core_jalview creation

diff --git a/buildcore.xml b/buildcore.xml
new file mode 100644 (file)
index 0000000..f4dff04
--- /dev/null
+++ b/buildcore.xml
@@ -0,0 +1,60 @@
+<project name="JSmol" default="toJs" basedir=".">
+ 
+   <property name="site.path" value="site/swingjs" />
+   <property name="core.name" value="_jalview" />
+
+
+   <target name="toJs" id="toJs">
+                       
+       <!-- create a NON svn local directory only containing JS files
+       
+       <echo>Deleting the site directory.</echo>
+               <delete quiet="true" dir="site" />
+    -->
+       
+       <!-- make core files -->
+
+       <echo>creating and compressing core files - warnings are OK; "does not exist" is trouble</echo>
+       <echo>reading core class list from file coreclasses</echo>      
+       <loadresource property="coreclasses">
+       <file file="coreclasses"/>
+    </loadresource>
+ 
+    <antcall target="call-core">
+        <param name="call-core.name" value="${core.name}" />
+        <param name="call-core.list" value="
+                       core/coreswingjs.js
+               ${coreclasses}
+               " />
+    </antcall>
+    
+    <echo>......Now copy an html file in site/ and add   core:"core${core.name}",    to the Info block.</echo>         
+    
+  </target>
+
+
+         <target name="call-core" id="call-core">
+               <echo>......Creating core${call-core.name}.js</echo>
+               <concat destfile="${site.path}/js/core/tmp.js">
+                       <filelist dir="${site.path}/j2s" files="${call-core.list}" />
+               </concat> 
+
+               <replace dir="${site.path}/js/core" includes="tmp.js" token="Clazz." value="Clazz_"/>
+               <replace dir="${site.path}/js/core" includes="tmp.js" token="Clazz__" value="Clazz._"/>
+               <echo>......Generating ${site.path}/j2s/core/core${call-core.name}.js</echo>    
+               <concat destfile="${site.path}/j2s/core/core${call-core.name}.js"><filelist dir="${site.path}/js" files="
+                       core/coretop2.js
+                       core/tmp.js
+                       core/corebottom2.js
+                       " />
+               </concat>
+               <echo>......Generating ${site.path}/j2s/core/core${call-core.name}.z.js</echo>  
+               <java jar="tools/closure_compiler.jar" fork="true" dir="${site.path}/j2s/core" failonerror="false">
+                       <arg line="--js core${call-core.name}.js --js_output_file core${call-core.name}.z.js" />
+           </java>
+               <delete quiet="true" file="${site.path}/js/core/tmp.js" />
+         </target>
+
+               
+       
+</project>

diff --git a/coreclasses b/coreclasses
new file mode 100644 (file)
index 0000000..40ff83b
--- /dev/null
+++ b/coreclasses
@@ -0,0 +1,304 @@
+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/FeaturesSourceI.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/JalviewJS.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/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/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/FastaFile.js
+jalview/io/FeaturesFile.js
+jalview/io/FileFormat.js
+jalview/io/FileFormatI.js
+jalview/io/FileFormats.js
+jalview/io/FileLoader.js
+jalview/io/FileParse.js
+jalview/io/FormatAdapter.js
+jalview/io/IdentifyFile.js
+jalview/io/PIRFile.js
+jalview/io/ScoreMatrixFile.js
+jalview/io/SequenceAnnotationReport.js
+jalview/javascript/log4j/Level.js
+jalview/javascript/log4j/Logger.js
+jalview/javascript/log4j/Priority.js
+jalview/jbgui/GAlignFrame.js
+jalview/jbgui/GAlignmentPanel.js
+jalview/jbgui/GDesktop.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/LinkedIdentityHashSet.js
+jalview/util/MessageManager.js
+jalview/util/ParseHtmlBodyAndLinks.js
+jalview/util/Platform.js
+jalview/util/StringUtils.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/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
+java/awt/AWTKeyStroke.js
+java/awt/AlphaComposite.js
+java/awt/Composite.js
+java/awt/GridLayout.js
+java/awt/IllegalComponentStateException.js
+java/awt/Image.js
+java/awt/datatransfer/ClipboardOwner.js
+java/awt/dnd/DropTargetListener.js
+java/awt/event/ActionEvent.js
+java/awt/event/ComponentAdapter.js
+java/awt/event/FocusAdapter.js
+java/awt/event/KeyAdapter.js
+java/awt/event/MouseAdapter.js
+java/awt/event/MouseMotionAdapter.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/print/Printable.js
+java/io/BufferedInputStream.js
+java/io/BufferedReader.js
+java/io/ByteArrayInputStream.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/Reader.js
+java/lang/Readable.js
+java/lang/Runtime.js
+java/lang/StringBuilder.js
+java/math/RoundingMode.js
+java/net/MalformedURLException.js
+java/net/URLConnection.js
+java/net/URLStreamHandler.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/ArrayDeque.js
+java/util/BitSet.js
+java/util/Calendar.js
+java/util/Deque.js
+java/util/GregorianCalendar.js
+java/util/LinkedHashMap.js
+java/util/ListResourceBundle.js
+java/util/NavigableMap.js
+java/util/NavigableSet.js
+java/util/Objects.js
+java/util/Properties.js
+java/util/PropertyResourceBundle.js
+java/util/ResourceBundle.js
+java/util/SortedMap.js
+java/util/SortedSet.js
+java/util/StringTokenizer.js
+java/util/TimeZone.js
+java/util/TreeMap.js
+java/util/concurrent/ConcurrentHashMap.js
+java/util/concurrent/ConcurrentMap.js
+java/util/concurrent/atomic/AtomicBoolean.js
+java/util/concurrent/atomic/AtomicInteger.js
+java/util/concurrent/locks/Lock.js
+java/util/concurrent/locks/ReadWriteLock.js
+java/util/concurrent/locks/ReentrantReadWriteLock.js
+java/util/regex/Pattern.js
+javajs/api/GenericLineReader.js
+javajs/api/JSONEncodable.js
+javajs/util/AjaxURLStreamHandler.js
+javajs/util/BS.js
+javajs/util/Rdr.js
+javajs/util/SB.js
+javax/swing/ComponentInputMap.js
+javax/swing/InputMap.js
+javax/swing/JInternalFrame.js
+javax/swing/JScrollPane.js
+javax/swing/JTabbedPane.js
+javax/swing/JToolTip.js
+javax/swing/JViewport.js
+javax/swing/JWindow.js
+javax/swing/KeyStroke.js
+javax/swing/Popup.js
+javax/swing/PopupFactory.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/MenuListener.js
+javax/swing/plaf/ComponentInputMapUIResource.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/plaf/JSAppletUI.js
+swingjs/plaf/JSDesktopIconUI.js
+swingjs/plaf/JSInternalFrameUI.js
+swingjs/plaf/JSScrollPaneUI.js
+swingjs/plaf/JSTabbedPaneUI.js
+swingjs/plaf/JSToolTipUI.js
+swingjs/plaf/JSViewportUI.js

diff --git a/tools/ant-contrib.jar b/tools/ant-contrib.jar
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index 0000000..ea817cd
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diff --git a/tools/closure_compiler.jar b/tools/closure_compiler.jar
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index 0000000..53037b0
Binary files /dev/null and b/tools/closure_compiler.jar differ