From 36d803e4a1f98728e91e80de5fa0b95e0cadb0d4 Mon Sep 17 00:00:00 2001 From: hansonr Date: Sat, 25 Jul 2015 07:57:16 +0100 Subject: [PATCH] JAL-1807 - Bob's last(?) before leaving Dundee -- adds fast file loading using j2s/core/corejalview.z.js created by buildSite.xml --- buildSite.xml | 941 +++++++++++--------- site/j2s/awt2swing/Scrollbar.js | 4 + site/j2s/core/coreswingjs.js | 140 ++- site/j2s/core/coreswingjs.z.js | 930 +++++++++---------- site/j2s/core/package.js | 42 +- site/j2s/jalview/analysis/Conservation.js | 3 +- site/j2s/jalview/appletgui/AlignFrame.js | 22 +- site/j2s/jalview/appletgui/AnnotationLabels.js | 10 +- site/j2s/jalview/appletgui/AnnotationPanel.js | 4 +- site/j2s/jalview/appletgui/FeatureRenderer.js | 4 +- site/j2s/jalview/appletgui/FeatureSettings.js | 8 +- site/j2s/jalview/appletgui/IdCanvas.js | 6 +- site/j2s/jalview/appletgui/RotatableCanvas.js | 8 +- site/j2s/jalview/appletgui/ScalePanel.js | 6 +- site/j2s/jalview/appletgui/SeqCanvas.js | 8 +- site/j2s/jalview/appletgui/SequenceRenderer.js | 10 +- site/j2s/jalview/appletgui/TitledPanel.js | 4 +- site/j2s/jalview/appletgui/TreeCanvas.js | 8 +- site/j2s/jalview/appletgui/UserDefinedColours.js | 2 +- site/j2s/jalview/bin/JalviewLite.js | 10 +- site/j2s/jalview/jsdev/GenericFileAdapter.js | 11 + site/j2s/jalview/renderer/AnnotationRenderer.js | 10 +- .../renderer/seqfeatures/FeatureRenderer.js | 6 +- .../jalview/schemes/AnnotationColourGradient.js | 8 +- site/j2s/jalview/schemes/Blosum62ColourScheme.js | 2 +- site/j2s/jalview/schemes/ClustalxColourScheme.js | 4 +- site/j2s/jalview/schemes/NucleotideColourScheme.js | 4 +- site/j2s/jalview/schemes/PIDColourScheme.js | 2 +- site/j2s/jalview/schemes/RNAHelicesColour.js | 4 +- .../jalview/schemes/RNAInteractionColourScheme.js | 4 +- site/j2s/jalview/schemes/ResidueColourScheme.js | 4 +- site/j2s/jalview/schemes/ScoreColourScheme.js | 2 +- site/j2s/jalview/schemes/TCoffeeColourScheme.js | 2 +- site/j2s/jalview/schemes/UserColourScheme.js | 2 +- site/j2s/java/awt/Color.js | 8 + site/j2s/java/util/ArrayList.js | 2 +- site/j2s/java/util/ResourceBundle.js | 2 +- site/j2s/swingjs/JSEvent.js | 4 + site/j2s/swingjs/JSGraphics2D.js | 15 +- site/j2s/swingjs/JSToolkit.js | 1 + site/j2s/swingjs/api/Interface.js | 13 + site/js/core/corebottom2.js | 2 +- site/js/core/coretop2.js | 2 +- site/test.htm | 8 +- src/fr/orsay/lri/varna/models/rna/RNA.java | 9 +- src/jalview/analysis/Conservation.java | 2 +- src/jalview/appletgui/AlignFrame.java | 20 +- src/jalview/appletgui/AnnotationLabels.java | 8 +- src/jalview/appletgui/AnnotationPanel.java | 2 +- src/jalview/appletgui/AppletJmol.java | 2 +- src/jalview/appletgui/FeatureRenderer.java | 2 +- src/jalview/appletgui/FeatureSettings.java | 8 +- src/jalview/appletgui/IdCanvas.java | 4 +- src/jalview/appletgui/RotatableCanvas.java | 6 +- src/jalview/appletgui/ScalePanel.java | 4 +- src/jalview/appletgui/SeqCanvas.java | 6 +- src/jalview/appletgui/SequenceRenderer.java | 8 +- src/jalview/appletgui/TitledPanel.java | 2 +- src/jalview/appletgui/Tooltip.java | 6 +- src/jalview/appletgui/TreeCanvas.java | 6 +- src/jalview/appletgui/UserDefinedColours.java | 2 +- src/jalview/bin/JalviewLite.java | 8 +- src/jalview/io/AppletFormatAdapter.java | 31 +- src/jalview/io/IdentifyFile.java | 7 +- src/jalview/jsdev/GenericFileAdapter.java | 11 + src/jalview/renderer/AnnotationRenderer.java | 14 +- .../renderer/seqfeatures/FeatureRenderer.java | 4 +- src/jalview/schemes/AnnotationColourGradient.java | 6 +- src/jalview/schemes/Blosum62ColourScheme.java | 2 +- src/jalview/schemes/ClustalxColourScheme.java | 2 +- src/jalview/schemes/ColourSchemeI.java | 2 +- src/jalview/schemes/NucleotideColourScheme.java | 2 +- src/jalview/schemes/PIDColourScheme.java | 2 +- src/jalview/schemes/RNAHelicesColour.java | 2 +- .../schemes/RNAInteractionColourScheme.java | 2 +- src/jalview/schemes/ResidueColourScheme.java | 2 +- src/jalview/schemes/ScoreColourScheme.java | 2 +- src/jalview/schemes/TCoffeeColourScheme.java | 6 +- src/jalview/schemes/UserColourScheme.java | 2 +- src/swingjs/JSImage.java | 14 +- 80 files changed, 1310 insertions(+), 1200 deletions(-) diff --git a/buildSite.xml b/buildSite.xml index e5c75c2..9d98c85 100644 --- a/buildSite.xml +++ b/buildSite.xml @@ -17,6 +17,13 @@ + ...adding package.js from ${project.path}/package + + + + + + ...adding to /j2s all src property and css files -- adjust as necessary @@ -41,7 +48,7 @@ ...replacing JavaObject with Clazz._O - ...removing all $fz references for sub/superclass common private function names + ...removing all $fz references for sub/superclass common private function names (not recommended, actually -- see note in Bob's log) ...changing Clazz.pu$h() to Clazz.pu$h(self.c$) (only a partial fix) @@ -71,394 +78,27 @@ --> - - - - - - - - ......Creating core${call-core.name}.js - - - - - + swingjs/JSPlainDocument.js + swingjs/JSAbstractDocument.js + swingjs/JSDocumentEvent.js + swingjs/JSPosition.js + swingjs/api/HTML5CanvasContext2D.js + javax/swing/DefaultListCellRenderer.js + javax/swing/ListCellRenderer.js + javax/swing/border/EmptyBorder.js + jssun/swing/DefaultLookup.js + javax/swing/plaf/DimensionUIResource.js + javax/swing/plaf/InsetsUIResource.js + swingjs/plaf/JSEventHandler.js + JU/AjaxURLStreamHandlerFactory.js + java/net/URLStreamHandlerFactory.js + JU/AjaxURLStreamHandler.js + java/net/URLStreamHandler.js + JU/AjaxURLConnection.js + java/net/URLConnection.js + java/net/UnknownServiceException.js + + jalview/bin/JalviewLite.js + javax/swing/JButton.js + jalview/util/MessageManager.js + java/util/logging/Logger.js + java/util/logging/LogRecord.js + java/util/logging/Level.js + java/text/MessageFormat.js + java/util/PropertyResourceBundle.js + jalview/javascript/JalviewLiteJsApi.js + jalview/api/StructureSelectionManagerProvider.js + awt2swing/Util.js + jalview/analysis/SequenceIdMatcher.js + jalview/appletgui/AlignFrame.js + awt2swing/Canvas.js + awt2swing/Panel.js + jalview/api/AlignViewControllerGuiI.js + jalview/appletgui/EmbmenuFrame.js + awt2swing/Frame.js + awt2swing/Label.js + awt2swing/PopupMenu.js + jalview/util/Platform.js + awt2swing/CheckboxMenuItem.js + awt2swing/Menu.js + awt2swing/MenuBar.js + awt2swing/MenuItem.js + jalview/analysis/AlignmentSorter.js + jalview/datamodel/SequenceI.js + jalview/datamodel/ASequenceI.js + jalview/util/Comparison.js + jalview/util/QuickSort.js + jalview/analysis/AnnotationSorter.js + jalview/analysis/AlignmentUtils.js + jalview/analysis/CodonComparator.js + jalview/datamodel/AlignedCodonFrame.js + jalview/datamodel/Mapping.js + jalview/datamodel/AlignedCodon.js + jalview/datamodel/IncompleteCodonException.js + jalview/datamodel/SequenceFeature.js + jalview/util/MapList.js + jalview/util/MappingUtils.js + jalview/commands/EditCommand.js + jalview/commands/CommandI.js + jalview/analysis/AlignSeq.js + jalview/schemes/ResidueProperties.js + jalview/analysis/scoremodels/FeatureScoreModel.js + jalview/api/analysis/ScoreModelI.js + jalview/api/analysis/ViewBasedAnalysisI.js + jalview/analysis/scoremodels/PIDScoreModel.js + jalview/schemes/ScoreMatrix.js + jalview/analysis/scoremodels/PairwiseSeqScoreModel.js + jalview/datamodel/Sequence.js + jalview/datamodel/ASequence.js + jalview/jsdev/RegExp.js + com/stevesoft/pat/Regex.js + com/stevesoft/pat/RegRes.js + com/stevesoft/pat/UniValidator.js + com/stevesoft/pat/Validator.js + com/stevesoft/pat/patInf.js + com/stevesoft/pat/patInt.js + jalview/jsdev/api/RegExpInterface.js + com/stevesoft/pat/NoPattern.js + com/stevesoft/pat/Pattern.js + com/stevesoft/pat/MessageManager.js + com/stevesoft/pat/Pthings.js + com/stevesoft/pat/Any.js + com/stevesoft/pat/BackG.js + com/stevesoft/pat/BackMatch.js + com/stevesoft/pat/Backup.js + com/stevesoft/pat/Boundary.js + com/stevesoft/pat/Bracket.js + com/stevesoft/pat/Or.js + com/stevesoft/pat/CaseMgr.js + com/stevesoft/pat/Ctrl.js + com/stevesoft/pat/Custom.js + com/stevesoft/pat/PatternSub.js + com/stevesoft/pat/CustomEndpoint.js + com/stevesoft/pat/DotMulti.js + com/stevesoft/pat/End.js + com/stevesoft/pat/FastMulti.js + com/stevesoft/pat/RegSyntaxError.js + com/stevesoft/pat/RegSyntax.js + com/stevesoft/pat/Group.js + com/stevesoft/pat/Multi.js + com/stevesoft/pat/Multi_stage2.js + com/stevesoft/pat/NullPattern.js + com/stevesoft/pat/OrMark.js + com/stevesoft/pat/SubMark.js + com/stevesoft/pat/Prop.js + com/stevesoft/pat/Bits.js + com/stevesoft/pat/Range.js + com/stevesoft/pat/oneChar.js + com/stevesoft/pat/RegOpt.js + com/stevesoft/pat/FastBracket.js + java/util/BitSet.js + com/stevesoft/pat/ReplaceRule.js + com/stevesoft/pat/Transformer.js + com/stevesoft/pat/Replacer.js + com/stevesoft/pat/AmpersandRule.js + com/stevesoft/pat/ChangeRule.js + com/stevesoft/pat/SpecialRule.js + com/stevesoft/pat/PopRule.js + com/stevesoft/pat/PushRule.js + com/stevesoft/pat/RuleHolder.js + com/stevesoft/pat/StringBufferLike.js + com/stevesoft/pat/BasicStringBufferLike.js + com/stevesoft/pat/WantMoreTextReplaceRule.js + com/stevesoft/pat/wrap/StringWrap.js + com/stevesoft/pat/StringLike.js + com/stevesoft/pat/wrap/StringBufferWrap.js + com/stevesoft/pat/TransPat.js + com/stevesoft/pat/Rthings.js + com/stevesoft/pat/Skip.js + com/stevesoft/pat/Skipped.js + com/stevesoft/pat/Start.js + com/stevesoft/pat/StrPos.js + com/stevesoft/pat/lookAhead.js + com/stevesoft/pat/parsePerl.js + com/stevesoft/pat/StringRule.js + jalview/datamodel/AlignmentAnnotation.js + jalview/analysis/Rna.js + jalview/analysis/SecStrConsensus.js + jalview/analysis/WUSSParseException.js + java/util/Stack.js + jalview/datamodel/Annotation.js + jalview/datamodel/GraphLine.js + jalview/datamodel/DBRefEntry.js + jalview/datamodel/DBRefSource.js + jalview/datamodel/PDBEntry.js + jalview/util/StringUtils.js + java/util/regex/Pattern.js + java/util/regex/Matcher.js + java/util/regex/MatchResult.js + jalview/util/Format.js + jalview/util/ReverseListIterator.js + jalview/commands/OrderCommand.js + jalview/datamodel/AlignmentOrder.js + jalview/datamodel/ColumnSelection.js + jalview/util/ShiftList.js + jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js + jalview/datamodel/SearchResults.js + jalview/datamodel/SequenceGroup.js + jalview/datamodel/AnnotatedCollectionI.js + jalview/datamodel/SequenceCollectionI.js + jalview/analysis/AAFrequency.js + jalview/analysis/CodingUtils.js + jalview/analysis/Conservation.js + jalview/datamodel/Alignment.js + jalview/datamodel/AlignmentI.js + jalview/datamodel/HiddenSequences.js + java/util/LinkedHashSet.js + java/util/LinkedHashMap.js + jalview/datamodel/CigarArray.js + jalview/datamodel/CigarBase.js + jalview/datamodel/CigarCigar.js + jalview/datamodel/CigarSimple.js + jalview/datamodel/SeqCigar.js + jalview/analysis/SeqsetUtils.js + jalview/datamodel/FeatureProperties.js + jalview/util/DBRefUtils.js + java/util/TreeMap.js + jalview/appletgui/AlignViewport.js + jalview/structure/CommandListener.js + jalview/structure/SelectionSource.js + jalview/structure/VamsasSource.js + jalview/viewmodel/AlignmentViewport.js + jalview/api/AlignViewportI.js + jalview/api/ViewStyleI.js + jalview/viewmodel/styles/ViewStyle.js + jalview/workers/AlignCalcManager.js + jalview/api/AlignCalcManagerI.js + java/util/ArrayDeque.js + java/util/Deque.js + jalview/datamodel/AlignmentView.js + jalview/schemes/Blosum62ColourScheme.js + jalview/schemes/ResidueColourScheme.js + jalview/schemes/ColourSchemeI.js + jalview/schemes/PIDColourScheme.js + jalview/workers/ComplementConsensusThread.js + jalview/workers/ConsensusThread.js + jalview/api/AlignCalcWorkerI.js + jalview/workers/AlignCalcWorker.js + jalview/workers/ConservationThread.js + jalview/workers/StrucConsensusThread.js + jalview/analysis/StructureFrequency.js + jalview/schemes/ColourSchemeProperty.js + jalview/schemes/BuriedColourScheme.js + jalview/schemes/ScoreColourScheme.js + jalview/schemes/ClustalxColourScheme.js + jalview/schemes/Consensus.js + jalview/schemes/HelixColourScheme.js + jalview/schemes/HydrophobicColourScheme.js + jalview/schemes/NucleotideColourScheme.js + jalview/schemes/PurinePyrimidineColourScheme.js + jalview/schemes/RNAHelicesColour.js + jalview/util/ColorUtils.js + jalview/schemes/StrandColourScheme.js + jalview/schemes/TCoffeeColourScheme.js + jalview/schemes/TaylorColourScheme.js + jalview/schemes/TurnColourScheme.js + jalview/schemes/UserColourScheme.js + jalview/schemes/ZappoColourScheme.js + jalview/structure/StructureSelectionManager.js + MCview/PDBfile.js + jalview/io/AlignFile.js + jalview/io/FileParse.js + jalview/io/AppletFormatAdapter.js + jalview/io/IdentifyFile.js + jalview/jsdev/GenericFileAdapter.js + java/util/zip/GZIPInputStream.js + java/util/zip/InflaterInputStream.js + JU/InflaterInputStream.js + java/util/zip/CRC32.js + JU/CRC32.js + JU/Checksum.js + java/util/zip/CheckedInputStream.js + java/util/zip/Inflater.js + JU/Inflater.js + JU/ZStream.js + JU/Adler32.js + JU/Inflate.js + JU/GZIPHeader.js + JU/InfBlocks.js + JU/InfTree.js + JU/InfCodes.js + java/io/ByteArrayOutputStream.js + java/io/OutputStream.js + java/util/zip/ZipException.js + MCview/Atom.js + MCview/PDBChain.js + MCview/Bond.js + MCview/Residue.js + jalview/structure/AtomSpec.js + jalview/structure/SecondaryStructureListener.js + jalview/structure/SequenceListener.js + jalview/structure/StructureListener.js + jalview/structure/StructureMapping.js + jalview/structure/VamsasListener.js + jalview/appletgui/AlignmentPanel.js + jalview/api/AlignmentViewPanel.js + jalview/api/OOMHandlerI.js + awt2swing/Scrollbar.js + javax/swing/JScrollBar.js + java/awt/Adjustable.js + java/awt/event/AdjustmentEvent.js + jalview/appletgui/AnnotationLabels.js + awt2swing/Checkbox.js + jalview/appletgui/CutAndPasteTransfer.js + awt2swing/Button.js + awt2swing/TextArea.js + javax/swing/JTextArea.js + jalview/api/ComplexAlignFile.js + jalview/appletgui/AppletJmol.js + jalview/appletgui/JVDialog.js + jalview/appletgui/SplitFrame.js + java/awt/GridLayout.js + jalview/io/AnnotationFile.js + jalview/io/NewickFile.js + jalview/datamodel/SequenceNode.js + jalview/datamodel/BinaryNode.js + jalview/appletgui/EditNameDialog.js + awt2swing/TextField.js + java/awt/event/TextEvent.js + jalview/appletgui/PaintRefresher.js + jalview/appletgui/Tooltip.js + jalview/util/ParseHtmlBodyAndLinks.js + jalview/appletgui/AnnotationPanel.js + jalview/renderer/AwtRenderPanelI.js + jalview/appletgui/UserDefinedColours.js + jalview/appletgui/AnnotationColourChooser.js + awt2swing/Choice.js + javax/swing/JComboBox.js + javax/swing/event/ListDataListener.js + javax/swing/DefaultComboBoxModel.js + javax/swing/AbstractListModel.js + javax/swing/ListModel.js + javax/swing/event/ListDataEvent.js + javax/swing/MutableComboBoxModel.js + javax/swing/ComboBoxModel.js + jalview/schemes/AnnotationColourGradient.js + jalview/schemes/FollowerColourScheme.js + jalview/renderer/AnnotationRenderer.js + jalview/appletgui/FeatureColourChooser.js + jalview/schemes/GraduatedColor.js + jalview/appletgui/FeatureRenderer.js + jalview/renderer/seqfeatures/FeatureRenderer.js + jalview/viewmodel/seqfeatures/FeatureRendererModel.js + jalview/api/FeatureRenderer.js + java/util/concurrent/ConcurrentHashMap.js + jalview/viewmodel/seqfeatures/FeatureRendererSettings.js + jalview/viewmodel/seqfeatures/FeaturesDisplayed.js + jalview/api/FeaturesDisplayedI.js + java/awt/AlphaComposite.js + java/awt/Composite.js + jssun/java2d/SunCompositeContext.js + java/awt/CompositeContext.js + java/awt/image/BufferedImage.js + java/awt/Image.js + java/awt/image/DirectColorModel.js + java/awt/image/PackedColorModel.js + java/awt/image/Raster.js + java/awt/image/MultiPixelPackedSampleModel.js + java/awt/image/SampleModel.js + java/awt/image/DataBuffer.js + jssun/java2d/StateTrackable.js + jssun/java2d/StateTrackableDelegate.js + jssun/java2d/StateTracker.js + java/awt/image/DataBufferByte.js + java/awt/image/DataBufferInt.js + java/awt/image/RasterFormatException.js + java/awt/image/SinglePixelPackedSampleModel.js + jssun/awt/image/OffScreenImageSource.js + java/awt/image/WritableRaster.js + jssun/java2d/loops/CompositeType.js + awt2swing/ScrollPane.js + javax/swing/JScrollPane.js + javax/swing/ScrollPaneConstants.js + javax/swing/ScrollPaneLayout.js + jalview/io/FeaturesFile.js + jalview/datamodel/SequenceDummy.js + java/awt/event/MouseAdapter.js + jalview/appletgui/FeatureSettings.js + jalview/api/FeatureSettingsControllerI.js + jalview/appletgui/IdPanel.js + jalview/appletgui/APopupMenu.js + jalview/analysis/AlignmentAnnotationUtils.js + jalview/appletgui/SliderPanel.js + jalview/commands/ChangeCaseCommand.js + jalview/io/SequenceAnnotationReport.js + jalview/util/UrlLink.js + jalview/appletgui/IdCanvas.js + jalview/appletgui/IdwidthAdjuster.js + jalview/appletgui/ScalePanel.js + jalview/appletgui/SeqPanel.js + jalview/structure/SelectionListener.js + jalview/appletgui/SeqCanvas.js + jalview/appletgui/SequenceRenderer.js + jalview/api/SequenceRenderer.js + jalview/appletgui/AnnotationColumnChooser.js + jalview/appletgui/AnnotationRowFilter.js + jalview/appletgui/TitledPanel.js + java/awt/CardLayout.js + java/io/ObjectStreamField.js + jalview/appletgui/Finder.js + jalview/analysis/Finder.js + java/awt/event/KeyAdapter.js + jalview/appletgui/FontChooser.js + jalview/appletgui/OverviewPanel.js + jalview/appletgui/PCAPanel.js + jalview/appletgui/RotatableCanvas.js + jalview/api/RotatableCanvasI.js + jalview/math/RotatableMatrix.js + jalview/viewmodel/PCAModel.js + jalview/analysis/PCA.js + jalview/datamodel/BinarySequence.js + jalview/math/Matrix.js + jalview/datamodel/SequencePoint.js + jalview/appletgui/PairwiseAlignPanel.js + jalview/appletgui/RedundancyPanel.js + jalview/appletgui/TreePanel.js + jalview/analysis/NJTree.js + jalview/datamodel/NodeTransformI.js + jalview/appletgui/TreeCanvas.js + jalview/commands/RemoveGapColCommand.js + jalview/commands/RemoveGapsCommand.js + jalview/commands/SlideSequencesCommand.js + jalview/commands/TrimRegionCommand.js + jalview/controller/AlignViewController.js + jalview/api/AlignViewControllerI.js + jalview/analysis/Grouping.js + jalview/io/AlignmentProperties.js + jalview/schemes/RNAHelicesColourChooser.js + jalview/schemes/RNAInteractionColourScheme.js + java/net/URLEncoder.js + jalview/io/JnetAnnotationMaker.js + jalview/javascript/JSFunctionExec.js + netscape/javascript/JSException.js + netscape/javascript/JSObject.js + jalview/javascript/JsSelectionSender.js + jalview/javascript/JsCallBack.js + jalview/javascript/MouseOverListener.js + jalview/javascript/MouseOverStructureListener.js + jalview/ext/jmol/JmolCommands.js + jalview/structure/StructureMappingcommandSet.js + java/util/Properties.js + jssun/util/ResourceBundleEnumeration.js + jalview/io/FastaFile.js + swingjs/plaf/JSMenuBarUI.js + swingjs/plaf/JSMenuUI.js + swingjs/plaf/JSMenuItemUI.js + swingjs/plaf/JSCheckBoxMenuItemUI.js + swingjs/plaf/JSCheckBoxUI.js + swingjs/plaf/JSLabelUI.js + swingjs/plaf/JSPopupMenuUI.js + swingjs/plaf/JSPopupMenuSeparatorUI.js + swingjs/plaf/JSScrollBarUI.js + swingjs/JSImagekit.js + swingjs/JSImage.js + jssun/awt/image/IntegerInterleavedRaster.js + jssun/awt/image/IntegerComponentRaster.js + jssun/awt/image/SunWritableRaster.js + jssun/awt/image/DataStealer.js + "/> + - - - - - - - - ......Generating core${call-core.name}.z.js - - - - + - - ......Creating JSmol.${call-min.minname}.js - - - - - - - + + + + ......Creating core${call-core.name}.js + + + + + + + + + + + + ......Generating core${call-core.name}.z.js + + + + + + diff --git a/site/j2s/awt2swing/Scrollbar.js b/site/j2s/awt2swing/Scrollbar.js index 58f1258..6e376e3 100644 --- a/site/j2s/awt2swing/Scrollbar.js +++ b/site/j2s/awt2swing/Scrollbar.js @@ -5,4 +5,8 @@ Clazz.defineMethod (c$, "addChangeListener", function (l) { this.addAdjustmentListener (l); }, "javax.swing.event.ChangeListener"); +Clazz.defineMethod (c$, "removeChangeListener", +function (l) { +this.removeAdjustmentListener (l); +}, "javax.swing.event.ChangeListener"); }); diff --git a/site/j2s/core/coreswingjs.js b/site/j2s/core/coreswingjs.js index 3699911..fecb71b 100644 --- a/site/j2s/core/coreswingjs.js +++ b/site/j2s/core/coreswingjs.js @@ -24627,6 +24627,7 @@ c$ = Clazz_p0p (); Clazz_declarePackage ("java.awt"); Clazz_load (null, "java.awt.Font", ["java.awt.font.TextAttribute", "java.awt.geom.AffineTransform", "swingjs.JSToolkit"], function () { c$ = Clazz_decorateAsClass (function () { +this.fm = null; this.family = null; this.name = null; this.style = 0; @@ -24637,6 +24638,14 @@ this.nonIdentityTx = false; this.hash = 0; Clazz_instantialize (this, arguments); }, java.awt, "Font"); +Clazz_defineMethod (c$, "getFontMetrics", +function () { +return this.fm; +}); +Clazz_defineMethod (c$, "setFontMetrics", +function (fm) { +this.fm = fm; +}, "java.awt.FontMetrics"); Clazz_makeConstructor (c$, function (name, style, size) { this.name = (name != null) ? name : "Default"; @@ -24645,13 +24654,6 @@ this.size = size; this.pointSize = size; }, "~S,~N,~N"); Clazz_makeConstructor (c$, - function (name, style, sizePts) { -this.name = (name != null) ? name : "Default"; -this.style = (style & -4) == 0 ? style : 0; -this.size = Clazz_doubleToInt (sizePts + 0.5); -this.pointSize = sizePts; -}, "~S,~N,~N"); -Clazz_makeConstructor (c$, function (font) { this.name = font.name; this.style = font.style; @@ -24819,12 +24821,16 @@ var attributes = Clazz_newArray (-1, [java.awt.font.TextAttribute.FAMILY, java. return attributes; }); Clazz_defineMethod (c$, "deriveFont", -function (style, size) { -return new java.awt.Font (this.name, style, size); +function (style, sizePts) { +var f = new java.awt.Font (this.name, style, Clazz_doubleToInt (sizePts + 0.5)); +f.pointSize = sizePts; +return f; }, "~N,~N"); Clazz_defineMethod (c$, "deriveFont", -function (size) { -return new java.awt.Font (this.name, this.style, size); +function (sizePts) { +var f = new java.awt.Font (this.name, this.style, Clazz_doubleToInt (sizePts + 0.5)); +f.pointSize = sizePts; +return f; }, "~N"); Clazz_defineMethod (c$, "deriveFont", function (style) { @@ -28656,7 +28662,7 @@ return true; }return clipRect.intersects (x, y, width, height); }, "~N,~N,~N,~N"); Clazz_declarePackage ("jssun.font"); -Clazz_load (["java.awt.FontMetrics", "java.util.Hashtable"], "jssun.font.FontDesignMetrics", ["java.lang.IndexOutOfBoundsException", "java.awt.Toolkit", "swingjs.JSToolkit"], function () { +Clazz_load (["java.awt.FontMetrics", "java.util.Hashtable"], "jssun.font.FontDesignMetrics", ["java.lang.Character", "$.IndexOutOfBoundsException", "java.awt.Toolkit", "swingjs.JSToolkit"], function () { c$ = Clazz_decorateAsClass (function () { this.ascent = 0; this.descent = 0; @@ -28747,6 +28753,17 @@ if (this.height < 0) { this.height = this.getAscent () + Clazz_floatToInt (jssun.font.FontDesignMetrics.roundingUpValue + this.descent + this.leading); }return this.height; }); +Clazz_defineMethod (c$, "charWidth", +function (codePoint) { +if (!Character.isValidCodePoint (codePoint)) { +codePoint = 0xffff; +}if (codePoint < 256) { +return this.getWidths ()[codePoint]; +} else { +var buffer = Clazz_newCharArray (2, '\0'); +var len = Character.toChars (codePoint, buffer, 0); +return this.charsWidth (buffer, 0, len); +}}, "~N"); Clazz_pu$h(self.c$); c$ = Clazz_decorateAsClass (function () { this.key = null; @@ -28778,7 +28795,7 @@ Clazz_defineStatics (c$, "recentIndex", 0); }); Clazz_declarePackage ("java.awt"); -Clazz_load (["java.awt.font.FontRenderContext"], "java.awt.FontMetrics", ["java.lang.Character"], function () { +Clazz_load (["java.awt.font.FontRenderContext"], "java.awt.FontMetrics", null, function () { c$ = Clazz_decorateAsClass (function () { this.font = null; Clazz_instantialize (this, arguments); @@ -28795,18 +28812,6 @@ Clazz_defineMethod (c$, "getFontRenderContext", function () { return java.awt.FontMetrics.DEFAULT_FRC; }); -Clazz_defineMethod (c$, "getLeading", -function () { -return 0; -}); -Clazz_defineMethod (c$, "getAscent", -function () { -return this.font.getSize (); -}); -Clazz_defineMethod (c$, "getDescent", -function () { -return 0; -}); Clazz_defineMethod (c$, "getHeight", function () { return this.getLeading () + this.getAscent () + this.getDescent (); @@ -28819,39 +28824,10 @@ Clazz_defineMethod (c$, "getMaxDescent", function () { return this.getDescent (); }); -Clazz_defineMethod (c$, "getMaxDecent", -function () { -return this.getMaxDescent (); -}); Clazz_defineMethod (c$, "getMaxAdvance", function () { -return -1; +return this.charWidth ('M'); }); -Clazz_defineMethod (c$, "charWidth", -function (codePoint) { -if (!Character.isValidCodePoint (codePoint)) { -codePoint = 0xffff; -}if (codePoint < 256) { -return this.getWidths ()[codePoint]; -} else { -var buffer = Clazz_newCharArray (2, '\0'); -var len = Character.toChars (codePoint, buffer, 0); -return this.charsWidth (buffer, 0, len); -}}, "~N"); -Clazz_defineMethod (c$, "charWidth", -function (ch) { -if (ch.charCodeAt (0) < 256) { -return this.getWidths ()[ch.charCodeAt (0)]; -}var data = Clazz_newCharArray (-1, [ch]); -return this.charsWidth (data, 0, 1); -}, "~S"); -Clazz_defineMethod (c$, "stringWidth", -function (str) { -var len = str.length; -var data = Clazz_newCharArray (len, '\0'); -str.getChars (0, len, data, 0); -return this.charsWidth (data, 0, len); -}, "~S"); Clazz_defineMethod (c$, "charsWidth", function (data, off, len) { return this.stringWidth ( String.instantialize (data, off, len)); @@ -28860,14 +28836,6 @@ Clazz_defineMethod (c$, "bytesWidth", function (data, off, len) { return this.stringWidth ( String.instantialize (data, 0, off, len)); }, "~A,~N,~N"); -Clazz_defineMethod (c$, "getWidths", -function () { -var widths = Clazz_newIntArray (256, 0); -for (var ch = String.fromCharCode (0); ch.charCodeAt (0) < 256; ch = String.fromCharCode (ch.charCodeAt (0) + 1)) { -widths[ch.charCodeAt (0)] = this.charWidth (ch); -} -return widths; -}); Clazz_overrideMethod (c$, "toString", function () { return this.getClass ().getName () + "[font=" + this.getFont () + "ascent=" + this.getAscent () + ", descent=" + this.getDescent () + ", height=" + this.getHeight () + "]"; @@ -49607,7 +49575,7 @@ lines[pt] = text.substring (i, len); return lines; }, "~S,~S"); Clazz_declarePackage ("swingjs"); -Clazz_load (["jssun.awt.SunToolkit"], "swingjs.JSToolkit", ["java.io.BufferedInputStream", "$.ByteArrayInputStream", "$.InputStream", "java.lang.Boolean", "$.Thread", "java.util.Hashtable", "JU.AU", "$.Rdr", "$.SB", "java.awt.Dimension", "java.awt.image.ColorModel", "javax.swing.UIManager", "jssun.awt.AppContext", "swingjs.JSComponentPeer", "$.JSImage", "swingjs.api.Interface"], function () { +Clazz_load (["jssun.awt.SunToolkit"], "swingjs.JSToolkit", ["java.io.BufferedInputStream", "$.ByteArrayInputStream", "$.InputStream", "java.lang.Boolean", "$.Thread", "java.util.Hashtable", "JU.AU", "$.Rdr", "$.SB", "java.awt.Dimension", "java.awt.image.ColorModel", "javax.swing.UIManager", "jssun.awt.AppContext", "swingjs.JSComponentPeer", "swingjs.api.Interface"], function () { c$ = Clazz_decorateAsClass (function () { this.imageKit = null; Clazz_instantialize (this, arguments); @@ -49752,9 +49720,12 @@ return font.getName (); }, "java.awt.Font"); Clazz_overrideMethod (c$, "getFontMetrics", function (font) { -var fm = swingjs.JSToolkit.getInstance ("swingjs.JSFontMetrics"); -fm.setFont (font); -return fm; +var fm = font.getFontMetrics (); +if (fm == null) { +fm = swingjs.JSToolkit.getInstance ("swingjs.JSFontMetrics"); +(fm).setFont (font); +font.setFontMetrics (fm); +}return fm; }, "java.awt.Font"); c$.getCSSColor = Clazz_defineMethod (c$, "getCSSColor", function (c) { @@ -49977,11 +49948,7 @@ throw e; }, "java.net.URL"); Clazz_defineMethod (c$, "createImage", function (data, imageoffset, imagelength) { -if (data == null) { -var width = imageoffset; -var height = imagelength; -return new swingjs.JSImage (null, width, height); -}return this.getImagekit ().createImageFromBytes (data, imageoffset, imagelength); +return this.getImagekit ().createImageFromBytes (data, imageoffset, imagelength); }, "~A,~N,~N"); Clazz_overrideMethod (c$, "checkImage", function (image, width, height, observer) { @@ -50084,8 +50051,9 @@ Clazz_superConstructor (this, swingjs.JSEvent, [t, 1201, r, null, false]); Clazz_declarePackage ("swingjs"); Clazz_load (["java.awt.FontMetrics"], "swingjs.JSFontMetrics", ["swingjs.JSToolkit"], function () { c$ = Clazz_decorateAsClass (function () { -this.widths = null; +this.fwidths = null; this.iwidths = null; +this.FIRST_PRINTABLE = 32; Clazz_instantialize (this, arguments); }, swingjs, "JSFontMetrics", java.awt.FontMetrics); Clazz_makeConstructor (c$, @@ -50110,12 +50078,12 @@ return Clazz_doubleToInt (this.font.getSize () / 4) + 1; }); Clazz_defineMethod (c$, "charWidth", function (pt) { -return (pt.charCodeAt (0) < 256 ? Clazz_floatToInt (this.getWidthsFloat ()[pt.charCodeAt (0)]) : this.stringWidth ("" + pt)); -}, "~S"); -Clazz_defineMethod (c$, "charWidth", -function (pt) { -return (pt < 256 ? Clazz_floatToInt (this.getWidthsFloat ()[pt]) : this.stringWidth ("" + String.fromCharCode (pt))); -}, "~N"); +{ +var spt; +return ((pt + 0 == pt ? pt : (pt = (spt = pt).charCodeAt(0))) < 256 ? +Clazz_floatToInt(this.getWidthsFloat()[pt]) +: this.stringWidth(isChar ? spt : String.fromCharCode (pt))); +}}, "~N"); Clazz_overrideMethod (c$, "stringWidth", function (s) { return Clazz_floatToInt (swingjs.JSToolkit.getStringWidth (null, this.font, s)); @@ -50125,19 +50093,19 @@ function () { if (this.iwidths != null) return this.iwidths; this.iwidths = Clazz_newIntArray (256, 0); this.getWidthsFloat (); -for (var ch = 0; ch < 256; ch++) { -this.iwidths[ch] = Clazz_floatToInt (this.widths[ch]); +for (var ch = this.FIRST_PRINTABLE; ch < 256; ch++) { +this.iwidths[ch] = Clazz_floatToInt (this.fwidths[ch]); } return this.iwidths; }); Clazz_defineMethod (c$, "getWidthsFloat", function () { -if (this.widths != null) return this.widths; -this.widths = Clazz_newFloatArray (256, 0); -for (var ch = 0; ch < 256; ch++) { -this.widths[ch] = swingjs.JSToolkit.getStringWidth (null, this.font, "" + String.fromCharCode (ch)); +if (this.fwidths != null) return this.fwidths; +this.fwidths = Clazz_newFloatArray (256, 0); +for (var ch = this.FIRST_PRINTABLE; ch < 256; ch++) { +this.fwidths[ch] = swingjs.JSToolkit.getStringWidth (null, this.font, "" + String.fromCharCode (ch)); } -return this.widths; +return this.fwidths; }); }); Clazz_declarePackage ("swingjs"); diff --git a/site/j2s/core/coreswingjs.z.js b/site/j2s/core/coreswingjs.z.js index 033e4d8..c4485ff 100644 --- a/site/j2s/core/coreswingjs.z.js +++ b/site/j2s/core/coreswingjs.z.js @@ -1,24 +1,24 @@ -(function(J,la,ta,ua,A,va,p,j,n,k,q,E,wa,g,F,z,H,x,M,t,I,r,L,y,v,w,ma,D,C,K,B,U,xa,u,R,na,Q,V,N,O,aa,ya,oa,pa,W,X,ca,da,ea,fa,ga,Y,ha,qa,S,ra,za,c,d,G,Aa,P){(function(a){a._Loader.registerPackages("java",["io","lang","lang.reflect","util"]);var b=java.util;a._Loader.ignore("net.sf.j2s.ajax.HttpRequest java.util.MapEntry.Type 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1:return this.m11;case 2:return this.m12}break; -case 2:switch(b){case 0:return this.m20;case 1:return this.m21;case 2:return this.m22}}this.err();return 0},"~N,~N");c(c$,"setRow33",function(a,b){switch(a){case 0:this.m00=b[0];this.m01=b[1];this.m02=b[2];break;case 1:this.m10=b[0];this.m11=b[1];this.m12=b[2];break;case 2:this.m20=b[0];this.m21=b[1];this.m22=b[2];break;default:this.err()}},"~N,~A");c(c$,"getRow33",function(a,b){switch(a){case 0:b[0]=this.m00;b[1]=this.m01;b[2]=this.m02;return;case 1:b[0]=this.m10;b[1]=this.m11;b[2]=this.m12;return; -case 2:b[0]=this.m20;b[1]=this.m21;b[2]=this.m22;return}this.err()},"~N,~A");c(c$,"setColumn33",function(a,b){switch(a){case 0:this.m00=b[0];this.m10=b[1];this.m20=b[2];break;case 1:this.m01=b[0];this.m11=b[1];this.m21=b[2];break;case 2:this.m02=b[0];this.m12=b[1];this.m22=b[2];break;default:this.err()}},"~N,~A");c(c$,"getColumn33",function(a,b){switch(a){case 0:b[0]=this.m00;b[1]=this.m10;b[2]=this.m20;break;case 1:b[0]=this.m01;b[1]=this.m11;b[2]=this.m21;break;case 2:b[0]=this.m02;b[1]=this.m12; -b[2]=this.m22;break;default:this.err()}},"~N,~A");c(c$,"add33",function(a){this.m00+=a.m00;this.m01+=a.m01;this.m02+=a.m02;this.m10+=a.m10;this.m11+=a.m11;this.m12+=a.m12;this.m20+=a.m20;this.m21+=a.m21;this.m22+=a.m22},"JU.M34");c(c$,"sub33",function(a){this.m00-=a.m00;this.m01-=a.m01;this.m02-=a.m02;this.m10-=a.m10;this.m11-=a.m11;this.m12-=a.m12;this.m20-=a.m20;this.m21-=a.m21;this.m22-=a.m22},"JU.M34");c(c$,"mul33",function(a){this.m00*=a;this.m01*=a;this.m02*=a;this.m10*=a;this.m11*=a;this.m12*= -a;this.m20*=a;this.m21*=a;this.m22*=a},"~N");c(c$,"transpose33",function(){var a=this.m01;this.m01=this.m10;this.m10=a;a=this.m02;this.m02=this.m20;this.m20=a;a=this.m12;this.m12=this.m21;this.m21=a});c(c$,"setXRot",function(a){var b=Math.cos(a);a=Math.sin(a);this.m00=1;this.m10=this.m02=this.m01=0;this.m11=b;this.m12=-a;this.m20=0;this.m21=a;this.m22=b},"~N");c(c$,"setYRot",function(a){var b=Math.cos(a);a=Math.sin(a);this.m00=b;this.m01=0;this.m02=a;this.m10=0;this.m11=1;this.m12=0;this.m20=-a;this.m21= -0;this.m22=b},"~N");c(c$,"setZRot",function(a){var b=Math.cos(a);a=Math.sin(a);this.m00=b;this.m01=-a;this.m02=0;this.m10=a;this.m11=b;this.m21=this.m20=this.m12=0;this.m22=1},"~N");c(c$,"determinant3",function(){return this.m00*(this.m11*this.m22-this.m21*this.m12)-this.m01*(this.m10*this.m22-this.m20*this.m12)+this.m02*(this.m10*this.m21-this.m20*this.m11)});c(c$,"err",function(){throw new ArrayIndexOutOfBoundsException("matrix column/row out of bounds");})});p("JU");n(["JU.M34"],"JU.M4",["JU.T3"], -function(){c$=q(function(){this.m33=this.m32=this.m31=this.m30=this.m23=this.m13=this.m03=0;k(this,arguments)},JU,"M4",JU.M34);c$.newA16=c(c$,"newA16",function(a){var b=new JU.M4;b.m00=a[0];b.m01=a[1];b.m02=a[2];b.m03=a[3];b.m10=a[4];b.m11=a[5];b.m12=a[6];b.m13=a[7];b.m20=a[8];b.m21=a[9];b.m22=a[10];b.m23=a[11];b.m30=a[12];b.m31=a[13];b.m32=a[14];b.m33=a[15];return b},"~A");c$.newM4=c(c$,"newM4",function(a){var b=new JU.M4;if(null==a)return b.setIdentity(),b;b.setToM3(a);b.m03=a.m03;b.m13=a.m13;b.m23= -a.m23;b.m30=a.m30;b.m31=a.m31;b.m32=a.m32;b.m33=a.m33;return b},"JU.M4");c$.newMV=c(c$,"newMV",function(a,b){var c=new JU.M4;c.setMV(a,b);return c},"JU.M3,JU.T3");c(c$,"setZero",function(){this.clear33();this.m03=this.m13=this.m23=this.m30=this.m31=this.m32=this.m33=0});c(c$,"setIdentity",function(){this.setZero();this.m00=this.m11=this.m22=this.m33=1});c(c$,"setM4",function(a){this.setM33(a);this.m03=a.m03;this.m13=a.m13;this.m23=a.m23;this.m30=a.m30;this.m31=a.m31;this.m32=a.m32;this.m33=a.m33; -return this},"JU.M4");c(c$,"setMV",function(a,b){this.setM33(a);this.setTranslation(b);this.m33=1},"JU.M3,JU.T3");c(c$,"setToM3",function(a){this.setM33(a);this.m03=this.m13=this.m23=this.m30=this.m31=this.m32=0;this.m33=1},"JU.M34");c(c$,"setToAA",function(a){this.setIdentity();this.setAA33(a)},"JU.A4");c(c$,"setA",function(a){this.m00=a[0];this.m01=a[1];this.m02=a[2];this.m03=a[3];this.m10=a[4];this.m11=a[5];this.m12=a[6];this.m13=a[7];this.m20=a[8];this.m21=a[9];this.m22=a[10];this.m23=a[11];this.m30= -a[12];this.m31=a[13];this.m32=a[14];this.m33=a[15]},"~A");c(c$,"setTranslation",function(a){this.m03=a.x;this.m13=a.y;this.m23=a.z},"JU.T3");c(c$,"setElement",function(a,b,c){if(3>a&&3>b)this.set33(a,b,c);else{(3a&&3>b)return this.get33(a,b);if(3< -a||3a&&this.setRow33(a,b);switch(a){case 0:this.m03=b[3];return;case 1:this.m13=b[3];return;case 2:this.m23=b[3];return;case 3:this.m30=b[0];this.m31=b[1];this.m32=b[2];this.m33=b[3];return}this.err()},"~N,~A");d(c$,"getRow",function(a,b){3>a&&this.getRow33(a,b);switch(a){case 0:b[3]=this.m03;return;case 1:b[3]=this.m13; -return;case 2:b[3]=this.m23;return;case 3:b[0]=this.m30;b[1]=this.m31;b[2]=this.m32;b[3]=this.m33;return}this.err()},"~N,~A");c(c$,"setColumn4",function(a,b,c,d,f){0==a?(this.m00=b,this.m10=c,this.m20=d,this.m30=f):1==a?(this.m01=b,this.m11=c,this.m21=d,this.m31=f):2==a?(this.m02=b,this.m12=c,this.m22=d,this.m32=f):3==a?(this.m03=b,this.m13=c,this.m23=d,this.m33=f):this.err()},"~N,~N,~N,~N,~N");c(c$,"setColumnA",function(a,b){3>a&&this.setColumn33(a,b);switch(a){case 0:this.m30=b[3];break;case 1:this.m31= -b[3];break;case 2:this.m32=b[3];break;case 3:this.m03=b[0];this.m13=b[1];this.m23=b[2];this.m33=b[3];break;default:this.err()}},"~N,~A");c(c$,"getColumn",function(a,b){3>a&&this.getColumn33(a,b);switch(a){case 0:b[3]=this.m30;break;case 1:b[3]=this.m31;break;case 2:b[3]=this.m32;break;case 3:b[0]=this.m03;b[1]=this.m13;b[2]=this.m23;b[3]=this.m33;break;default:this.err()}},"~N,~A");c(c$,"sub",function(a){this.sub33(a);this.m03-=a.m03;this.m13-=a.m13;this.m23-=a.m23;this.m30-=a.m30;this.m31-=a.m31; -this.m32-=a.m32;this.m33-=a.m33},"JU.M4");c(c$,"transpose",function(){this.transpose33();var a=this.m03;this.m03=this.m30;this.m30=a;a=this.m13;this.m13=this.m31;this.m31=a;a=this.m23;this.m23=this.m32;this.m32=a});c(c$,"invert",function(){var a=this.determinant4();if(0==a)return this;a=1/a;this.set(this.m11*(this.m22*this.m33-this.m23*this.m32)+this.m12*(this.m23*this.m31-this.m21*this.m33)+this.m13*(this.m21*this.m32-this.m22*this.m31),this.m21*(this.m02*this.m33-this.m03*this.m32)+this.m22*(this.m03* -this.m31-this.m01*this.m33)+this.m23*(this.m01*this.m32-this.m02*this.m31),this.m31*(this.m02*this.m13-this.m03*this.m12)+this.m32*(this.m03*this.m11-this.m01*this.m13)+this.m33*(this.m01*this.m12-this.m02*this.m11),this.m01*(this.m13*this.m22-this.m12*this.m23)+this.m02*(this.m11*this.m23-this.m13*this.m21)+this.m03*(this.m12*this.m21-this.m11*this.m22),this.m12*(this.m20*this.m33-this.m23*this.m30)+this.m13*(this.m22*this.m30-this.m20*this.m32)+this.m10*(this.m23*this.m32-this.m22*this.m33),this.m22* -(this.m00*this.m33-this.m03*this.m30)+this.m23*(this.m02*this.m30-this.m00*this.m32)+this.m20*(this.m03*this.m32-this.m02*this.m33),this.m32*(this.m00*this.m13-this.m03*this.m10)+this.m33*(this.m02*this.m10-this.m00*this.m12)+this.m30*(this.m03*this.m12-this.m02*this.m13),this.m02*(this.m13*this.m20-this.m10*this.m23)+this.m03*(this.m10*this.m22-this.m12*this.m20)+this.m00*(this.m12*this.m23-this.m13*this.m22),this.m13*(this.m20*this.m31-this.m21*this.m30)+this.m10*(this.m21*this.m33-this.m23*this.m31)+ -this.m11*(this.m23*this.m30-this.m20*this.m33),this.m23*(this.m00*this.m31-this.m01*this.m30)+this.m20*(this.m01*this.m33-this.m03*this.m31)+this.m21*(this.m03*this.m30-this.m00*this.m33),this.m33*(this.m00*this.m11-this.m01*this.m10)+this.m30*(this.m01*this.m13-this.m03*this.m11)+this.m31*(this.m03*this.m10-this.m00*this.m13),this.m03*(this.m11*this.m20-this.m10*this.m21)+this.m00*(this.m13*this.m21-this.m11*this.m23)+this.m01*(this.m10*this.m23-this.m13*this.m20),this.m10*(this.m22*this.m31-this.m21* -this.m32)+this.m11*(this.m20*this.m32-this.m22*this.m30)+this.m12*(this.m21*this.m30-this.m20*this.m31),this.m20*(this.m02*this.m31-this.m01*this.m32)+this.m21*(this.m00*this.m32-this.m02*this.m30)+this.m22*(this.m01*this.m30-this.m00*this.m31),this.m30*(this.m02*this.m11-this.m01*this.m12)+this.m31*(this.m00*this.m12-this.m02*this.m10)+this.m32*(this.m01*this.m10-this.m00*this.m11),this.m00*(this.m11*this.m22-this.m12*this.m21)+this.m01*(this.m12*this.m20-this.m10*this.m22)+this.m02*(this.m10*this.m21- -this.m11*this.m20));this.scale(a);return 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c},"JU.M3,JU.T3");c(c$,"setZero",function(){this.clear33();this.m03=this.m13=this.m23=this.m30=this.m31=this.m32=this.m33=0});c(c$,"setIdentity",function(){this.setZero();this.m00=this.m11=this.m22=this.m33=1});c(c$,"setM4",function(a){this.setM33(a);this.m03=a.m03;this.m13=a.m13;this.m23=a.m23;this.m30=a.m30;this.m31=a.m31;this.m32=a.m32;this.m33=a.m33;return this},"JU.M4");c(c$,"setMV",function(a,b){this.setM33(a);this.setTranslation(b);this.m33= +1},"JU.M3,JU.T3");c(c$,"setToM3",function(a){this.setM33(a);this.m03=this.m13=this.m23=this.m30=this.m31=this.m32=0;this.m33=1},"JU.M34");c(c$,"setToAA",function(a){this.setIdentity();this.setAA33(a)},"JU.A4");c(c$,"setA",function(a){this.m00=a[0];this.m01=a[1];this.m02=a[2];this.m03=a[3];this.m10=a[4];this.m11=a[5];this.m12=a[6];this.m13=a[7];this.m20=a[8];this.m21=a[9];this.m22=a[10];this.m23=a[11];this.m30=a[12];this.m31=a[13];this.m32=a[14];this.m33=a[15]},"~A");c(c$,"setTranslation",function(a){this.m03= +a.x;this.m13=a.y;this.m23=a.z},"JU.T3");c(c$,"setElement",function(a,b,c){if(3>a&&3>b)this.set33(a,b,c);else{(3a&&3>b)return this.get33(a,b);if(3a&&this.setRow33(a,b);switch(a){case 0:this.m03=b[3];return;case 1:this.m13=b[3];return;case 2:this.m23=b[3];return;case 3:this.m30=b[0];this.m31=b[1];this.m32=b[2];this.m33=b[3];return}this.err()},"~N,~A");d(c$,"getRow",function(a,b){3>a&&this.getRow33(a,b);switch(a){case 0:b[3]=this.m03;return;case 1:b[3]=this.m13;return;case 2:b[3]=this.m23;return;case 3:b[0]=this.m30;b[1]=this.m31;b[2]=this.m32;b[3]=this.m33; +return}this.err()},"~N,~A");c(c$,"setColumn4",function(a,b,c,d,f){0==a?(this.m00=b,this.m10=c,this.m20=d,this.m30=f):1==a?(this.m01=b,this.m11=c,this.m21=d,this.m31=f):2==a?(this.m02=b,this.m12=c,this.m22=d,this.m32=f):3==a?(this.m03=b,this.m13=c,this.m23=d,this.m33=f):this.err()},"~N,~N,~N,~N,~N");c(c$,"setColumnA",function(a,b){3>a&&this.setColumn33(a,b);switch(a){case 0:this.m30=b[3];break;case 1:this.m31=b[3];break;case 2:this.m32=b[3];break;case 3:this.m03=b[0];this.m13=b[1];this.m23=b[2];this.m33= +b[3];break;default:this.err()}},"~N,~A");c(c$,"getColumn",function(a,b){3>a&&this.getColumn33(a,b);switch(a){case 0:b[3]=this.m30;break;case 1:b[3]=this.m31;break;case 2:b[3]=this.m32;break;case 3:b[0]=this.m03;b[1]=this.m13;b[2]=this.m23;b[3]=this.m33;break;default:this.err()}},"~N,~A");c(c$,"sub",function(a){this.sub33(a);this.m03-=a.m03;this.m13-=a.m13;this.m23-=a.m23;this.m30-=a.m30;this.m31-=a.m31;this.m32-=a.m32;this.m33-=a.m33},"JU.M4");c(c$,"transpose",function(){this.transpose33();var a= +this.m03;this.m03=this.m30;this.m30=a;a=this.m13;this.m13=this.m31;this.m31=a;a=this.m23;this.m23=this.m32;this.m32=a});c(c$,"invert",function(){var a=this.determinant4();if(0==a)return this;a=1/a;this.set(this.m11*(this.m22*this.m33-this.m23*this.m32)+this.m12*(this.m23*this.m31-this.m21*this.m33)+this.m13*(this.m21*this.m32-this.m22*this.m31),this.m21*(this.m02*this.m33-this.m03*this.m32)+this.m22*(this.m03*this.m31-this.m01*this.m33)+this.m23*(this.m01*this.m32-this.m02*this.m31),this.m31*(this.m02* +this.m13-this.m03*this.m12)+this.m32*(this.m03*this.m11-this.m01*this.m13)+this.m33*(this.m01*this.m12-this.m02*this.m11),this.m01*(this.m13*this.m22-this.m12*this.m23)+this.m02*(this.m11*this.m23-this.m13*this.m21)+this.m03*(this.m12*this.m21-this.m11*this.m22),this.m12*(this.m20*this.m33-this.m23*this.m30)+this.m13*(this.m22*this.m30-this.m20*this.m32)+this.m10*(this.m23*this.m32-this.m22*this.m33),this.m22*(this.m00*this.m33-this.m03*this.m30)+this.m23*(this.m02*this.m30-this.m00*this.m32)+this.m20* +(this.m03*this.m32-this.m02*this.m33),this.m32*(this.m00*this.m13-this.m03*this.m10)+this.m33*(this.m02*this.m10-this.m00*this.m12)+this.m30*(this.m03*this.m12-this.m02*this.m13),this.m02*(this.m13*this.m20-this.m10*this.m23)+this.m03*(this.m10*this.m22-this.m12*this.m20)+this.m00*(this.m12*this.m23-this.m13*this.m22),this.m13*(this.m20*this.m31-this.m21*this.m30)+this.m10*(this.m21*this.m33-this.m23*this.m31)+this.m11*(this.m23*this.m30-this.m20*this.m33),this.m23*(this.m00*this.m31-this.m01*this.m30)+ +this.m20*(this.m01*this.m33-this.m03*this.m31)+this.m21*(this.m03*this.m30-this.m00*this.m33),this.m33*(this.m00*this.m11-this.m01*this.m10)+this.m30*(this.m01*this.m13-this.m03*this.m11)+this.m31*(this.m03*this.m10-this.m00*this.m13),this.m03*(this.m11*this.m20-this.m10*this.m21)+this.m00*(this.m13*this.m21-this.m11*this.m23)+this.m01*(this.m10*this.m23-this.m13*this.m20),this.m10*(this.m22*this.m31-this.m21*this.m32)+this.m11*(this.m20*this.m32-this.m22*this.m30)+this.m12*(this.m21*this.m30-this.m20* +this.m31),this.m20*(this.m02*this.m31-this.m01*this.m32)+this.m21*(this.m00*this.m32-this.m02*this.m30)+this.m22*(this.m01*this.m30-this.m00*this.m31),this.m30*(this.m02*this.m11-this.m01*this.m12)+this.m31*(this.m00*this.m12-this.m02*this.m10)+this.m32*(this.m01*this.m10-this.m00*this.m11),this.m00*(this.m11*this.m22-this.m12*this.m21)+this.m01*(this.m12*this.m20-this.m10*this.m22)+this.m02*(this.m10*this.m21-this.m11*this.m20));this.scale(a);return this});c(c$,"set",function(a,b,c,d,f,l,g,j,k,n, +p,q,r,t,u,v){this.m00=a;this.m01=b;this.m02=c;this.m03=d;this.m10=f;this.m11=l;this.m12=g;this.m13=j;this.m20=k;this.m21=n;this.m22=p;this.m23=q;this.m30=r;this.m31=t;this.m32=u;this.m33=v},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"determinant4",function(){return(this.m00*this.m11-this.m01*this.m10)*(this.m22*this.m33-this.m23*this.m32)-(this.m00*this.m12-this.m02*this.m10)*(this.m21*this.m33-this.m23*this.m31)+(this.m00*this.m13-this.m03*this.m10)*(this.m21*this.m32-this.m22*this.m31)+ +(this.m01*this.m12-this.m02*this.m11)*(this.m20*this.m33-this.m23*this.m30)-(this.m01*this.m13-this.m03*this.m11)*(this.m20*this.m32-this.m22*this.m30)+(this.m02*this.m13-this.m03*this.m12)*(this.m20*this.m31-this.m21*this.m30)});c(c$,"scale",function(a){this.mul33(a);this.m03*=a;this.m13*=a;this.m23*=a;this.m30*=a;this.m31*=a;this.m32*=a;this.m33*=a},"~N");c(c$,"mul",function(a){this.mul2(this,a)},"JU.M4");c(c$,"mul2",function(a,b){this.set(a.m00*b.m00+a.m01*b.m10+a.m02*b.m20+a.m03*b.m30,a.m00*b.m01+ +a.m01*b.m11+a.m02*b.m21+a.m03*b.m31,a.m00*b.m02+a.m01*b.m12+a.m02*b.m22+a.m03*b.m32,a.m00*b.m03+a.m01*b.m13+a.m02*b.m23+a.m03*b.m33,a.m10*b.m00+a.m11*b.m10+a.m12*b.m20+a.m13*b.m30,a.m10*b.m01+a.m11*b.m11+a.m12*b.m21+a.m13*b.m31,a.m10*b.m02+a.m11*b.m12+a.m12*b.m22+a.m13*b.m32,a.m10*b.m03+a.m11*b.m13+a.m12*b.m23+a.m13*b.m33,a.m20*b.m00+a.m21*b.m10+a.m22*b.m20+a.m23*b.m30,a.m20*b.m01+a.m21*b.m11+a.m22*b.m21+a.m23*b.m31,a.m20*b.m02+a.m21*b.m12+a.m22*b.m22+a.m23*b.m32,a.m20*b.m03+a.m21*b.m13+a.m22*b.m23+ +a.m23*b.m33,a.m30*b.m00+a.m31*b.m10+a.m32*b.m20+a.m33*b.m30,a.m30*b.m01+a.m31*b.m11+a.m32*b.m21+a.m33*b.m31,a.m30*b.m02+a.m31*b.m12+a.m32*b.m22+a.m33*b.m32,a.m30*b.m03+a.m31*b.m13+a.m32*b.m23+a.m33*b.m33)},"JU.M4,JU.M4");c(c$,"transform",function(a){this.transform2(a,a)},"JU.T4");c(c$,"transform2",function(a,b){b.set4(this.m00*a.x+this.m01*a.y+this.m02*a.z+this.m03*a.w,this.m10*a.x+this.m11*a.y+this.m12*a.z+this.m13*a.w,this.m20*a.x+this.m21*a.y+this.m22*a.z+this.m23*a.w,this.m30*a.x+this.m31*a.y+ +this.m32*a.z+this.m33*a.w)},"JU.T4,JU.T4");c(c$,"rotTrans",function(a){this.rotTrans2(a,a)},"JU.T3");c(c$,"rotTrans2",function(a,b){b.set(this.m00*a.x+this.m01*a.y+this.m02*a.z+this.m03,this.m10*a.x+this.m11*a.y+this.m12*a.z+this.m13,this.m20*a.x+this.m21*a.y+this.m22*a.z+this.m23);return b},"JU.T3,JU.T3");c(c$,"setAsXYRotation",function(a){this.setIdentity();var b=Math.cos(a);a=Math.sin(a);this.m22=b;this.m23=-a;this.m32=a;this.m33=b;return this},"~N");c(c$,"setAsYZRotation",function(a){this.setIdentity(); +var b=Math.cos(a);a=Math.sin(a);this.m00=b;this.m03=-a;this.m30=a;this.m33=b;return this},"~N");c(c$,"setAsXZRotation",function(a){this.setIdentity();var b=Math.cos(a);a=Math.sin(a);this.m11=b;this.m13=-a;this.m31=a;this.m33=b;return this},"~N");d(c$,"equals",function(a){return!j(a,JU.M4)?!1:this.m00==a.m00&&this.m01==a.m01&&this.m02==a.m02&&this.m03==a.m03&&this.m10==a.m10&&this.m11==a.m11&&this.m12==a.m12&&this.m13==a.m13&&this.m20==a.m20&&this.m21==a.m21&&this.m22==a.m22&&this.m23==a.m23&&this.m30== +a.m30&&this.m31==a.m31&&this.m32==a.m32&&this.m33==a.m33},"~O");d(c$,"hashCode",function(){return 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-0:swingjs.JSAppletThread.$JSAppletThread$1$(),D(swingjs.JSAppletThread$1,this,P("m",b))))},"Runnable,~N");c$.$JSAppletThread$1$=function(){w(self.c$);c$=G(swingjs,"JSAppletThread$1",null,Runnable);d(c$,"run",function(){this.b$["swingjs.JSAppletThread"].run1(this.f$.m)});c$=v()}});p("swingjs");n(null,"swingjs.JSMouse",["JU.V3","java.awt.Toolkit","java.awt.event.MouseEvent"],function(){c$=q(function(){this.ap=null;this.wheeling=this.isMouseDown=!1;this.modifiersWhenPressed10=this.yWhenPressed=this.xWhenPressed= +0:swingjs.JSAppletThread.$JSAppletThread$1$(),D(swingjs.JSAppletThread$1,this,P("m",b))))},"Runnable,~N");c$.$JSAppletThread$1$=function(){v(self.c$);c$=G(swingjs,"JSAppletThread$1",null,Runnable);d(c$,"run",function(){this.b$["swingjs.JSAppletThread"].run1(this.f$.m)});c$=w()}});p("swingjs");n(null,"swingjs.JSMouse",["JU.V3","java.awt.Toolkit","java.awt.event.MouseEvent"],function(){c$=q(function(){this.ap=null;this.wheeling=this.isMouseDown=!1;this.modifiersWhenPressed10=this.yWhenPressed=this.xWhenPressed= 0;k(this,arguments)},swingjs,"JSMouse");g(c$,function(a){this.ap=a},"swingjs.JSAppletPanel");c(c$,"processEvent",function(a,b,c,d,f){-1!=a&&(d=swingjs.JSMouse.applyLeftMouse(d));switch(a){case -1:this.wheeled(f,b,d);break;case 501:this.xWhenPressed=b;this.yWhenPressed=c;this.modifiersWhenPressed10=d;this.pressed(f,b,c,d,!1);break;case 506:this.dragged(f,b,c,d);break;case 504:this.entry(f,b,c,!1);break;case 505:this.entry(f,b,c,!0);break;case 503:this.moved(f,b,c,d);break;case 502:this.released(f, b,c,d);b==this.xWhenPressed&&(c==this.yWhenPressed&&d==this.modifiersWhenPressed10)&&this.clicked(f,b,c,d,1);break;default:return!1}return!0},"~N,~N,~N,~N,~N");c(c$,"processTwoPointGesture",function(a){if(!(2>a[0].length)){var b=a[0],c=a[1],d=b[0],f=b[c.length-1];a=d[0];var g=f[0],d=d[1],f=f[1],j=JU.V3.new3(g-a,f-d,0),k=j.length(),n=c[0],p=c[c.length-1],c=n[0],q=p[0],n=n[1],p=p[1],r=JU.V3.new3(q-c,p-n,0),t=r.length();1>k||1>t||(j.normalize(),r.normalize(),j=j.dot(r),0.8j&&(j=JU.V3.new3(c-a,n-d,0),r=JU.V3.new3(q-g,p-f,0),b=r.length()-j.length(),this.wheeled(System.currentTimeMillis(),0>b?-1:1,32)))}},"~A");c(c$,"translateXYBy",function(){},"~N,~N");c(c$,"mouseClicked",function(a){this.clicked(a.getWhen(),a.getX(),a.getY(),a.getModifiers(),a.getClickCount())},"java.awt.event.MouseEvent");c(c$,"mouseEntered",function(a){this.entry(a.getWhen(),a.getX(),a.getY(),!1)},"java.awt.event.MouseEvent");c(c$,"mouseExited", @@ -2115,8 +2115,8 @@ new javax.swing.plaf.DimensionUIResource(146,12),"ProgressBar.verticalSize",new 5),"Spinner.editorAlignment",new Integer(11),"SplitPane.background",q,"SplitPane.dividerSize",new Integer(7),"SplitPaneDivider.draggingColor",p,"TabbedPane.selected",null,"TabbedPane.textIconGap",J,"TabbedPane.tabsOverlapBorder",Boolean.FALSE,"TabbedPane.labelShift",new Integer(1),"TabbedPane.selectedLabelShift",new Integer(-1),"TabbedPane.tabInsets",F,"TabbedPane.selectedTabPadInsets",G,"TabbedPane.tabAreaInsets",H,"TabbedPane.contentBorderInsets",I,"TabbedPane.tabRunOverlay",new Integer(2),"Table.background", w,"Table.dropLineShortColor",j,"Table.gridColor",n,"Table.focusCellBackground",w,"Table.focusCellForeground",r,"TextField.font",d,"TextField.background",w,"TextField.foreground",v,"TextField.margin",x,"FormattedTextField.font",d,"FormattedTextField.background",w,"FormattedTextField.foreground",v,"FormattedTextField.caretForeground",v,"FormattedTextField.margin",x,"PasswordField.font",g,"PasswordField.background",w,"PasswordField.foreground",v,"PasswordField.margin",x,"PasswordField.echoChar",new Character("*"), "TextArea.font",g,"TextArea.background",w,"TextArea.foreground",v,"TextArea.margin",x,"TextPane.font",c,"TextPane.background",k,"TextPane.foreground",v,"TextPane.margin",z,"EditorPane.font",c,"EditorPane.background",k,"EditorPane.foreground",v,"EditorPane.margin",z,"TitledBorder.titleColor",r,"Tree.paintLines",Boolean.TRUE,"Tree.lineTypeDashed",Boolean.FALSE,"Tree.background",w,"Tree.foreground",v,"Tree.hash",n,"Tree.textForeground",v,"Tree.textBackground",a.get("text"),"Tree.leftChildIndent",new Integer(7), -"Tree.rightChildIndent",new Integer(13),"Tree.rowHeight",new Integer(16),"Tree.scrollsOnExpand",Boolean.TRUE,"Tree.timeFactor",b]);a.putDefaults(b)},"javax.swing.UIDefaults");d(c$,"getName",function(){return"SwingJS"});d(c$,"getID",function(){return"SwingJS"});d(c$,"getDescription",function(){return"SwingJS L&F"});d(c$,"isNativeLookAndFeel",function(){return!0});d(c$,"isSupportedLookAndFeel",function(){return!0});c$.$HTML5LookAndFeel$1$=function(){w(self.c$);c$=G(swingjs.plaf,"HTML5LookAndFeel$1", -null,javax.swing.UIDefaults.ActiveValue);d(c$,"createValue",function(){return new javax.swing.DefaultListCellRenderer.UIResource},"javax.swing.UIDefaults");c$=v()}});p("swingjs.plaf");n(["javax.swing.plaf.ComponentUI","swingjs.plaf.JSEventHandler"],"swingjs.plaf.JSComponentUI","java.lang.IllegalArgumentException $.NullPointerException java.awt.Color $.Component $.Dimension $.Point $.Toolkit java.awt.event.FocusEvent swingjs.JSToolkit swingjs.api.DOMNode".split(" "),function(){c$=q(function(){this.components= +"Tree.rightChildIndent",new Integer(13),"Tree.rowHeight",new Integer(16),"Tree.scrollsOnExpand",Boolean.TRUE,"Tree.timeFactor",b]);a.putDefaults(b)},"javax.swing.UIDefaults");d(c$,"getName",function(){return"SwingJS"});d(c$,"getID",function(){return"SwingJS"});d(c$,"getDescription",function(){return"SwingJS L&F"});d(c$,"isNativeLookAndFeel",function(){return!0});d(c$,"isSupportedLookAndFeel",function(){return!0});c$.$HTML5LookAndFeel$1$=function(){v(self.c$);c$=G(swingjs.plaf,"HTML5LookAndFeel$1", +null,javax.swing.UIDefaults.ActiveValue);d(c$,"createValue",function(){return new javax.swing.DefaultListCellRenderer.UIResource},"javax.swing.UIDefaults");c$=w()}});p("swingjs.plaf");n(["javax.swing.plaf.ComponentUI","swingjs.plaf.JSEventHandler"],"swingjs.plaf.JSComponentUI","java.lang.IllegalArgumentException $.NullPointerException java.awt.Color $.Component $.Dimension $.Point $.Toolkit java.awt.event.FocusEvent swingjs.JSToolkit swingjs.api.DOMNode".split(" "),function(){c$=q(function(){this.components= this.focusNode=this.scrollNode=this.valueNode=this.textNode=this.enableNode=this.domNode=this.outerNode=this.c=this.id=null;this.num=0;this.isTainted=!0;this.y=this.x=0;this.preferredSize=null;this.isContainer=!1;this.body=this.document=this.classID=this.scrollerNode=this.currentText=this.parent=null;this.needPreferred=!1;k(this,arguments)},swingjs.plaf,"JSComponentUI",javax.swing.plaf.ComponentUI,swingjs.plaf.JSEventHandler);g(c$,function(){r(this,swingjs.plaf.JSComponentUI,[]);this.setDoc()});c(c$, "setDoc",function(){this.document=document;this.body=document.body});d(c$,"installUI",function(){},"javax.swing.JComponent");d(c$,"uninstallUI",function(){this.uninstallJSUI()},"javax.swing.JComponent");c(c$,"$",function(a){return swingjs.JSToolkit.getJQuery().$(a)},"swingjs.api.DOMNode");c(c$,"setTainted",function(){this.isTainted=!0});c(c$,"set",function(a){this.c=a;this.newID();this.needPreferred&&this.getPreferredSize(this.c);this.installJSUI();return this},"javax.swing.JComponent");c(c$,"newID", function(){this.classID=this.c.getUIClassID();null==this.id&&(this.num=++swingjs.plaf.JSComponentUI.incr,this.id=this.c.getHTMLName(this.classID)+"_"+this.num)});c(c$,"setCssFont",function(a,b){if(null!=b){var c=b.getStyle(),d=b.getFamily();"Dialog"===d&&(d="Arial");swingjs.api.DOMNode.setStyles(a,["font-family",d,"font-size",b.getSize()+"px","font-style",0==(c&2)?"normal":"italic","font-weight",0==(c&1)?"normal":"bold"])}this.c.isBackgroundSet()&&this.setBackground(this.c.getBackground());this.setForeground(this.c.getForeground()); @@ -2152,8 +2152,8 @@ null)},"javax.swing.JComponent");c(c$,"getInputMap",function(){return null},"~N, 0,!0),"released")}else c=javax.swing.SwingUtilities.getUIInputMap(a,2),null!=c&&c.clear()},"javax.swing.AbstractButton");d(c$,"stateChanged",function(a){a.getSource().repaint()},"javax.swing.event.ChangeEvent");d(c$,"focusGained",function(){},"java.awt.event.FocusEvent");d(c$,"focusLost",function(a){a=a.getSource().getModel();a.setArmed(!1);a.setPressed(!1)},"java.awt.event.FocusEvent");d(c$,"mouseMoved",function(){},"java.awt.event.MouseEvent");d(c$,"mouseDragged",function(){},"java.awt.event.MouseEvent"); d(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");d(c$,"mousePressed",function(a){if(javax.swing.SwingUtilities.isLeftMouseButton(a)){var b=a.getSource();if(b.contains(a.getX(),a.getY())){b.getUI().verifyButtonClick(!1);var c=b.getMultiClickThreshhold(),d=this.lastPressedTimestamp;a=this.lastPressedTimestamp=a.getWhen();-1!=d&&a-d maxX) { -gg.drawString (string, (i - startx - 1) * avcharWidth, y); +awt2swing.Util.drawString (gg, string, (i - startx - 1) * avcharWidth, y); maxX = (i - startx + 1) * avcharWidth + fm.stringWidth (string); }gg.drawLine (((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + 2, ((i - startx - 1) * avcharWidth) + (Clazz.doubleToInt (avcharWidth / 2)), y + (fm.getDescent () * 2)); } else { @@ -203,7 +203,7 @@ continue; }gg.fillPolygon ( Clazz.newIntArray (-1, [res * avcharWidth - Clazz.doubleToInt (avcharHeight / 4), res * avcharWidth + Clazz.doubleToInt (avcharHeight / 4), res * avcharWidth]), Clazz.newIntArray (-1, [y - Clazz.doubleToInt (avcharHeight / 2), y - Clazz.doubleToInt (avcharHeight / 2), y + 8]), 3); } }if (this.reveal != null && this.reveal[0] > startx && this.reveal[0] < endx) { -gg.drawString (jalview.util.MessageManager.getString ("label.reveal_columns"), this.reveal[0] * avcharWidth, 0); +awt2swing.Util.drawString (gg, jalview.util.MessageManager.getString ("label.reveal_columns"), this.reveal[0] * avcharWidth, 0); }}}, "java.awt.Graphics,~N,~N,~N,~N"); c$.$ScalePanel$1$ = function () { Clazz.pu$h(self.c$); diff --git a/site/j2s/jalview/appletgui/SeqCanvas.js b/site/j2s/jalview/appletgui/SeqCanvas.js index faa6bae..1d1a64d 100644 --- a/site/j2s/jalview/appletgui/SeqCanvas.js +++ b/site/j2s/jalview/appletgui/SeqCanvas.js @@ -1,5 +1,5 @@ Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel"], "jalview.appletgui.SeqCanvas", ["jalview.appletgui.AnnotationPanel", "$.FeatureRenderer", "$.PaintRefresher", "$.SequenceRenderer", "jalview.util.Comparison", "java.awt.Color"], function () { +Clazz.load (["awt2swing.Panel"], "jalview.appletgui.SeqCanvas", ["awt2swing.Util", "jalview.appletgui.AnnotationPanel", "$.FeatureRenderer", "$.PaintRefresher", "$.SequenceRenderer", "jalview.util.Comparison", "java.awt.Color"], function () { c$ = Clazz.decorateAsClass (function () { this.fr = null; this.sr = null; @@ -54,7 +54,7 @@ for (var i = scalestartx; i < endx; i += 10) { var value = i; if (this.av.hasHiddenColumns ()) { value = this.av.getColumnSelection ().adjustForHiddenColumns (value); -}g.drawString (String.valueOf (value), (i - startx - 1) * this.avcharWidth, ypos - (Clazz.doubleToInt (this.avcharHeight / 2))); +}awt2swing.Util.drawString (g, String.valueOf (value), (i - startx - 1) * this.avcharWidth, ypos - (Clazz.doubleToInt (this.avcharHeight / 2))); g.drawLine (((i - startx - 1) * this.avcharWidth) + (Clazz.doubleToInt (this.avcharWidth / 2)), (ypos + 2) - (Clazz.doubleToInt (this.avcharHeight / 2)), ((i - startx - 1) * this.avcharWidth) + (Clazz.doubleToInt (this.avcharWidth / 2)), ypos - 2); } }, "java.awt.Graphics,~N,~N,~N"); @@ -81,7 +81,7 @@ break; } if (value != -1) { var x = this.LABEL_WEST - fm.stringWidth (String.valueOf (value)) - Clazz.doubleToInt (this.avcharWidth / 2); -g.drawString (value + "", x, (ypos + (i * this.avcharHeight)) - (Clazz.doubleToInt (this.avcharHeight / 5))); +awt2swing.Util.drawString (g, value + "", x, (ypos + (i * this.avcharHeight)) - (Clazz.doubleToInt (this.avcharHeight / 5))); }} }, "java.awt.Graphics,~N,~N,~N"); Clazz.defineMethod (c$, "drawEastScale", @@ -102,7 +102,7 @@ continue; break; } if (value != -1) { -g.drawString (String.valueOf (value), 0, (ypos + (i * this.avcharHeight)) - (Clazz.doubleToInt (this.avcharHeight / 5))); +awt2swing.Util.drawString (g, String.valueOf (value), 0, (ypos + (i * this.avcharHeight)) - (Clazz.doubleToInt (this.avcharHeight / 5))); }} }, "java.awt.Graphics,~N,~N,~N"); Clazz.defineMethod (c$, "fastPaint", diff --git a/site/j2s/jalview/appletgui/SequenceRenderer.js b/site/j2s/jalview/appletgui/SequenceRenderer.js index 103924e..908e633 100644 --- a/site/j2s/jalview/appletgui/SequenceRenderer.js +++ b/site/j2s/jalview/appletgui/SequenceRenderer.js @@ -1,5 +1,5 @@ Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["jalview.api.SequenceRenderer"], "jalview.appletgui.SequenceRenderer", ["jalview.util.Comparison", "java.awt.Color", "$.Font"], function () { +Clazz.load (["jalview.api.SequenceRenderer"], "jalview.appletgui.SequenceRenderer", ["awt2swing.Util", "jalview.util.Comparison", "java.awt.Color", "$.Font"], function () { c$ = Clazz.decorateAsClass (function () { this.av = null; this.fm = null; @@ -41,7 +41,7 @@ col = fr.findFeatureColour (col, seq, position); Clazz.defineMethod (c$, "getBoxColour", function (cs, seq, i) { if (cs != null) { -this.resBoxColour = cs.findColour (seq.getCharAt (i), i, seq); +this.resBoxColour = cs.findColourSeq (seq.getCharAt (i), i, seq); } else if (this.forOverview && !jalview.util.Comparison.isGap (seq.getCharAt (i))) { this.resBoxColour = java.awt.Color.lightGray; } else { @@ -141,7 +141,7 @@ this.graphics.setFont (boldFont); this.graphics.setFont (this.av.font); bold = false; }}charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2); -this.graphics.drawString (String.valueOf (s), charOffset + avCharWidth * (i - start), y1); +awt2swing.Util.drawString (this.graphics, String.valueOf (s), charOffset + avCharWidth * (i - start), y1); } }, "jalview.datamodel.SequenceI,~N,~N,~N"); Clazz.defineMethod (c$, "getDisplayChar", @@ -177,7 +177,7 @@ for (var i = start; i <= end; i++) { if (i < seq.getLength ()) { s = seq.getCharAt (i); }charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2); -this.graphics.drawString (String.valueOf (s), charOffset + x1 + avCharWidth * (i - start), y1 + avCharHeight - pady); +awt2swing.Util.drawString (this.graphics, String.valueOf (s), charOffset + x1 + avCharWidth * (i - start), y1 + avCharHeight - pady); } }}, "jalview.datamodel.SequenceI,~N,~N,~N,~N"); Clazz.defineMethod (c$, "drawCursor", @@ -191,6 +191,6 @@ this.graphics.setColor (java.awt.Color.white); var s = seq.getCharAt (res); if (this.av.validCharWidth) { charOffset = Clazz.doubleToInt ((this.av.getCharWidth () - this.fm.charWidth (s)) / 2); -this.graphics.drawString (String.valueOf (s), charOffset + x1, (y1 + this.av.getCharHeight ()) - pady); +awt2swing.Util.drawString (this.graphics, String.valueOf (s), charOffset + x1, (y1 + this.av.getCharHeight ()) - pady); }}, "jalview.datamodel.SequenceI,~N,~N,~N"); }); diff --git a/site/j2s/jalview/appletgui/TitledPanel.js b/site/j2s/jalview/appletgui/TitledPanel.js index 026a455..480b54d 100644 --- a/site/j2s/jalview/appletgui/TitledPanel.js +++ b/site/j2s/jalview/appletgui/TitledPanel.js @@ -1,5 +1,5 @@ Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.Insets"], "jalview.appletgui.TitledPanel", null, function () { +Clazz.load (["awt2swing.Panel", "java.awt.Insets"], "jalview.appletgui.TitledPanel", ["awt2swing.Util"], function () { c$ = Clazz.decorateAsClass (function () { this.title = null; this.$insets = null; @@ -30,7 +30,7 @@ var width = g.getFontMetrics ().stringWidth (this.getTitle ()); g.setColor (this.getBackground ()); g.fillRect (10, 0, width, 10); g.setColor (this.getForeground ()); -g.drawString (this.getTitle (), 10, 10); +awt2swing.Util.drawString (g, this.getTitle (), 10, 10); }, "java.awt.Graphics"); Clazz.defineMethod (c$, "getTitle", function () { diff --git a/site/j2s/jalview/appletgui/TreeCanvas.js b/site/j2s/jalview/appletgui/TreeCanvas.js index 69da9f2..43b95d7 100644 --- a/site/j2s/jalview/appletgui/TreeCanvas.js +++ b/site/j2s/jalview/appletgui/TreeCanvas.js @@ -1,5 +1,5 @@ Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.util.Hashtable"], "jalview.appletgui.TreeCanvas", ["jalview.analysis.Conservation", "jalview.appletgui.PaintRefresher", "jalview.datamodel.SequenceGroup", "$.SequenceI", "$.SequenceNode", "jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "$.UserColourScheme", "jalview.util.Format", "$.MappingUtils", "java.awt.Color", "$.Dimension", "$.Point", "$.Rectangle", "java.util.Vector"], function () { +Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.util.Hashtable"], "jalview.appletgui.TreeCanvas", ["awt2swing.Util", "jalview.analysis.Conservation", "jalview.appletgui.PaintRefresher", "jalview.datamodel.SequenceGroup", "$.SequenceI", "$.SequenceNode", "jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "$.UserColourScheme", "jalview.util.Format", "$.MappingUtils", "java.awt.Color", "$.Dimension", "$.Point", "$.Rectangle", "java.util.Vector"], function () { c$ = Clazz.decorateAsClass (function () { this.tree = null; this.scrollPane = null; @@ -90,7 +90,7 @@ if (this.showDistances) { nodeLabel = nodeLabel + " : "; }nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ()); }}if (!nodeLabel.equals ("")) { -g.drawString (nodeLabel, xstart + 2, ypos - 2); +awt2swing.Util.drawString (g, nodeLabel, xstart + 2, ypos - 2); }var name = (this.markPlaceholders && node.isPlaceholder ()) ? (" * " + node.getName ()) : node.getName (); var fm = g.getFontMetrics (this.$font); var charWidth = fm.stringWidth (name) + 3; @@ -102,7 +102,7 @@ if (selected != null && selected.getSequences (null).contains (node.element ())) g.setColor (java.awt.Color.gray); g.fillRect (xend + 10, ypos - charHeight + 3, charWidth, charHeight); g.setColor (java.awt.Color.white); -}g.drawString (name, xend + 10, ypos); +}awt2swing.Util.drawString (g, name, xend + 10, ypos); g.setColor (java.awt.Color.black); } else { this.drawNode (g, node.left (), chunk, scale, width, offx, offy); @@ -133,7 +133,7 @@ if (this.showDistances) { nodeLabel = nodeLabel + " : "; }nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ()); }}if (!nodeLabel.equals ("")) { -g.drawString (nodeLabel, xstart + 2, ypos - 2); +awt2swing.Util.drawString (g, nodeLabel, xstart + 2, ypos - 2); }}}, "java.awt.Graphics,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N"); Clazz.defineMethod (c$, "findElement", function (x, y) { diff --git a/site/j2s/jalview/appletgui/UserDefinedColours.js b/site/j2s/jalview/appletgui/UserDefinedColours.js index c0ad316..01a51a6 100644 --- a/site/j2s/jalview/appletgui/UserDefinedColours.js +++ b/site/j2s/jalview/appletgui/UserDefinedColours.js @@ -274,7 +274,7 @@ var button = new awt2swing.Button (); var col = java.awt.Color.white; if (this.oldColourScheme != null) { try { -col = this.oldColourScheme.findColour (aa.charAt (0), -1, null); +col = this.oldColourScheme.findColourSeq (aa.charAt (0), -1, null); } catch (ex) { if (Clazz.exceptionOf (ex, Exception)) { } else { diff --git a/site/j2s/jalview/bin/JalviewLite.js b/site/j2s/jalview/bin/JalviewLite.js index 0b04f24..a905d67 100644 --- a/site/j2s/jalview/bin/JalviewLite.js +++ b/site/j2s/jalview/bin/JalviewLite.js @@ -1,5 +1,5 @@ Clazz.declarePackage ("jalview.bin"); -Clazz.load (["jalview.api.StructureSelectionManagerProvider", "jalview.javascript.JalviewLiteJsApi", "java.lang.Thread", "javax.swing.JApplet", "jalview.util.MessageManager", "java.util.Hashtable", "$.Vector", "javax.swing.JButton"], "jalview.bin.JalviewLite", ["jalview.analysis.SequenceIdMatcher", "jalview.appletgui.AlignFrame", "$.EmbmenuFrame", "$.FeatureSettings", "$.SplitFrame", "jalview.datamodel.Alignment", "$.AlignmentOrder", "$.ColumnSelection", "$.PDBEntry", "$.SequenceGroup", "jalview.io.AnnotationFile", "$.AppletFormatAdapter", "$.FileParse", "$.IdentifyFile", "$.JnetAnnotationMaker", "$.NewickFile", "jalview.javascript.JSFunctionExec", "$.JsSelectionSender", "$.MouseOverListener", "$.MouseOverStructureListener", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.ColourSchemeProperty", "$.UserColourScheme", "jalview.structure.SelectionListener", "$.StructureSelectionManager", "java.awt.Color", "$.EventQueue", "$.Font", "java.awt.event.ActionListener", "$.WindowAdapter", "java.io.BufferedReader", "$.InputStreamReader", "java.lang.Error", "$.StringBuffer", "java.net.URL", "java.util.StringTokenizer", "netscape.javascript.JSObject"], function () { +Clazz.load (["jalview.api.StructureSelectionManagerProvider", "jalview.javascript.JalviewLiteJsApi", "java.lang.Thread", "javax.swing.JApplet", "jalview.util.MessageManager", "java.util.Hashtable", "$.Vector", "javax.swing.JButton"], "jalview.bin.JalviewLite", ["awt2swing.Util", "jalview.analysis.SequenceIdMatcher", "jalview.appletgui.AlignFrame", "$.EmbmenuFrame", "$.FeatureSettings", "$.SplitFrame", "jalview.datamodel.Alignment", "$.AlignmentOrder", "$.ColumnSelection", "$.PDBEntry", "$.SequenceGroup", "jalview.io.AnnotationFile", "$.AppletFormatAdapter", "$.FileParse", "$.IdentifyFile", "$.JnetAnnotationMaker", "$.NewickFile", "jalview.javascript.JSFunctionExec", "$.JsSelectionSender", "$.MouseOverListener", "$.MouseOverStructureListener", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.ColourSchemeProperty", "$.UserColourScheme", "jalview.structure.SelectionListener", "$.StructureSelectionManager", "java.awt.Color", "$.EventQueue", "$.Font", "java.awt.event.ActionListener", "$.WindowAdapter", "java.io.BufferedReader", "$.InputStreamReader", "java.lang.Error", "$.StringBuffer", "java.net.URL", "java.util.StringTokenizer", "netscape.javascript.JSObject"], function () { c$ = Clazz.decorateAsClass (function () { this.embedded = false; this.enableSplitFrame = false; @@ -818,13 +818,13 @@ g.setColor ( new java.awt.Color (200, 200, 200)); g.setColor (java.awt.Color.cyan); g.fillRect (0, 0, this.getSize ().width, this.getSize ().height); g.setColor (java.awt.Color.red); -g.drawString (jalview.util.MessageManager.getString ("label.jalview_cannot_open_file"), 5, 15); -g.drawString ("\"" + this.startupFile + "\"", 5, 30); +awt2swing.Util.drawString (g, jalview.util.MessageManager.getString ("label.jalview_cannot_open_file"), 5, 15); +awt2swing.Util.drawString (g, "\"" + this.startupFile + "\"", 5, 30); } else if (this.embedded && !this.haveShownLoadMessage) { g.setColor (java.awt.Color.black); g.setFont ( new java.awt.Font ("Arial", 1, 24)); -g.drawString (jalview.util.MessageManager.getString ("label.jalview_applet"), 50, Clazz.doubleToInt (this.getSize ().height / 2) - 30); -g.drawString (jalview.util.MessageManager.getString ("label.loading_data") + "...", 50, Clazz.doubleToInt (this.getSize ().height / 2)); +awt2swing.Util.drawString (g, jalview.util.MessageManager.getString ("label.jalview_applet"), 50, Clazz.doubleToInt (this.getSize ().height / 2) - 30); +awt2swing.Util.drawString (g, jalview.util.MessageManager.getString ("label.loading_data") + "...", 50, Clazz.doubleToInt (this.getSize ().height / 2)); this.haveShownLoadMessage = true; }}, "java.awt.Graphics"); Clazz.defineMethod (c$, "getAppletWindow", diff --git a/site/j2s/jalview/jsdev/GenericFileAdapter.js b/site/j2s/jalview/jsdev/GenericFileAdapter.js index 6df0a9f..3c4f852 100644 --- a/site/j2s/jalview/jsdev/GenericFileAdapter.js +++ b/site/j2s/jalview/jsdev/GenericFileAdapter.js @@ -82,4 +82,15 @@ if (!forceURL && !jalview.jsdev.GenericFileAdapter.isJS ()) return new java.io. if (fileName.indexOf ("//") < 0) fileName = "file://" + fileName; return new java.io.BufferedReader ( new java.io.InputStreamReader ( new java.net.URL (fileName).openStream ())); }, "~S,~B"); +Clazz.defineStatics (c$, +"TCOFFEE_SCORE", "TCoffeeScore", +"Phylip_FILE", 1, +"Phylip_FILE_EXT", "phy", +"Phylip_FILE_DESC", "PHYLIP", +"JSON_FILE", 2, +"JSON_FILE_EXT", "json", +"JSON_FILE_DESC", "JSON", +"Html_FILE", 3, +"Html_FILE_EXT", "html", +"Html_FILE_DESC", "HTML"); }); diff --git a/site/j2s/jalview/renderer/AnnotationRenderer.js b/site/j2s/jalview/renderer/AnnotationRenderer.js index 221e5d3..4fa68cb 100644 --- a/site/j2s/jalview/renderer/AnnotationRenderer.js +++ b/site/j2s/jalview/renderer/AnnotationRenderer.js @@ -1,5 +1,5 @@ Clazz.declarePackage ("jalview.renderer"); -Clazz.load (["jalview.util.Platform", "java.awt.Color"], "jalview.renderer.AnnotationRenderer", ["jalview.analysis.AAFrequency", "$.CodingUtils", "$.StructureFrequency", "jalview.jsdev.RegExp", "jalview.schemes.NucleotideColourScheme", "$.ResidueProperties", "$.ZappoColourScheme", "java.awt.BasicStroke", "java.awt.geom.AffineTransform", "java.util.BitSet"], function () { +Clazz.load (["jalview.util.Platform", "java.awt.Color"], "jalview.renderer.AnnotationRenderer", ["awt2swing.Util", "jalview.analysis.AAFrequency", "$.CodingUtils", "$.StructureFrequency", "jalview.jsdev.RegExp", "jalview.schemes.NucleotideColourScheme", "$.ResidueProperties", "$.ZappoColourScheme", "java.awt.BasicStroke", "java.awt.geom.AffineTransform", "java.util.BitSet"], function () { c$ = Clazz.decorateAsClass (function () { this.debugRedraw = false; this.charWidth = 0; @@ -270,9 +270,9 @@ g.setColor (java.awt.Color.black); } else { g.setColor (row_annotations[column].colour); }if (column == 0 || row.graph > 0) { -g.drawString (displayChar, (x * this.charWidth) + charOffset, y + iconOffset); +awt2swing.Util.drawString (g, displayChar, (x * this.charWidth) + charOffset, y + iconOffset); } else if (row_annotations[column - 1] == null || (labelAllCols || !displayChar.equals (row_annotations[column - 1].displayCharacter) || (displayChar.length < 2 && row_annotations[column].secondaryStructure == ' '))) { -g.drawString (displayChar, x * this.charWidth + charOffset, y + iconOffset); +awt2swing.Util.drawString (g, displayChar, x * this.charWidth + charOffset, y + iconOffset); }g.setFont (ofont); }}if (row.hasIcons) { var ss = validRes ? row_annotations[column].secondaryStructure : '-'; @@ -663,9 +663,9 @@ lm = g.getFontMetrics ().getLineMetrics (dc, 0, 1, g); var colour = null; if (isCdnaProfile) { var codonTranslation = jalview.schemes.ResidueProperties.codonTranslate ( String.instantialize (dc)); -colour = this.profcolour.findColour (codonTranslation.charAt (0), column, null); +colour = this.profcolour.findColourSeq (codonTranslation.charAt (0), column, null); } else { -colour = this.profcolour.findColour (dc[0], column, null); +colour = this.profcolour.findColourSeq (dc[0], column, null); }g.setColor (colour === java.awt.Color.white ? java.awt.Color.lightGray : colour); hght = (ht + (scl - lm.getDescent () - lm.getBaselineOffsets ()[lm.getBaselineIndex ()])); g.drawChars (dc, 0, dc.length, x * this.charWidth, Clazz.doubleToInt (hght)); diff --git a/site/j2s/jalview/renderer/seqfeatures/FeatureRenderer.js b/site/j2s/jalview/renderer/seqfeatures/FeatureRenderer.js index 7dc84b1..e4a1026 100644 --- a/site/j2s/jalview/renderer/seqfeatures/FeatureRenderer.js +++ b/site/j2s/jalview/renderer/seqfeatures/FeatureRenderer.js @@ -1,5 +1,5 @@ Clazz.declarePackage ("jalview.renderer.seqfeatures"); -Clazz.load (["jalview.viewmodel.seqfeatures.FeatureRendererModel"], "jalview.renderer.seqfeatures.FeatureRenderer", ["jalview.util.Comparison", "java.awt.AlphaComposite", "$.Color", "java.awt.image.BufferedImage", "java.lang.Float"], function () { +Clazz.load (["jalview.viewmodel.seqfeatures.FeatureRendererModel"], "jalview.renderer.seqfeatures.FeatureRenderer", ["awt2swing.Util", "jalview.util.Comparison", "java.awt.AlphaComposite", "$.Color", "java.awt.image.BufferedImage", "java.lang.Float"], function () { c$ = Clazz.decorateAsClass (function () { this.fm = null; this.charOffset = 0; @@ -46,7 +46,7 @@ if (this.offscreenRender || !this.av_validCharWidth) { continue; }g.setColor (java.awt.Color.white); this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2); -g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady); +awt2swing.Util.drawString (g, String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady); } }}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N"); Clazz.defineMethod (c$, "renderScoreFeature", @@ -82,7 +82,7 @@ if (this.offscreenRender || !this.av_validCharWidth) { continue; }g.setColor (java.awt.Color.black); this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2); -g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady); +awt2swing.Util.drawString (g, String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady); } }}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N,~A"); Clazz.defineMethod (c$, "findFeatureColour", diff --git a/site/j2s/jalview/schemes/AnnotationColourGradient.js b/site/j2s/jalview/schemes/AnnotationColourGradient.js index a1b8db6..adc6c46 100644 --- a/site/j2s/jalview/schemes/AnnotationColourGradient.js +++ b/site/j2s/jalview/schemes/AnnotationColourGradient.js @@ -121,11 +121,11 @@ Clazz.defineMethod (c$, "getMaxColour", function () { return new java.awt.Color (Clazz.floatToInt (this.r1 + this.rr), Clazz.floatToInt (this.g1 + this.gg), Clazz.floatToInt (this.b1 + this.bb)); }); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColour", function (c) { return java.awt.Color.red; }, "~S"); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { var currentColour = java.awt.Color.white; var annotation = (this.seqAssociated && this.seqannot != null ? this.seqannot.get (seq) : this.annotation); @@ -140,7 +140,7 @@ currentColour = aj.colour; } else if (annotation.hasIcons && annotation.graph == 0) { if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.' && aj.secondaryStructure != '-') { if (this.colourScheme != null) { -currentColour = this.colourScheme.findColour (c, j, seq); +currentColour = this.colourScheme.findColourSeq (c, j, seq); } else { if (annotation.isRNA ()) { currentColour = jalview.schemes.ColourSchemeProperty.rnaHelices[Clazz.floatToInt (aj.value)]; @@ -150,7 +150,7 @@ currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.re return java.awt.Color.white; }} else if (this.noGradient) { if (this.colourScheme != null) { -currentColour = this.colourScheme.findColour (c, j, seq); +currentColour = this.colourScheme.findColourSeq (c, j, seq); } else { if (aj.colour != null) { currentColour = aj.colour; diff --git a/site/j2s/jalview/schemes/Blosum62ColourScheme.js b/site/j2s/jalview/schemes/Blosum62ColourScheme.js index 87c4a51..465bc97 100644 --- a/site/j2s/jalview/schemes/Blosum62ColourScheme.js +++ b/site/j2s/jalview/schemes/Blosum62ColourScheme.js @@ -1,7 +1,7 @@ Clazz.declarePackage ("jalview.schemes"); Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.Blosum62ColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () { c$ = Clazz.declareType (jalview.schemes, "Blosum62ColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (res, j, seq) { if ('a' <= res && res <= 'z') { res = String.fromCharCode (res.charCodeAt (0) - (32)); diff --git a/site/j2s/jalview/schemes/ClustalxColourScheme.js b/site/j2s/jalview/schemes/ClustalxColourScheme.js index 0556777..36419d0 100644 --- a/site/j2s/jalview/schemes/ClustalxColourScheme.js +++ b/site/j2s/jalview/schemes/ClustalxColourScheme.js @@ -171,11 +171,11 @@ this.residueColour[17] = this.colours[0]; this.residueColour[18] = this.colours[10]; this.residueColour[19] = this.colours[0]; }); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColour", function (c) { return java.awt.Color.pink; }, "~S"); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { var currentColour; if (this.cons2.length <= j || (this.includeGaps && this.threshold != 0 && !this.aboveThreshold (c, j))) { diff --git a/site/j2s/jalview/schemes/NucleotideColourScheme.js b/site/j2s/jalview/schemes/NucleotideColourScheme.js index abdfb5e..6594167 100644 --- a/site/j2s/jalview/schemes/NucleotideColourScheme.js +++ b/site/j2s/jalview/schemes/NucleotideColourScheme.js @@ -5,11 +5,11 @@ Clazz.makeConstructor (c$, function () { Clazz.superConstructor (this, jalview.schemes.NucleotideColourScheme, [jalview.schemes.ResidueProperties.nucleotideIndex, jalview.schemes.ResidueProperties.nucleotide, 0]); }); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColour", function (c) { return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; }, "~S"); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { var currentColour; if ((this.threshold == 0) || this.aboveThreshold (c, j)) { diff --git a/site/j2s/jalview/schemes/PIDColourScheme.js b/site/j2s/jalview/schemes/PIDColourScheme.js index bdf6f24..77099d7 100644 --- a/site/j2s/jalview/schemes/PIDColourScheme.js +++ b/site/j2s/jalview/schemes/PIDColourScheme.js @@ -12,7 +12,7 @@ Clazz.superConstructor (this, jalview.schemes.PIDColourScheme, []); this.pidColours = jalview.schemes.ResidueProperties.pidColours; this.thresholds = jalview.schemes.ResidueProperties.pidThresholds; }); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { if ('a' <= c && c <= 'z') { c = String.fromCharCode (c.charCodeAt (0) - (32)); diff --git a/site/j2s/jalview/schemes/RNAHelicesColour.js b/site/j2s/jalview/schemes/RNAHelicesColour.js index c7d3af2..abfa7ae 100644 --- a/site/j2s/jalview/schemes/RNAHelicesColour.js +++ b/site/j2s/jalview/schemes/RNAHelicesColour.js @@ -51,11 +51,11 @@ if (!this.helixcolorhash.containsKey (Integer.toString (j))) { this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white)); }} }}); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColour", function (c) { return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]]; }, "~S"); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { this.refresh (); var currentColour = java.awt.Color.white; diff --git a/site/j2s/jalview/schemes/RNAInteractionColourScheme.js b/site/j2s/jalview/schemes/RNAInteractionColourScheme.js index 6935253..5c8425b 100644 --- a/site/j2s/jalview/schemes/RNAInteractionColourScheme.js +++ b/site/j2s/jalview/schemes/RNAInteractionColourScheme.js @@ -1,11 +1,11 @@ Clazz.declarePackage ("jalview.schemes"); Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.RNAInteractionColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () { c$ = Clazz.declareType (jalview.schemes, "RNAInteractionColourScheme", jalview.schemes.ResidueColourScheme); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColour", function (c) { return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]]; }, "~S"); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { var currentColour; if ((this.threshold == 0) || this.aboveThreshold (c, j)) { diff --git a/site/j2s/jalview/schemes/ResidueColourScheme.js b/site/j2s/jalview/schemes/ResidueColourScheme.js index 9b2382f..23a1c72 100644 --- a/site/j2s/jalview/schemes/ResidueColourScheme.js +++ b/site/j2s/jalview/schemes/ResidueColourScheme.js @@ -26,11 +26,11 @@ Clazz.makeConstructor (c$, function () { this.symbolIndex = null; }); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColour", function (c) { return this.colors == null ? java.awt.Color.white : this.colors[this.symbolIndex[c.charCodeAt (0)]]; }, "~S"); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { var currentColour; if (this.colors != null && this.symbolIndex != null && (this.threshold == 0) || this.aboveThreshold (c, j)) { diff --git a/site/j2s/jalview/schemes/ScoreColourScheme.js b/site/j2s/jalview/schemes/ScoreColourScheme.js index f097a40..2ba5128 100644 --- a/site/j2s/jalview/schemes/ScoreColourScheme.js +++ b/site/j2s/jalview/schemes/ScoreColourScheme.js @@ -24,7 +24,7 @@ red = 0.0; }this.colors[i] = this.makeColour (red); } }, "~A,~A,~N,~N"); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { if (this.threshold > 0) { if (!this.aboveThreshold (c, j)) { diff --git a/site/j2s/jalview/schemes/TCoffeeColourScheme.js b/site/j2s/jalview/schemes/TCoffeeColourScheme.js index 6350ad9..185348c 100644 --- a/site/j2s/jalview/schemes/TCoffeeColourScheme.js +++ b/site/j2s/jalview/schemes/TCoffeeColourScheme.js @@ -28,7 +28,7 @@ scores[i++] = (an != null) ? an.colour : java.awt.Color.white; this.seqMap.put (al.sequenceRef, scores); }} }, "jalview.datamodel.AnnotatedCollectionI,java.util.Map"); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { var cols; if (this.seqMap == null || (cols = this.seqMap.get (seq)) == null) { diff --git a/site/j2s/jalview/schemes/UserColourScheme.js b/site/j2s/jalview/schemes/UserColourScheme.js index ee83987..9167b50 100644 --- a/site/j2s/jalview/schemes/UserColourScheme.js +++ b/site/j2s/jalview/schemes/UserColourScheme.js @@ -143,7 +143,7 @@ throw ex; } } }, "~S"); -Clazz.defineMethod (c$, "findColour", +Clazz.overrideMethod (c$, "findColourSeq", function (c, j, seq) { var currentColour; var index = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)]; diff --git a/site/j2s/java/awt/Color.js b/site/j2s/java/awt/Color.js index c726fe1..431d7e7 100644 --- a/site/j2s/java/awt/Color.js +++ b/site/j2s/java/awt/Color.js @@ -40,9 +40,17 @@ case 2: this.value = (a[1] ? a[0] : 0xff000000 | a[0]); break; case 3: +var n = a[0] + a[1] + a[2]; +if (n > 0 && n < 3.001) +this.setFloat(a[0], a[1], a[2], 1); +else this.setColor4(a[0], a[1], a[2], 255); break; case 4: +var n = a[0] + a[1] + a[2] + a[3]; +if (n > 0 && n < 4.001) +this.setFloat(a[0], a[1], a[2], a[3]); +else this.setColor4(a[0], a[1], a[2], a[3]); break; } diff --git a/site/j2s/java/util/ArrayList.js b/site/j2s/java/util/ArrayList.js index 71e92a9..78c4c54 100644 --- a/site/j2s/java/util/ArrayList.js +++ b/site/j2s/java/util/ArrayList.js @@ -310,7 +310,7 @@ return i-this.firstIndex; },"~O"); Clazz.overrideMethod(c$,"remove", function(location){ -if (0+location != location) return this.removeObject(location) +if (0 + location != location)return this.removeObject(location) var result; var size=this.size(); if(0<=location&&location -Jmol._checkLoad = false; - -Jmol._isAsync = false; +Jmol._checkLoad = false; // gets a list of classes loaded when true +Jmol._debugCode = false; // this should not be necessary +Jmol._isAsync = false; // do not set this true. Jmol.getProfile() // records repeat calls to overridden or overloaded Java methods @@ -37,7 +37,7 @@ Info = { defaultColour: "Zappo", width: 1050, height: 550, - debug: true, + debug: false, color: "#F0F0F0", zIndexBase: 20000, z:{monitorZIndex:100}, diff --git a/src/fr/orsay/lri/varna/models/rna/RNA.java b/src/fr/orsay/lri/varna/models/rna/RNA.java index d72bb20..2f6e5d7 100644 --- a/src/fr/orsay/lri/varna/models/rna/RNA.java +++ b/src/fr/orsay/lri/varna/models/rna/RNA.java @@ -1,22 +1,21 @@ package fr.orsay.lri.varna.models.rna; /** - * jsapplet?yes! test 2 Bob changes + * no significant reference in applet? * -lots of changes * @author Bob Hanson * */ public class RNA { public int getSize() { - // all // TODO Auto-generated method stub + // TODO Auto-generated method stub return 0; } public String getStructDBN(boolean b) { - //over // TODO Auto-generated method stub + // TODO Auto-generated method stub return null; } -// the place + } diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 94da265..1ac9d86 100644 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -719,7 +719,7 @@ public class Conservation + (maxB * vprop))); } } - DebugJS._("Conservation"); +// DebugJS._("Conservation"); } diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 3699fca..c639445 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -2938,32 +2938,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // TODO: update this text for each release or centrally store it for // lite and application g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString(MessageManager.formatMessage( + awt2swing.Util.drawString(g, MessageManager.formatMessage( "label.jalviewLite_release", new String[] { version }), x, y += fh); g.setFont(new Font("Helvetica", Font.BOLD, 12)); - g.drawString(MessageManager.formatMessage( + awt2swing.Util.drawString(g, MessageManager.formatMessage( "label.jaview_build_date", new String[] { builddate }), x, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g.drawString(MessageManager.getString("label.jalview_authors_1"), + awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_authors_1"), x, y += fh * 1.5); - g.drawString(MessageManager.getString("label.jalview_authors_2"), + awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh + 8); - g.drawString( + awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_dev_managers"), x, y += fh); - g.drawString(MessageManager + awt2swing.Util.drawString(g, MessageManager .getString("label.jalview_distribution_lists"), x, y += fh); - g.drawString(MessageManager.getString("label.jalview_please_cite"), + awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8); - g.drawString( + awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_cite_1_authors"), x, y += fh); - g.drawString( + awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_cite_1_title"), x, y += fh); - g.drawString(MessageManager.getString("label.jalview_cite_1_ref"), + awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_cite_1_ref"), x, y += fh); } } diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index cf24f85..083578b 100644 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -831,7 +831,7 @@ public class AnnotationLabels extends Panel implements ActionListener, y += aa[i].height; offset = -(aa[i].height - fy) / 2; - g.drawString(aa[i].label, x, y + offset); + awt2swing.Util.drawString(g, aa[i].label, x, y + offset); } } g.translate(0, +scrollOffset); @@ -845,15 +845,15 @@ public class AnnotationLabels extends Panel implements ActionListener, else if (!dragCancelled && dragEvent != null && aa != null) { g.setColor(Color.lightGray); - g.drawString(aa[selectedRow].label, dragEvent.getX(), + awt2swing.Util.drawString(g, aa[selectedRow].label, dragEvent.getX(), dragEvent.getY()); } if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) { g.setColor(Color.black); - g.drawString(MessageManager.getString("label.right_click"), 2, 8); - g.drawString(MessageManager.getString("label.to_add_annotation"), 2, + awt2swing.Util.drawString(g, MessageManager.getString("label.right_click"), 2, 8); + awt2swing.Util.drawString(g, MessageManager.getString("label.to_add_annotation"), 2, 18); } } diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index 3b3252c..72dbfff 100644 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -637,7 +637,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, g.setColor(Color.black); if (av.validCharWidth) { - g.drawString(MessageManager + awt2swing.Util.drawString(g, MessageManager .getString("label.alignment_has_no_annotations"), 20, 15); } diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index aa18f5f..cc4090f 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -670,7 +670,7 @@ public class AppletJmol //extends EmbmenuFrame implements // g.fillRect(0, 0, currentSize.width, currentSize.height); // g.setColor(Color.white); // g.setFont(new Font("Verdana", Font.BOLD, 14)); -// g.drawString(MessageManager.getString("label.retrieving_pdb_data"), +// awt2swing.Util.drawString(g, MessageManager.getString("label.retrieving_pdb_data"), // 20, currentSize.height / 2); // } // else diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 2d996c7..f46810d 100644 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -168,7 +168,7 @@ public class FeatureRenderer extends g.setColor(Color.black); Font f = new Font("Verdana", Font.PLAIN, 10); g.setFont(f); - g.drawString(MessageManager.getString("label.label"), 0, 0); + awt2swing.Util.drawString(g, MessageManager.getString("label.label"), 0, 0); } else { diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index d8a6140..9bb1426 100644 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -187,12 +187,12 @@ public class FeatureSettings extends Panel implements ItemListener, public void PaintComponent(Graphics g) { g.setColor(Color.black); - g.drawString(MessageManager + awt2swing.Util.drawString(g, MessageManager .getString("label.no_features_added_to_this_alignment"), 10, 20); - g.drawString(MessageManager + awt2swing.Util.drawString(g, MessageManager .getString("label.features_can_be_added_from_searches_1"), 10, 40); - g.drawString(MessageManager + awt2swing.Util.drawString(g, MessageManager .getString("label.features_can_be_added_from_searches_2"), 10, 60); } @@ -772,7 +772,7 @@ public class FeatureSettings extends Panel implements ItemListener, * // g.setFont(g.getFont().deriveFont( // * AffineTransform.getScaleInstance( // * width/g.getFontMetrics().stringWidth("Label"), // - * height/g.getFontMetrics().getHeight()))); g.drawString("Label", + * height/g.getFontMetrics().getHeight()))); awt2swing.Util.drawString(g, "Label", * width/2, 0); */ diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java index a045541..0e142ae 100644 --- a/src/jalview/appletgui/IdCanvas.java +++ b/src/jalview/appletgui/IdCanvas.java @@ -85,7 +85,7 @@ public class IdCanvas extends Panel gg.setColor(Color.black); } - gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0, + awt2swing.Util.drawString(gg, s.getDisplayId(av.getShowJVSuffix()), 0, ((i - starty) * charHeight) + ypos + charHeight - (charHeight / 5)); @@ -297,7 +297,7 @@ public class IdCanvas extends Panel avcharHeight); gg.setColor(currentTextColor); - gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0, + awt2swing.Util.drawString(gg, seq.getDisplayId(av.getShowJVSuffix()), 0, (((i - starty) * avcharHeight) + avcharHeight) - (avcharHeight / 5)); diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java index 2602e89..ad580d1 100644 --- a/src/jalview/appletgui/RotatableCanvas.java +++ b/src/jalview/appletgui/RotatableCanvas.java @@ -331,7 +331,7 @@ public class RotatableCanvas extends Panel implements MouseListener, if (points == null) { g.setFont(new Font("Verdana", Font.PLAIN, 18)); - g.drawString(MessageManager.getString("label.calculating_pca") + awt2swing.Util.drawString(g, MessageManager.getString("label.calculating_pca") + "....", 20, getSize().height / 2); } else @@ -362,7 +362,7 @@ public class RotatableCanvas extends Panel implements MouseListener, if (tooltip != null) { ig.setColor(Color.red); - ig.drawString(tooltip, toolx, tooly); + awt2swing.Util.drawString(ig, tooltip, toolx, tooly); } g.drawImage(img, 0, 0, this); @@ -428,7 +428,7 @@ public class RotatableCanvas extends Panel implements MouseListener, if (showLabels) { g.setColor(Color.red); - g.drawString( + awt2swing.Util.drawString(g, ((SequencePoint) points.elementAt(i)).sequence.getName(), x - 3, y - 4); } diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java index 371b0c7..281a3ea 100644 --- a/src/jalview/appletgui/ScalePanel.java +++ b/src/jalview/appletgui/ScalePanel.java @@ -413,7 +413,7 @@ public class ScalePanel extends Panel implements MouseMotionListener, .adjustForHiddenColumns(i)); if ((i - startx - 1) * avcharWidth > maxX) { - gg.drawString(string, (i - startx - 1) * avcharWidth, y); + awt2swing.Util.drawString(gg, string, (i - startx - 1) * avcharWidth, y); maxX = (i - startx + 1) * avcharWidth + fm.stringWidth(string); } @@ -465,7 +465,7 @@ public class ScalePanel extends Panel implements MouseMotionListener, if (reveal != null && reveal[0] > startx && reveal[0] < endx) { - gg.drawString(MessageManager.getString("label.reveal_columns"), + awt2swing.Util.drawString(gg, MessageManager.getString("label.reveal_columns"), reveal[0] * avcharWidth, 0); } } diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index a85e783..0526e63 100644 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -104,7 +104,7 @@ public class SeqCanvas extends Panel value = av.getColumnSelection().adjustForHiddenColumns(value); } - g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth, + awt2swing.Util.drawString(g, String.valueOf(value), (i - startx - 1) * avcharWidth, ypos - (avcharHeight / 2)); g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2), @@ -155,7 +155,7 @@ public class SeqCanvas extends Panel { int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) - avcharWidth / 2; - g.drawString(value + "", x, (ypos + (i * avcharHeight)) + awt2swing.Util.drawString(g, value + "", x, (ypos + (i * avcharHeight)) - (avcharHeight / 5)); } } @@ -194,7 +194,7 @@ public class SeqCanvas extends Panel if (value != -1) { - g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight)) + awt2swing.Util.drawString(g, String.valueOf(value), 0, (ypos + (i * avcharHeight)) - (avcharHeight / 5)); } } diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index e2e98cb..b0733e4 100644 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -116,7 +116,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { if (cs != null) { - resBoxColour = cs.findColour(seq.getCharAt(i), i, seq); + resBoxColour = cs.findColourSeq(seq.getCharAt(i), i, seq); } else if (forOverview && !Comparison.isGap(seq.getCharAt(i))) { @@ -308,7 +308,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } charOffset = (avCharWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + avCharWidth + awt2swing.Util.drawString(graphics, String.valueOf(s), charOffset + avCharWidth * (i - start), y1); } @@ -370,7 +370,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } charOffset = (avCharWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + x1 + awt2swing.Util.drawString(graphics, String.valueOf(s), charOffset + x1 + avCharWidth * (i - start), y1 + avCharHeight - pady); } } @@ -391,7 +391,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + x1, + awt2swing.Util.drawString(graphics, String.valueOf(s), charOffset + x1, (y1 + av.getCharHeight()) - pady); } } diff --git a/src/jalview/appletgui/TitledPanel.java b/src/jalview/appletgui/TitledPanel.java index 4594ba2..f4cf685 100644 --- a/src/jalview/appletgui/TitledPanel.java +++ b/src/jalview/appletgui/TitledPanel.java @@ -39,7 +39,7 @@ public class TitledPanel extends Panel g.setColor(getBackground()); g.fillRect(10, 0, width, 10); g.setColor(getForeground()); - g.drawString(getTitle(), 10, 10); + awt2swing.Util.drawString(g, getTitle(), 10, 10); } /** diff --git a/src/jalview/appletgui/Tooltip.java b/src/jalview/appletgui/Tooltip.java index 4ed029b..06c6004 100644 --- a/src/jalview/appletgui/Tooltip.java +++ b/src/jalview/appletgui/Tooltip.java @@ -98,20 +98,20 @@ public class Tooltip // extends Canvas implements MouseListener, // { // if (lindex > 0) // { -// g.drawString(tip[i].substring(0, lindex), 3, (i + 1) * fontHeight +// awt2swing.Util.drawString(g, tip[i].substring(0, lindex), 3, (i + 1) * fontHeight // - 3); // x += fm.stringWidth(tip[i].substring(0, lindex) + 3); // } // g.drawImage(linkImage, x, i * fontHeight + 1, this); // if (lindex + 6 < tip[i].length()) // { -// g.drawString(tip[i].substring(lindex + 6), +// awt2swing.Util.drawString(g, tip[i].substring(lindex + 6), // x + linkImage.getWidth(this), (i + 1) * fontHeight - 3); // } // } // else // { -// g.drawString(tip[i], 3, (i + 1) * fontHeight - 3); +// awt2swing.Util.drawString(g, tip[i], 3, (i + 1) * fontHeight - 3); // } // } // } diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index 3f149d0..a16cc8c 100644 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -207,7 +207,7 @@ public class TreeCanvas extends Panel implements MouseListener, } if (!nodeLabel.equals("")) { - g.drawString(nodeLabel, xstart + 2, ypos - 2); + awt2swing.Util.drawString(g, nodeLabel, xstart + 2, ypos - 2); } String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node @@ -231,7 +231,7 @@ public class TreeCanvas extends Panel implements MouseListener, g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight); g.setColor(Color.white); } - g.drawString(name, xend + 10, ypos); + awt2swing.Util.drawString(g, name, xend + 10, ypos); g.setColor(Color.black); } else @@ -294,7 +294,7 @@ public class TreeCanvas extends Panel implements MouseListener, if (!nodeLabel.equals("")) { - g.drawString(nodeLabel, xstart + 2, ypos - 2); + awt2swing.Util.drawString(g, nodeLabel, xstart + 2, ypos - 2); } } diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java index af8a155..af1d25c 100644 --- a/src/jalview/appletgui/UserDefinedColours.java +++ b/src/jalview/appletgui/UserDefinedColours.java @@ -406,7 +406,7 @@ public class UserDefinedColours extends Panel implements ActionListener, { try { - col = oldColourScheme.findColour(aa.charAt(0), -1, null); + col = oldColourScheme.findColourSeq(aa.charAt(0), -1, null); } catch (Exception ex) { } diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 2befd9a..07fdce5 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1797,18 +1797,18 @@ public class JalviewLite extends JApplet implements g.setColor(Color.cyan); g.fillRect(0, 0, getSize().width, getSize().height); g.setColor(Color.red); - g.drawString( + awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_cannot_open_file"), 5, 15); - g.drawString("\"" + startupFile + "\"", 5, 30); + awt2swing.Util.drawString(g, "\"" + startupFile + "\"", 5, 30); } else if (embedded && !haveShownLoadMessage) { g.setColor(Color.black); g.setFont(new Font("Arial", Font.BOLD, 24)); - g.drawString(MessageManager.getString("label.jalview_applet"), 50, + awt2swing.Util.drawString(g, MessageManager.getString("label.jalview_applet"), 50, getSize().height / 2 - 30); - g.drawString(MessageManager.getString("label.loading_data") + "...", + awt2swing.Util.drawString(g, MessageManager.getString("label.loading_data") + "...", 50, getSize().height / 2); haveShownLoadMessage = true; } diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index c908b15..ad3224a 100644 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -34,7 +34,6 @@ import java.util.List; import javajs.J2SIgnoreImport; -import jalview.jsdev.Constants; import jalview.jsdev.GenericFileAdapter; /** @@ -90,7 +89,7 @@ public class AppletFormatAdapter */ public static final String[] READABLE_FORMATS = new String[] { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", - "PDB", "JnetFile", "RNAML", Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC, IdentifyFile.GFF3File, + "PDB", "JnetFile", "RNAML", GenericFileAdapter.Phylip_FILE_DESC, GenericFileAdapter.JSON_FILE_DESC, IdentifyFile.GFF3File, "HTML" }; /** @@ -99,9 +98,9 @@ public class AppletFormatAdapter */ public static final String[] READABLE_EXTENSIONS = new String[] { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", - "sto,stk", "xml,rnaml", Constants.Phylip_FILE_EXT, Constants.JSON_FILE_EXT, + "sto,stk", "xml,rnaml", GenericFileAdapter.Phylip_FILE_EXT, GenericFileAdapter.JSON_FILE_EXT, ".gff2,gff3", - "jar,jvp", Constants.Html_FILE_EXT }; + "jar,jvp", GenericFileAdapter.Html_FILE_EXT }; /** * List of readable formats by application in order corresponding to @@ -109,8 +108,8 @@ public class AppletFormatAdapter */ public static final String[] READABLE_FNAMES = new String[] { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", - "RNAML", Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC, IdentifyFile.GFF3File, "Jalview", - Constants.Html_FILE_DESC }; + "RNAML", GenericFileAdapter.Phylip_FILE_DESC, GenericFileAdapter.JSON_FILE_DESC, IdentifyFile.GFF3File, "Jalview", + GenericFileAdapter.Html_FILE_DESC }; /** * List of valid format strings for use by callers of the formatSequences @@ -118,7 +117,7 @@ public class AppletFormatAdapter */ public static final String[] WRITEABLE_FORMATS = new String[] { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", - "STH", Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC }; + "STH", GenericFileAdapter.Phylip_FILE_DESC, GenericFileAdapter.JSON_FILE_DESC }; /** * List of extensions corresponding to file format types in WRITABLE_FNAMES @@ -126,7 +125,7 @@ public class AppletFormatAdapter */ public static final String[] WRITABLE_EXTENSIONS = new String[] { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", - "sto,stk", Constants.Phylip_FILE_EXT, Constants.JSON_FILE_EXT, "jvp" }; + "sto,stk", GenericFileAdapter.Phylip_FILE_EXT, GenericFileAdapter.JSON_FILE_EXT, "jvp" }; /** * List of writable formats by the application. Order must correspond with the @@ -134,7 +133,7 @@ public class AppletFormatAdapter */ public static final String[] WRITABLE_FNAMES = new String[] { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", - Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC, "Jalview" }; + GenericFileAdapter.Phylip_FILE_DESC, GenericFileAdapter.JSON_FILE_DESC, "Jalview" }; public static String INVALID_CHARACTERS = "Contains invalid characters"; @@ -297,11 +296,11 @@ public class AppletFormatAdapter { alignFile = GenericFileAdapter.getFile("PhylipFile", inFile, type); } - else if (format.equals(Constants.JSON_FILE_DESC)) + else if (format.equals(GenericFileAdapter.JSON_FILE_DESC)) { alignFile = GenericFileAdapter.getFile("JSONFile", inFile, type); } - else if (format.equals(Constants.Html_FILE_DESC)) + else if (format.equals(GenericFileAdapter.Html_FILE_DESC)) { alignFile = GenericFileAdapter.getFile("HtmlFile", inFile, type); } @@ -422,7 +421,7 @@ public class AppletFormatAdapter { alignFile = GenericFileAdapter.getFile("SimpleBlastFile", source); } - else if (format.equals(Constants.Phylip_FILE_DESC)) + else if (format.equals(GenericFileAdapter.Phylip_FILE_DESC)) { alignFile = GenericFileAdapter.getFile("PhylipFile", source); } @@ -430,11 +429,11 @@ public class AppletFormatAdapter { alignFile = GenericFileAdapter.getFile("Gff3File", inFile, type); } - else if (format.equals(Constants.JSON_FILE_DESC)) + else if (format.equals(GenericFileAdapter.JSON_FILE_DESC)) { alignFile = GenericFileAdapter.getFile("JSONFile", source); } - else if (format.equals(Constants.Html_FILE_DESC)) + else if (format.equals(GenericFileAdapter.Html_FILE_DESC)) { alignFile = GenericFileAdapter.getFile("HtmlFile", source); } @@ -586,11 +585,11 @@ public class AppletFormatAdapter { afile = GenericFileAdapter.getFile("AMSAFile", alignment); } - else if (format.equalsIgnoreCase(Constants.Phylip_FILE_DESC)) + else if (format.equalsIgnoreCase(GenericFileAdapter.Phylip_FILE_DESC)) { afile = GenericFileAdapter.getFile("PhylipFile"); } - else if (format.equalsIgnoreCase(Constants.JSON_FILE_DESC)) + else if (format.equalsIgnoreCase(GenericFileAdapter.JSON_FILE_DESC)) { afile = GenericFileAdapter.getFile("JSONFile"); } diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index 14848c7..f7c4286 100644 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -20,7 +20,6 @@ */ package jalview.io; -import jalview.jsdev.Constants; import jalview.jsdev.GenericFileAdapter; import java.io.IOException; @@ -148,7 +147,7 @@ public class IdentifyFile // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>")) if (data.matches("])*>")) // BH was (?i)rnaml, but JavaScript regex does not support (?i); data is already upper case { - reply = Constants.Html_FILE_DESC; + reply = GenericFileAdapter.Html_FILE_DESC; break; } @@ -160,7 +159,7 @@ public class IdentifyFile if (data.indexOf("{\"") > -1) { - reply = Constants.JSON_FILE_DESC; + reply = GenericFileAdapter.JSON_FILE_DESC; break; } if ((data.length() < 1) || (data.indexOf("#") == 0)) @@ -290,7 +289,7 @@ public class IdentifyFile } else if (data.matches("\\s*\\d+\\s+\\d+\\s*")) { - reply = Constants.Phylip_FILE_DESC; + reply = GenericFileAdapter.Phylip_FILE_DESC; break; } diff --git a/src/jalview/jsdev/GenericFileAdapter.java b/src/jalview/jsdev/GenericFileAdapter.java index f112ebf..f73b53b 100644 --- a/src/jalview/jsdev/GenericFileAdapter.java +++ b/src/jalview/jsdev/GenericFileAdapter.java @@ -125,6 +125,17 @@ abstract public class GenericFileAdapter extends AlignFile { fileName = "file://" + fileName; return new BufferedReader(new InputStreamReader(new URL(fileName).openStream())); } + + public final static String TCOFFEE_SCORE = "TCoffeeScore"; + public static final int Phylip_FILE = 1; + public static final String Phylip_FILE_EXT = "phy"; + public static final String Phylip_FILE_DESC = "PHYLIP"; + public static final int JSON_FILE = 2; + public static final String JSON_FILE_EXT = "json"; + public static final String JSON_FILE_DESC = "JSON"; + public static final int Html_FILE = 3; + public static final String Html_FILE_EXT = "html"; + public static final String Html_FILE_DESC = "HTML"; } diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index debbf9a..231187f 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -533,7 +533,7 @@ public class AnnotationRenderer g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y - row.height, imgWidth, y, annotationPanel); g.setColor(Color.black); - // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2); + // awt2swing.Util.drawString(g, "Calculating "+aa[i].label+"....",20, y-row.height/2); continue; } @@ -547,7 +547,7 @@ public class AnnotationRenderer * annotationPanel.imgWidth, y, annotationPanel); * * g.setColor(Color.black); // - * g.drawString("Calculating Conservation.....",20, y-row.height/2); + * awt2swing.Util.drawString(g, "Calculating Conservation.....",20, y-row.height/2); * * continue; } else if (annotationPanel.av.updatingConservation && * aa[i].label.equals("Quality")) { @@ -556,7 +556,7 @@ public class AnnotationRenderer * row.height, annotationPanel.imgWidth, y, 0, y - row.height, * annotationPanel.imgWidth, y, annotationPanel); * g.setColor(Color.black); // / - * g.drawString("Calculating Quality....",20, y-row.height/2); + * awt2swing.Util.drawString(g, "Calculating Quality....",20, y-row.height/2); * * continue; } */ @@ -664,7 +664,7 @@ public class AnnotationRenderer if (column == 0 || row.graph > 0) { - g.drawString(displayChar, (x * charWidth) + charOffset, y + awt2swing.Util.drawString(g, displayChar, (x * charWidth) + charOffset, y + iconOffset); } else if (row_annotations[column - 1] == null @@ -673,7 +673,7 @@ public class AnnotationRenderer .equals(row_annotations[column - 1].displayCharacter) || (displayChar .length() < 2 && row_annotations[column].secondaryStructure == ' '))) { - g.drawString(displayChar, x * charWidth + charOffset, y + awt2swing.Util.drawString(g, displayChar, x * charWidth + charOffset, y + iconOffset); } g.setFont(ofont); @@ -1413,12 +1413,12 @@ public class AnnotationRenderer { final String codonTranslation = ResidueProperties .codonTranslate(new String(dc)); - colour = profcolour.findColour(codonTranslation.charAt(0), + colour = profcolour.findColourSeq(codonTranslation.charAt(0), column, null); } else { - colour = profcolour.findColour(dc[0], column, null); + colour = profcolour.findColourSeq(dc[0], column, null); } g.setColor(colour == Color.white ? Color.lightGray : colour); diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index e3280de..cc56b1f 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -76,7 +76,7 @@ public class FeatureRenderer extends FeatureRendererModel g.setColor(Color.white); charOffset = (av_charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), charOffset + awt2swing.Util.drawString(g, String.valueOf(s), charOffset + (av_charWidth * (i - start)), pady); } @@ -141,7 +141,7 @@ public class FeatureRenderer extends FeatureRendererModel g.setColor(Color.black); charOffset = (av_charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), charOffset + awt2swing.Util.drawString(g, String.valueOf(s), charOffset + (av_charWidth * (i - start)), pady); } } diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index e65d5f5..2198a4e 100644 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -257,7 +257,7 @@ public class AnnotationColourGradient extends FollowerColourScheme * @return DOCUMENT ME! */ @Override - public Color findColour(char c, int j, SequenceI seq) { + public Color findColourSeq(char c, int j, SequenceI seq) { Color currentColour = Color.white; AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot .get(seq) : this.annotation); @@ -289,7 +289,7 @@ public class AnnotationColourGradient extends FollowerColourScheme if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.' && aj.secondaryStructure != '-') { if (colourScheme != null) { - currentColour = colourScheme.findColour(c, j, seq); + currentColour = colourScheme.findColourSeq(c, j, seq); } else { if (annotation.isRNA()) { currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value]; @@ -305,7 +305,7 @@ public class AnnotationColourGradient extends FollowerColourScheme } } else if (noGradient) { if (colourScheme != null) { - currentColour = colourScheme.findColour(c, j, seq); + currentColour = colourScheme.findColourSeq(c, j, seq); } else { if (aj.colour != null) { currentColour = aj.colour; diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java index d5d2924..a435b5b 100644 --- a/src/jalview/schemes/Blosum62ColourScheme.java +++ b/src/jalview/schemes/Blosum62ColourScheme.java @@ -37,7 +37,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme } @Override - public Color findColour(char res, int j, SequenceI seq) + public Color findColourSeq(char res, int j, SequenceI seq) { if ('a' <= res && res <= 'z') { diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java index ca4316f..4fe4183 100644 --- a/src/jalview/schemes/ClustalxColourScheme.java +++ b/src/jalview/schemes/ClustalxColourScheme.java @@ -275,7 +275,7 @@ public class ClustalxColourScheme extends ResidueColourScheme } @Override - public Color findColour(char c, int j, SequenceI seq) + public Color findColourSeq(char c, int j, SequenceI seq) { Color currentColour; diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java index 1589356..03256c6 100644 --- a/src/jalview/schemes/ColourSchemeI.java +++ b/src/jalview/schemes/ColourSchemeI.java @@ -48,7 +48,7 @@ public interface ColourSchemeI * @return context dependent colour for the given symbol at the position in * the given sequence */ - public Color findColour(char c, int j, SequenceI seq); + public Color findColourSeq(char c, int j, SequenceI seq); /** * assign the given consensus profile for the colourscheme diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java index dff2bf3..1e44d91 100644 --- a/src/jalview/schemes/NucleotideColourScheme.java +++ b/src/jalview/schemes/NucleotideColourScheme.java @@ -67,7 +67,7 @@ public class NucleotideColourScheme extends ResidueColourScheme * @return DOCUMENT ME! */ @Override - public Color findColour(char c, int j, SequenceI seq) + public Color findColourSeq(char c, int j, SequenceI seq) { Color currentColour; if ((threshold == 0) || aboveThreshold(c, j)) diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java index c59d579..7c48a7d 100644 --- a/src/jalview/schemes/PIDColourScheme.java +++ b/src/jalview/schemes/PIDColourScheme.java @@ -42,7 +42,7 @@ public class PIDColourScheme extends ResidueColourScheme } @Override - public Color findColour(char c, int j, SequenceI seq) + public Color findColourSeq(char c, int j, SequenceI seq) { if ('a' <= c && c <= 'z') { diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java index be28d91..2f46cc2 100644 --- a/src/jalview/schemes/RNAHelicesColour.java +++ b/src/jalview/schemes/RNAHelicesColour.java @@ -178,7 +178,7 @@ public class RNAHelicesColour extends ResidueColourScheme * @return Color in RGB */ @Override - public Color findColour(char c, int j, SequenceI seq) + public Color findColourSeq(char c, int j, SequenceI seq) { refresh(); Color currentColour = Color.white; diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java index 794195a..0d22b64 100644 --- a/src/jalview/schemes/RNAInteractionColourScheme.java +++ b/src/jalview/schemes/RNAInteractionColourScheme.java @@ -57,7 +57,7 @@ public class RNAInteractionColourScheme extends ResidueColourScheme * @return DOCUMENT ME! */ @Override - public Color findColour(char c, int j, SequenceI seq) + public Color findColourSeq(char c, int j, SequenceI seq) { Color currentColour; if ((threshold == 0) || aboveThreshold(c, j)) diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 5294006..d7300e1 100644 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -107,7 +107,7 @@ public class ResidueColourScheme implements ColourSchemeI } @Override - public Color findColour(char c, int j, SequenceI seq) + public Color findColourSeq(char c, int j, SequenceI seq) { Color currentColour; diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java index beb7b59..e0430e8 100644 --- a/src/jalview/schemes/ScoreColourScheme.java +++ b/src/jalview/schemes/ScoreColourScheme.java @@ -93,7 +93,7 @@ public class ScoreColourScheme extends ResidueColourScheme * @return DOCUMENT ME! */ @Override - public Color findColour(char c, int j, SequenceI seq) + public Color findColourSeq(char c, int j, SequenceI seq) { if (threshold > 0) { diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java index 9e8feea..47261f6 100644 --- a/src/jalview/schemes/TCoffeeColourScheme.java +++ b/src/jalview/schemes/TCoffeeColourScheme.java @@ -26,7 +26,7 @@ import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.Annotation; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceI; -import jalview.jsdev.Constants; +import jalview.jsdev.GenericFileAdapter; import java.awt.Color; import java.util.ArrayList; @@ -91,7 +91,7 @@ public class TCoffeeColourScheme extends ResidueColourScheme : alignment.getContext(); int w = 0; for (AlignmentAnnotation al : alcontext - .findAnnotation(Constants.TCOFFEE_SCORE)) + .findAnnotation(GenericFileAdapter.TCOFFEE_SCORE)) { if (al.sequenceRef != null && !al.belowAlignment) { @@ -116,7 +116,7 @@ public class TCoffeeColourScheme extends ResidueColourScheme } @Override - public Color findColour(char c, int j, SequenceI seq) + public Color findColourSeq(char c, int j, SequenceI seq) { Color[] cols; diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index 80efaca..f75cf13 100644 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -229,7 +229,7 @@ public class UserColourScheme extends ResidueColourScheme } @Override - public Color findColour(char c, int j, SequenceI seq) + public Color findColourSeq(char c, int j, SequenceI seq) { Color currentColour; int index = ResidueProperties.aaIndex[c]; diff --git a/src/swingjs/JSImage.java b/src/swingjs/JSImage.java index 1501688..0de3895 100644 --- a/src/swingjs/JSImage.java +++ b/src/swingjs/JSImage.java @@ -8,21 +8,15 @@ import java.awt.image.ImageObserver; public class JSImage extends BufferedImage { // a BufferedImage in name only, actually; int typeRequested; - int[] pix; // not used in Java, but may be used in JavaScript + int[] pix; public DOMNode _imgNode; // used by JSGraphics2D directly private int width, height; - public JSImage() { - super(1,1, TYPE_INT_ARGB); - - } - - public JSImage setData(int width, int height, int[] argb) { - pix = argb; + public JSImage(int[] argb, int width, int height) { + super(width, height, TYPE_INT_ARGB); this.width = width; this.height = height; - getColorModel().createCompatibleWritableRaster(width, height); - return this; + pix = argb; } /** -- 1.7.10.2