildSite.xml

   1 <project name="swingjs" default="createSite" basedir=".">
   2
   3 <!-- buildSite.xml for building site/ -->
   4
   5
   6   <target name="createSite" id="createSite">
   7
   8         <property name="project.path" value="." />
   9
  10         <!-- create a NON svn local directory only containing JS files  -->
  11
  12     <echo>...adding JavaScript files from bin</echo>
  13         <copy todir="site/j2s"  overwrite="true" >
  14       <fileset dir="bin">
  15         <include name="**/*.js" />
  16         <exclude name="javajs/**/*.js" />
  17       </fileset>
  18     </copy>
  19
  20         <echo>...adding package.js from ${project.path}/package</echo>
  21         <copy todir="site/j2s/core">
  22           <fileset dir="${project.path}/package">
  23             <include name="package.js" />
  24           </fileset>
  25     </copy>
  26
  27
  28         <echo>...adding to /j2s all src property and css files -- adjust as necessary</echo>
  29         <copy todir="site/j2s"  overwrite="true" >
  30       <fileset dir="src">
  31         <include name="**/*.properties" />
  32         <include name="**/*.css" />
  33         <include name="**/*.png" />
  34       </fileset>
  35     </copy>
  36
  37         <echo>...adding resource directory</echo>
  38         <copy todir="site/j2s/jalview/resources"  overwrite="true" >
  39       <fileset dir="resources">
  40         <include name="**/*" />
  41       </fileset>
  42     </copy>
  43
  44         <!-- modify class names -->
  45
  46     <echo>removing j2s globals Class and JavaObject</echo>
  47     <echo>...replacing Class.forName with Clazz._4Name</echo>
  48         <replace dir="site/j2s" includes="**/*.js" token="Class.forName" value="Clazz._4Name"/>
  49     <echo>...replacing JavaObject with Clazz._O</echo>
  50         <replace dir="site/j2s" includes="**/*.js" token=" JavaObject" value=" Clazz._O"/>
  51     <echo>...removing all $fz references for sub/superclass common private function names (not recommended, actually -- see note in Bob's log)</echo>
  52         <replace dir="site/j2s" includes="**/*.js" token="($fz =" value=""/>
  53         <replace dir="site/j2s" includes="**/*.js" token=", $fz.isPrivate = true, $fz)" value=""/>
  54         <echo>...changing Clazz.pu$h() to Clazz.pu$h(self.c$) (only a partial fix)</echo>
  55         <replace dir="site/j2s" includes="**/*.js" token="Clazz.pu$h()" value="Clazz.pu$h(self.c$)"/>
  56         <replace dir="site/j2s" includes="**/*.js" token="Clazz.pu$h ()" value="Clazz.pu$h(self.c$)"/>
  57
  58
  59     <echo>...abbreviating class name "javajs.util", and "com.jcraft.jzlib" to "JU"</echo>
  60         <replace dir="site/j2s" includes="**/*.js" token="javajs.util" value="JU"/>
  61         <replace dir="site/j2s" includes="**/*.js" token="com.jcraft.jzlib" value="JU"/>
  62
  63
  64         <!-- make core files -->
  65
  66         <echo>creating and compressing core files - warnings are OK; "does not exist" is trouble</echo>
  67
  68         <!-- note: any changes in these next sections must be reflected also
  69                      in package.js -->
  70 <!--
  71     <property name="javaCoreFiles" value="
  72         java/lang/AbstractStringBuilder.js
  73         java/lang/Enum.js
  74         ...
  75         " />
  76
  77
  78
  79 -->
  80
  81         <echo>creating minimal corejalview.z.js</echo>
  82
  83     <antcall target="call-core">
  84         <param name="call-core.name" value="jalview" />
  85         <param name="call-core.list" value="
  86             java/io/InputStreamReader.js
  87             javax/swing/text/JTextComponent.js
  88             javax/swing/text/Keymap.js
  89             javax/swing/text/DefaultEditorKit.js
  90             javax/swing/text/EditorKit.js
  91             javax/swing/text/TextAction.js
  92             javax/swing/text/BadLocationException.js
  93             javax/swing/text/DefaultCaret.js
  94             javax/swing/text/Caret.js
  95             javax/swing/text/NavigationFilter.js
  96             javax/swing/text/AbstractDocument.js
  97             javax/swing/event/DocumentEvent.js
  98             javax/swing/text/DocumentFilter.js
  99             javax/swing/text/Element.js
 100             javax/swing/text/JSMinimalAbstractDocument.js
 101             javax/swing/text/Document.js
 102             javax/swing/text/MutableAttributeSet.js
 103             javax/swing/text/AttributeSet.js
 104             javax/swing/tree/TreeNode.js
 105             javax/swing/undo/AbstractUndoableEdit.js
 106             javax/swing/undo/UndoableEdit.js
 107             javax/swing/undo/CannotRedoException.js
 108             javax/swing/undo/CannotUndoException.js
 109             javax/swing/undo/CompoundEdit.js
 110             javax/swing/event/UndoableEditEvent.js
 111             javax/swing/event/UndoableEditListener.js
 112             javax/swing/text/SegmentCache.js
 113             javax/swing/text/Segment.js
 114             javax/swing/text/StateInvariantError.js
 115             javax/swing/text/StyleConstants.js
 116             javax/swing/text/StyleContext.js
 117             javax/swing/text/Style.js
 118             javax/swing/text/SimpleAttributeSet.js
 119             javax/swing/text/Utilities.js
 120             javax/swing/text/CompositeView.js
 121             javax/swing/text/View.js
 122             javax/swing/text/Position.js
 123             javax/swing/text/StyledDocument.js
 124             javax/swing/text/DefaultHighlighter.js
 125             javax/swing/text/Highlighter.js
 126             javax/swing/text/LayeredHighlighter.js
 127             swingjs/JSPlainDocument.js
 128             swingjs/JSAbstractDocument.js
 129             swingjs/JSDocumentEvent.js
 130             swingjs/JSPosition.js
 131             swingjs/api/HTML5CanvasContext2D.js
 132             javax/swing/DefaultListCellRenderer.js
 133             javax/swing/ListCellRenderer.js
 134             javax/swing/border/EmptyBorder.js
 135             jssun/swing/DefaultLookup.js
 136             javax/swing/plaf/DimensionUIResource.js
 137             javax/swing/plaf/InsetsUIResource.js
 138             swingjs/plaf/JSEventHandler.js
 139             JU/AjaxURLStreamHandlerFactory.js
 140             java/net/URLStreamHandlerFactory.js
 141             JU/AjaxURLStreamHandler.js
 142             java/net/URLStreamHandler.js
 143             JU/AjaxURLConnection.js
 144             java/net/URLConnection.js
 145             java/net/UnknownServiceException.js
 146
 147             jalview/bin/JalviewLite.js
 148             javax/swing/JButton.js
 149             jalview/util/MessageManager.js
 150             java/util/logging/Logger.js
 151             java/util/logging/LogRecord.js
 152             java/util/logging/Level.js
 153             java/text/MessageFormat.js
 154             java/util/PropertyResourceBundle.js
 155             jalview/javascript/JalviewLiteJsApi.js
 156             jalview/api/StructureSelectionManagerProvider.js
 157             awt2swing/Util.js
 158             jalview/analysis/SequenceIdMatcher.js
 159             jalview/appletgui/AlignFrame.js
 160             awt2swing/Canvas.js
 161             awt2swing/Panel.js
 162             jalview/api/AlignViewControllerGuiI.js
 163             jalview/appletgui/EmbmenuFrame.js
 164             awt2swing/Frame.js
 165             awt2swing/Label.js
 166             awt2swing/PopupMenu.js
 167             jalview/util/Platform.js
 168             awt2swing/CheckboxMenuItem.js
 169             awt2swing/Menu.js
 170             awt2swing/MenuBar.js
 171             awt2swing/MenuItem.js
 172             jalview/analysis/AlignmentSorter.js
 173             jalview/datamodel/SequenceI.js
 174             jalview/datamodel/ASequenceI.js
 175             jalview/util/Comparison.js
 176             jalview/util/QuickSort.js
 177             jalview/analysis/AnnotationSorter.js
 178             jalview/analysis/AlignmentUtils.js
 179             jalview/analysis/CodonComparator.js
 180             jalview/datamodel/AlignedCodonFrame.js
 181             jalview/datamodel/Mapping.js
 182             jalview/datamodel/AlignedCodon.js
 183             jalview/datamodel/IncompleteCodonException.js
 184             jalview/datamodel/SequenceFeature.js
 185             jalview/util/MapList.js
 186             jalview/util/MappingUtils.js
 187             jalview/commands/EditCommand.js
 188             jalview/commands/CommandI.js
 189             jalview/analysis/AlignSeq.js
 190             jalview/schemes/ResidueProperties.js
 191             jalview/analysis/scoremodels/FeatureScoreModel.js
 192             jalview/api/analysis/ScoreModelI.js
 193             jalview/api/analysis/ViewBasedAnalysisI.js
 194             jalview/analysis/scoremodels/PIDScoreModel.js
 195             jalview/schemes/ScoreMatrix.js
 196             jalview/analysis/scoremodels/PairwiseSeqScoreModel.js
 197             jalview/datamodel/Sequence.js
 198             jalview/datamodel/ASequence.js
 199             jalview/jsdev/RegExp.js
 200             com/stevesoft/pat/Regex.js
 201             com/stevesoft/pat/RegRes.js
 202             com/stevesoft/pat/UniValidator.js
 203             com/stevesoft/pat/Validator.js
 204             com/stevesoft/pat/patInf.js
 205             com/stevesoft/pat/patInt.js
 206             jalview/jsdev/api/RegExpInterface.js
 207             com/stevesoft/pat/NoPattern.js
 208             com/stevesoft/pat/Pattern.js
 209             com/stevesoft/pat/MessageManager.js
 210             com/stevesoft/pat/Pthings.js
 211             com/stevesoft/pat/Any.js
 212             com/stevesoft/pat/BackG.js
 213             com/stevesoft/pat/BackMatch.js
 214             com/stevesoft/pat/Backup.js
 215             com/stevesoft/pat/Boundary.js
 216             com/stevesoft/pat/Bracket.js
 217             com/stevesoft/pat/Or.js
 218             com/stevesoft/pat/CaseMgr.js
 219             com/stevesoft/pat/Ctrl.js
 220             com/stevesoft/pat/Custom.js
 221             com/stevesoft/pat/PatternSub.js
 222             com/stevesoft/pat/CustomEndpoint.js
 223             com/stevesoft/pat/DotMulti.js
 224             com/stevesoft/pat/End.js
 225             com/stevesoft/pat/FastMulti.js
 226             com/stevesoft/pat/RegSyntaxError.js
 227             com/stevesoft/pat/RegSyntax.js
 228             com/stevesoft/pat/Group.js
 229             com/stevesoft/pat/Multi.js
 230             com/stevesoft/pat/Multi_stage2.js
 231             com/stevesoft/pat/NullPattern.js
 232             com/stevesoft/pat/OrMark.js
 233             com/stevesoft/pat/SubMark.js
 234             com/stevesoft/pat/Prop.js
 235             com/stevesoft/pat/Bits.js
 236             com/stevesoft/pat/Range.js
 237             com/stevesoft/pat/oneChar.js
 238             com/stevesoft/pat/RegOpt.js
 239             com/stevesoft/pat/FastBracket.js
 240             java/util/BitSet.js
 241             com/stevesoft/pat/ReplaceRule.js
 242             com/stevesoft/pat/Transformer.js
 243             com/stevesoft/pat/Replacer.js
 244             com/stevesoft/pat/AmpersandRule.js
 245             com/stevesoft/pat/ChangeRule.js
 246             com/stevesoft/pat/SpecialRule.js
 247             com/stevesoft/pat/PopRule.js
 248             com/stevesoft/pat/PushRule.js
 249             com/stevesoft/pat/RuleHolder.js
 250             com/stevesoft/pat/StringBufferLike.js
 251             com/stevesoft/pat/BasicStringBufferLike.js
 252             com/stevesoft/pat/WantMoreTextReplaceRule.js
 253             com/stevesoft/pat/wrap/StringWrap.js
 254             com/stevesoft/pat/StringLike.js
 255             com/stevesoft/pat/wrap/StringBufferWrap.js
 256             com/stevesoft/pat/TransPat.js
 257             com/stevesoft/pat/Rthings.js
 258             com/stevesoft/pat/Skip.js
 259             com/stevesoft/pat/Skipped.js
 260             com/stevesoft/pat/Start.js
 261             com/stevesoft/pat/StrPos.js
 262             com/stevesoft/pat/lookAhead.js
 263             com/stevesoft/pat/parsePerl.js
 264             com/stevesoft/pat/StringRule.js
 265             jalview/datamodel/AlignmentAnnotation.js
 266             jalview/analysis/Rna.js
 267             jalview/analysis/SecStrConsensus.js
 268             jalview/analysis/WUSSParseException.js
 269             java/util/Stack.js
 270             jalview/datamodel/Annotation.js
 271             jalview/datamodel/GraphLine.js
 272             jalview/datamodel/DBRefEntry.js
 273             jalview/datamodel/DBRefSource.js
 274             jalview/datamodel/PDBEntry.js
 275             jalview/util/StringUtils.js
 276             java/util/regex/Pattern.js
 277             java/util/regex/Matcher.js
 278             java/util/regex/MatchResult.js
 279             jalview/util/Format.js
 280             jalview/util/ReverseListIterator.js
 281             jalview/commands/OrderCommand.js
 282             jalview/datamodel/AlignmentOrder.js
 283             jalview/datamodel/ColumnSelection.js
 284             jalview/util/ShiftList.js
 285             jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js
 286             jalview/datamodel/SearchResults.js
 287             jalview/datamodel/SequenceGroup.js
 288             jalview/datamodel/AnnotatedCollectionI.js
 289             jalview/datamodel/SequenceCollectionI.js
 290             jalview/analysis/AAFrequency.js
 291             jalview/analysis/CodingUtils.js
 292             jalview/analysis/Conservation.js
 293             jalview/datamodel/Alignment.js
 294             jalview/datamodel/AlignmentI.js
 295             jalview/datamodel/HiddenSequences.js
 296             java/util/LinkedHashSet.js
 297             java/util/LinkedHashMap.js
 298             jalview/datamodel/CigarArray.js
 299             jalview/datamodel/CigarBase.js
 300             jalview/datamodel/CigarCigar.js
 301             jalview/datamodel/CigarSimple.js
 302             jalview/datamodel/SeqCigar.js
 303             jalview/analysis/SeqsetUtils.js
 304             jalview/datamodel/FeatureProperties.js
 305             jalview/util/DBRefUtils.js
 306             java/util/TreeMap.js
 307             jalview/appletgui/AlignViewport.js
 308             jalview/structure/CommandListener.js
 309             jalview/structure/SelectionSource.js
 310             jalview/structure/VamsasSource.js
 311             jalview/viewmodel/AlignmentViewport.js
 312             jalview/api/AlignViewportI.js
 313             jalview/api/ViewStyleI.js
 314             jalview/viewmodel/styles/ViewStyle.js
 315             jalview/workers/AlignCalcManager.js
 316             jalview/api/AlignCalcManagerI.js
 317             java/util/ArrayDeque.js
 318             java/util/Deque.js
 319             jalview/datamodel/AlignmentView.js
 320             jalview/schemes/Blosum62ColourScheme.js
 321             jalview/schemes/ResidueColourScheme.js
 322             jalview/schemes/ColourSchemeI.js
 323             jalview/schemes/PIDColourScheme.js
 324             jalview/workers/ComplementConsensusThread.js
 325             jalview/workers/ConsensusThread.js
 326             jalview/api/AlignCalcWorkerI.js
 327             jalview/workers/AlignCalcWorker.js
 328             jalview/workers/ConservationThread.js
 329             jalview/workers/StrucConsensusThread.js
 330             jalview/analysis/StructureFrequency.js
 331             jalview/schemes/ColourSchemeProperty.js
 332             jalview/schemes/BuriedColourScheme.js
 333             jalview/schemes/ScoreColourScheme.js
 334             jalview/schemes/ClustalxColourScheme.js
 335             jalview/schemes/Consensus.js
 336             jalview/schemes/HelixColourScheme.js
 337             jalview/schemes/HydrophobicColourScheme.js
 338             jalview/schemes/NucleotideColourScheme.js
 339             jalview/schemes/PurinePyrimidineColourScheme.js
 340             jalview/schemes/RNAHelicesColour.js
 341             jalview/util/ColorUtils.js
 342             jalview/schemes/StrandColourScheme.js
 343             jalview/schemes/TCoffeeColourScheme.js
 344             jalview/schemes/TaylorColourScheme.js
 345             jalview/schemes/TurnColourScheme.js
 346             jalview/schemes/UserColourScheme.js
 347             jalview/schemes/ZappoColourScheme.js
 348             jalview/structure/StructureSelectionManager.js
 349             MCview/PDBfile.js
 350             jalview/io/AlignFile.js
 351             jalview/io/FileParse.js
 352             jalview/io/AppletFormatAdapter.js
 353             jalview/io/IdentifyFile.js
 354             jalview/jsdev/GenericFileAdapter.js
 355             java/util/zip/GZIPInputStream.js
 356             java/util/zip/InflaterInputStream.js
 357             JU/InflaterInputStream.js
 358             java/util/zip/CRC32.js
 359             JU/CRC32.js
 360             JU/Checksum.js
 361             java/util/zip/CheckedInputStream.js
 362             java/util/zip/Inflater.js
 363             JU/Inflater.js
 364             JU/ZStream.js
 365             JU/Adler32.js
 366             JU/Inflate.js
 367             JU/GZIPHeader.js
 368             JU/InfBlocks.js
 369             JU/InfTree.js
 370             JU/InfCodes.js
 371             java/io/ByteArrayOutputStream.js
 372             java/io/OutputStream.js
 373             java/util/zip/ZipException.js
 374             MCview/Atom.js
 375             MCview/PDBChain.js
 376             MCview/Bond.js
 377             MCview/Residue.js
 378             jalview/structure/AtomSpec.js
 379             jalview/structure/SecondaryStructureListener.js
 380             jalview/structure/SequenceListener.js
 381             jalview/structure/StructureListener.js
 382             jalview/structure/StructureMapping.js
 383             jalview/structure/VamsasListener.js
 384             jalview/appletgui/AlignmentPanel.js
 385             jalview/api/AlignmentViewPanel.js
 386             jalview/api/OOMHandlerI.js
 387             awt2swing/Scrollbar.js
 388             javax/swing/JScrollBar.js
 389             java/awt/Adjustable.js
 390             java/awt/event/AdjustmentEvent.js
 391             jalview/appletgui/AnnotationLabels.js
 392             awt2swing/Checkbox.js
 393             jalview/appletgui/CutAndPasteTransfer.js
 394             awt2swing/Button.js
 395             awt2swing/TextArea.js
 396             javax/swing/JTextArea.js
 397             jalview/api/ComplexAlignFile.js
 398             jalview/appletgui/AppletJmol.js
 399             jalview/appletgui/JVDialog.js
 400             jalview/appletgui/SplitFrame.js
 401             java/awt/GridLayout.js
 402             jalview/io/AnnotationFile.js
 403             jalview/io/NewickFile.js
 404             jalview/datamodel/SequenceNode.js
 405             jalview/datamodel/BinaryNode.js
 406             jalview/appletgui/EditNameDialog.js
 407             awt2swing/TextField.js
 408             java/awt/event/TextEvent.js
 409             jalview/appletgui/PaintRefresher.js
 410             jalview/appletgui/Tooltip.js
 411             jalview/util/ParseHtmlBodyAndLinks.js
 412             jalview/appletgui/AnnotationPanel.js
 413             jalview/renderer/AwtRenderPanelI.js
 414             jalview/appletgui/UserDefinedColours.js
 415             jalview/appletgui/AnnotationColourChooser.js
 416             awt2swing/Choice.js
 417             javax/swing/JComboBox.js
 418             javax/swing/event/ListDataListener.js
 419             javax/swing/DefaultComboBoxModel.js
 420             javax/swing/AbstractListModel.js
 421             javax/swing/ListModel.js
 422             javax/swing/event/ListDataEvent.js
 423             javax/swing/MutableComboBoxModel.js
 424             javax/swing/ComboBoxModel.js
 425             jalview/schemes/AnnotationColourGradient.js
 426             jalview/schemes/FollowerColourScheme.js
 427             jalview/renderer/AnnotationRenderer.js
 428             jalview/appletgui/FeatureColourChooser.js
 429             jalview/schemes/GraduatedColor.js
 430             jalview/appletgui/FeatureRenderer.js
 431             jalview/renderer/seqfeatures/FeatureRenderer.js
 432             jalview/viewmodel/seqfeatures/FeatureRendererModel.js
 433             jalview/api/FeatureRenderer.js
 434             java/util/concurrent/ConcurrentHashMap.js
 435             jalview/viewmodel/seqfeatures/FeatureRendererSettings.js
 436             jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
 437             jalview/api/FeaturesDisplayedI.js
 438             java/awt/AlphaComposite.js
 439             java/awt/Composite.js
 440             jssun/java2d/SunCompositeContext.js
 441             java/awt/CompositeContext.js
 442             java/awt/image/BufferedImage.js
 443             java/awt/Image.js
 444             java/awt/image/DirectColorModel.js
 445             java/awt/image/PackedColorModel.js
 446             java/awt/image/Raster.js
 447             java/awt/image/MultiPixelPackedSampleModel.js
 448             java/awt/image/SampleModel.js
 449             java/awt/image/DataBuffer.js
 450             jssun/java2d/StateTrackable.js
 451             jssun/java2d/StateTrackableDelegate.js
 452             jssun/java2d/StateTracker.js
 453             java/awt/image/DataBufferByte.js
 454             java/awt/image/DataBufferInt.js
 455             java/awt/image/RasterFormatException.js
 456             java/awt/image/SinglePixelPackedSampleModel.js
 457             jssun/awt/image/OffScreenImageSource.js
 458             java/awt/image/WritableRaster.js
 459             jssun/java2d/loops/CompositeType.js
 460             awt2swing/ScrollPane.js
 461             javax/swing/JScrollPane.js
 462             javax/swing/ScrollPaneConstants.js
 463             javax/swing/ScrollPaneLayout.js
 464             jalview/io/FeaturesFile.js
 465             jalview/datamodel/SequenceDummy.js
 466             java/awt/event/MouseAdapter.js
 467             jalview/appletgui/FeatureSettings.js
 468             jalview/api/FeatureSettingsControllerI.js
 469             jalview/appletgui/IdPanel.js
 470             jalview/appletgui/APopupMenu.js
 471             jalview/analysis/AlignmentAnnotationUtils.js
 472             jalview/appletgui/SliderPanel.js
 473             jalview/commands/ChangeCaseCommand.js
 474             jalview/io/SequenceAnnotationReport.js
 475             jalview/util/UrlLink.js
 476             jalview/appletgui/IdCanvas.js
 477             jalview/appletgui/IdwidthAdjuster.js
 478             jalview/appletgui/ScalePanel.js
 479             jalview/appletgui/SeqPanel.js
 480             jalview/structure/SelectionListener.js
 481             jalview/appletgui/SeqCanvas.js
 482             jalview/appletgui/SequenceRenderer.js
 483             jalview/api/SequenceRenderer.js
 484             jalview/appletgui/AnnotationColumnChooser.js
 485             jalview/appletgui/AnnotationRowFilter.js
 486             jalview/appletgui/TitledPanel.js
 487             java/awt/CardLayout.js
 488             java/io/ObjectStreamField.js
 489             jalview/appletgui/Finder.js
 490             jalview/analysis/Finder.js
 491             java/awt/event/KeyAdapter.js
 492             jalview/appletgui/FontChooser.js
 493             jalview/appletgui/OverviewPanel.js
 494             jalview/appletgui/PCAPanel.js
 495             jalview/appletgui/RotatableCanvas.js
 496             jalview/api/RotatableCanvasI.js
 497             jalview/math/RotatableMatrix.js
 498             jalview/viewmodel/PCAModel.js
 499             jalview/analysis/PCA.js
 500             jalview/datamodel/BinarySequence.js
 501             jalview/math/Matrix.js
 502             jalview/datamodel/SequencePoint.js
 503             jalview/appletgui/PairwiseAlignPanel.js
 504             jalview/appletgui/RedundancyPanel.js
 505             jalview/appletgui/TreePanel.js
 506             jalview/analysis/NJTree.js
 507             jalview/datamodel/NodeTransformI.js
 508             jalview/appletgui/TreeCanvas.js
 509             jalview/commands/RemoveGapColCommand.js
 510             jalview/commands/RemoveGapsCommand.js
 511             jalview/commands/SlideSequencesCommand.js
 512             jalview/commands/TrimRegionCommand.js
 513             jalview/controller/AlignViewController.js
 514             jalview/api/AlignViewControllerI.js
 515             jalview/analysis/Grouping.js
 516             jalview/io/AlignmentProperties.js
 517             jalview/schemes/RNAHelicesColourChooser.js
 518             jalview/schemes/RNAInteractionColourScheme.js
 519             java/net/URLEncoder.js
 520             jalview/io/JnetAnnotationMaker.js
 521             jalview/javascript/JSFunctionExec.js
 522             netscape/javascript/JSException.js
 523             netscape/javascript/JSObject.js
 524             jalview/javascript/JsSelectionSender.js
 525             jalview/javascript/JsCallBack.js
 526             jalview/javascript/MouseOverListener.js
 527             jalview/javascript/MouseOverStructureListener.js
 528             jalview/ext/jmol/JmolCommands.js
 529             jalview/structure/StructureMappingcommandSet.js
 530             java/util/Properties.js
 531             jssun/util/ResourceBundleEnumeration.js
 532             jalview/io/FastaFile.js
 533             swingjs/plaf/JSMenuBarUI.js
 534             swingjs/plaf/JSMenuUI.js
 535             swingjs/plaf/JSMenuItemUI.js
 536             swingjs/plaf/JSCheckBoxMenuItemUI.js
 537             swingjs/plaf/JSCheckBoxUI.js
 538             swingjs/plaf/JSLabelUI.js
 539             swingjs/plaf/JSPopupMenuUI.js
 540             swingjs/plaf/JSPopupMenuSeparatorUI.js
 541             swingjs/plaf/JSScrollBarUI.js
 542             swingjs/JSImagekit.js
 543             swingjs/JSImage.js
 544             jssun/awt/image/IntegerInterleavedRaster.js
 545             jssun/awt/image/IntegerComponentRaster.js
 546             jssun/awt/image/SunWritableRaster.js
 547             jssun/awt/image/DataStealer.js
 548                 "/>
 549     </antcall>
 550
 551         <!--
 552
 553         put classes in here temporarily to exclude them from the
 554         core load and make them easier to debug
 555
 556
 557         minimize additional JSmol JavaScript -->
 558
 559   </target>
 560
 561
 562           <target name="call-core" id="call-core">
 563                 <echo>......Creating core${call-core.name}.js</echo>
 564                 <concat destfile="site/js/core/tmp.js">
 565                         <filelist dir="site/j2s" files="${call-core.list}" />
 566                 </concat>
 567                 <!--
 568                         <echo>...removing unnecessary Clazz.defineStatics blocks</echo>
 569                   This next replacement does not work, because the j2s compiler does not
 570                   distinguish between final and non-final static variable.
 571                   We will have to do this on a case-by-case basis.
 572
 573                 <replaceregexp file="site/js/core2.js" match="(Clazz.defineStatics ?\(((?![\[\(]).)*?\);)" flags="gs" replace="/*\1*/" />
 574                 <copy file="site/js/core2.js" tofile="site/js/core${call-core.name}3.js" />
 575
 576
 577                         java/io/InputStreamReader.js
 578                     javax/swing/text/JTextComponent.js
 579                     javax/swing/text/DefaultCaret.js
 580                     javax/swing/text/Caret.js
 581                     javax/swing/text/NavigationFilter.js
 582                     javax/swing/text/AbstractDocument.js
 583                     javax/swing/event/DocumentEvent.js
 584                     javax/swing/text/Document.js
 585                     javax/swing/text/DocumentFilter.js
 586                     javax/swing/text/Element.js
 587                     javax/swing/text/MutableAttributeSet.js
 588                     javax/swing/text/AttributeSet.js
 589                     javax/swing/tree/TreeNode.js
 590                     javax/swing/undo/AbstractUndoableEdit.js
 591                     javax/swing/undo/UndoableEdit.js
 592                     javax/swing/undo/CannotRedoException.js
 593                     javax/swing/undo/CannotUndoException.js
 594                     javax/swing/undo/CompoundEdit.js
 595                     javax/swing/event/UndoableEditEvent.js
 596                     javax/swing/event/UndoableEditListener.js
 597                     javax/swing/text/BadLocationException.js
 598                     javax/swing/text/SegmentCache.js
 599                     javax/swing/text/Segment.js
 600                     javax/swing/text/SimpleAttributeSet.js
 601                     javax/swing/text/StyleConstants.js
 602                     javax/swing/text/StateInvariantError.js
 603                     javax/swing/text/StyleContext.js
 604                     javax/swing/text/Style.js
 605                     javax/swing/text/Utilities.js
 606                     javax/swing/text/CompositeView.js
 607                     javax/swing/text/View.js
 608                     javax/swing/text/Position.js
 609                     javax/swing/text/StyledDocument.js
 610                         javax/swing/text/DefaultEditorKit.js
 611                         javax/swing/text/EditorKit.js
 612                     javax/swing/text/TextAction.js
 613                     javax/swing/text/PlainDocument.js
 614                     javax/swing/text/DefaultHighlighter.js
 615                     javax/swing/text/Highlighter.js
 616                     javax/swing/text/LayeredHighlighter.js
 617                     javax/swing/text/Keymap.js
 618
 619                  -->
 620
 621                 <replace dir="site/js/core" includes="tmp.js" token="Clazz." value="Clazz_"/>
 622                 <replace dir="site/js/core" includes="tmp.js" token="Clazz__" value="Clazz._"/>
 623                 <replace dir="site/js/core" includes="tmp.js" token="($fz = " value=""/>
 624                 <replace dir="site/js/core" includes="tmp.js" token=", $fz.isPrivate = true, $fz)" value=""/>
 625                 <concat destfile="site/j2s/core/core${call-core.name}.js"><filelist dir="site/js" files="
 626                         core/coretop2.js
 627                         core/tmp.js
 628                         core/corebottom2.js
 629                         " />
 630                 </concat>
 631                 <echo>......Generating core${call-core.name}.z.js</echo>
 632                 <java jar="jars/closure_compiler.jar" fork="true" dir="site/j2s/core" failonerror="false">
 633                         <arg line="--js core${call-core.name}.js --js_output_file core${call-core.name}.z.js" />
 634             </java>
 635                 <delete quiet="true" file="site/js/core/tmp.js" />
 636           </target>
 637
 638 </project>