From: hansonr Date: Thu, 21 Jun 2018 00:24:25 +0000 (+0100) Subject: core_jalview creation X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~672 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1245a23bc7e335bf6aaf37ded9e666a2bc9db160;p=jalview.git core_jalview creation --- diff --git a/buildcore.xml b/buildcore.xml new file mode 100644 index 0000000..f4dff04 --- /dev/null +++ b/buildcore.xml @@ -0,0 +1,60 @@ + + + + + + + + + + + + + creating and compressing core files - warnings are OK; "does not exist" is trouble + reading core class list from file coreclasses + + + + + + + + + + ......Now copy an html file in site/ and add core:"core${core.name}", to the Info block. + + + + + + ......Creating core${call-core.name}.js + + + + + + + ......Generating ${site.path}/j2s/core/core${call-core.name}.js + + + ......Generating ${site.path}/j2s/core/core${call-core.name}.z.js + + + + + + + + + diff --git a/coreclasses b/coreclasses new file mode 100644 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 new file mode 100644 index 0000000..ea817cd Binary files /dev/null and b/tools/ant-contrib.jar differ diff --git a/tools/closure_compiler.jar b/tools/closure_compiler.jar new file mode 100644 index 0000000..53037b0 Binary files /dev/null and b/tools/closure_compiler.jar differ