Formatting
authoramwaterhouse <Andrew Waterhouse>
Wed, 7 Feb 2007 15:11:09 +0000 (15:11 +0000)
committeramwaterhouse <Andrew Waterhouse>
Wed, 7 Feb 2007 15:11:09 +0000 (15:11 +0000)
commit7bc226b58110fa26d9dbd3f0c78095d06909ffc3
treec796dc17be6013a8352d8015c813adc19e68e7e1
parentdd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d
Formatting
419 files changed:
src/com/stevesoft/pat/AmpersandRule.java
src/com/stevesoft/pat/Any.java
src/com/stevesoft/pat/BackG.java
src/com/stevesoft/pat/BackMatch.java
src/com/stevesoft/pat/BackRefRule.java
src/com/stevesoft/pat/Backup.java
src/com/stevesoft/pat/BasicStringBufferLike.java
src/com/stevesoft/pat/Bits.java
src/com/stevesoft/pat/Boundary.java
src/com/stevesoft/pat/Bracket.java
src/com/stevesoft/pat/CaseMgr.java
src/com/stevesoft/pat/ChangeRule.java
src/com/stevesoft/pat/CodeRule.java
src/com/stevesoft/pat/Ctrl.java
src/com/stevesoft/pat/Custom.java
src/com/stevesoft/pat/CustomEndpoint.java
src/com/stevesoft/pat/DirFileRegex.java
src/com/stevesoft/pat/DotMulti.java
src/com/stevesoft/pat/End.java
src/com/stevesoft/pat/FastBracket.java
src/com/stevesoft/pat/FastMulti.java
src/com/stevesoft/pat/FileRegex.java
src/com/stevesoft/pat/Group.java
src/com/stevesoft/pat/LeftRule.java
src/com/stevesoft/pat/Multi.java
src/com/stevesoft/pat/MultiMin.java
src/com/stevesoft/pat/Multi_stage2.java
src/com/stevesoft/pat/NoPattern.java
src/com/stevesoft/pat/NonDirFileRegex.java
src/com/stevesoft/pat/NotImplementedError.java
src/com/stevesoft/pat/NullPattern.java
src/com/stevesoft/pat/NullRule.java
src/com/stevesoft/pat/Or.java
src/com/stevesoft/pat/OrMark.java
src/com/stevesoft/pat/PartialBuffer.java
src/com/stevesoft/pat/Pattern.java
src/com/stevesoft/pat/PatternSub.java
src/com/stevesoft/pat/PopRule.java
src/com/stevesoft/pat/Prop.java
src/com/stevesoft/pat/Pthings.java
src/com/stevesoft/pat/PushRule.java
src/com/stevesoft/pat/RBuffer.java
src/com/stevesoft/pat/Range.java
src/com/stevesoft/pat/RegOpt.java
src/com/stevesoft/pat/RegRes.java
src/com/stevesoft/pat/RegSyntax.java
src/com/stevesoft/pat/RegSyntaxError.java
src/com/stevesoft/pat/Regex.java
src/com/stevesoft/pat/RegexReader.java
src/com/stevesoft/pat/RegexTokenizer.java
src/com/stevesoft/pat/RegexWriter.java
src/com/stevesoft/pat/ReplaceRule.java
src/com/stevesoft/pat/Replacer.java
src/com/stevesoft/pat/RightRule.java
src/com/stevesoft/pat/Rthings.java
src/com/stevesoft/pat/RuleHolder.java
src/com/stevesoft/pat/Skip.java
src/com/stevesoft/pat/Skip2.java
src/com/stevesoft/pat/SkipBMH.java
src/com/stevesoft/pat/Skipped.java
src/com/stevesoft/pat/SpecialRule.java
src/com/stevesoft/pat/Start.java
src/com/stevesoft/pat/StrPos.java
src/com/stevesoft/pat/StringBufferLike.java
src/com/stevesoft/pat/StringLike.java
src/com/stevesoft/pat/StringRule.java
src/com/stevesoft/pat/SubMark.java
src/com/stevesoft/pat/TransPat.java
src/com/stevesoft/pat/Transformer.java
src/com/stevesoft/pat/UniValidator.java
src/com/stevesoft/pat/Validator.java
src/com/stevesoft/pat/WantMoreTextReplaceRule.java
src/com/stevesoft/pat/lookAhead.java
src/com/stevesoft/pat/oneChar.java
src/com/stevesoft/pat/parsePerl.java
src/com/stevesoft/pat/patInf.java
src/com/stevesoft/pat/patInt.java
src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
src/com/stevesoft/pat/wrap/CharArrayWrap.java
src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
src/com/stevesoft/pat/wrap/StringBufferWrap.java
src/com/stevesoft/pat/wrap/StringWrap.java
src/com/stevesoft/pat/wrap/WriterWrap.java
src/ext/vamsas/IRegistry.java
src/ext/vamsas/IRegistryService.java
src/ext/vamsas/IRegistryServiceLocator.java
src/ext/vamsas/Jpred.java
src/ext/vamsas/JpredService.java
src/ext/vamsas/JpredServiceLocator.java
src/ext/vamsas/JpredSoapBindingStub.java
src/ext/vamsas/MuscleWS.java
src/ext/vamsas/MuscleWSService.java
src/ext/vamsas/MuscleWSServiceLocator.java
src/ext/vamsas/MuscleWSSoapBindingStub.java
src/ext/vamsas/RegistryServiceSoapBindingStub.java
src/ext/vamsas/ServiceHandle.java
src/ext/vamsas/ServiceHandles.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/Finder.java
src/jalview/analysis/NJTree.java
src/jalview/analysis/PCA.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/analysis/SequenceIdMatcher.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/EditNameDialog.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/FontChooser.java
src/jalview/appletgui/IdCanvas.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/IdwidthAdjuster.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/PCAPanel.java
src/jalview/appletgui/PaintRefresher.java
src/jalview/appletgui/PairwiseAlignPanel.java
src/jalview/appletgui/RedundancyPanel.java
src/jalview/appletgui/RotatableCanvas.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SequenceRenderer.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/Tooltip.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/TreePanel.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/commands/ChangeCaseCommand.java
src/jalview/commands/CommandI.java
src/jalview/commands/EditCommand.java
src/jalview/commands/OrderCommand.java
src/jalview/commands/RemoveGapColCommand.java
src/jalview/commands/RemoveGapsCommand.java
src/jalview/commands/TrimRegionCommand.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentOrder.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/Annotation.java
src/jalview/datamodel/BinaryNode.java
src/jalview/datamodel/BinarySequence.java
src/jalview/datamodel/CigarArray.java
src/jalview/datamodel/CigarBase.java
src/jalview/datamodel/CigarCigar.java
src/jalview/datamodel/CigarSimple.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/DBRefSource.java
src/jalview/datamodel/GraphLine.java
src/jalview/datamodel/HiddenSequences.java
src/jalview/datamodel/PDBEntry.java
src/jalview/datamodel/Provenance.java
src/jalview/datamodel/ProvenanceEntry.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/SeqCigar.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/SequenceNode.java
src/jalview/datamodel/SequencePoint.java
src/jalview/datamodel/UniprotEntry.java
src/jalview/datamodel/UniprotFile.java
src/jalview/datamodel/UniprotProteinName.java
src/jalview/datamodel/UniprotSequence.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/EPSOptions.java
src/jalview/gui/EditNameDialog.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/FontChooser.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/IdPanel.java
src/jalview/gui/IdwidthAdjuster.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PaintRefresher.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/RedundancyPanel.java
src/jalview/gui/RotatableCanvas.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SequenceRenderer.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/TextColourChooser.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/UserQuestionnaireCheck.java
src/jalview/gui/VamsasClient.java
src/jalview/gui/WebserviceInfo.java
src/jalview/io/AMSAFile.java
src/jalview/io/AlignFile.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BLCFile.java
src/jalview/io/ClustalFile.java
src/jalview/io/DBRefFetcher.java
src/jalview/io/DasSequenceFeatureFetcher.java
src/jalview/io/EBIFetchClient.java
src/jalview/io/FastaFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileLoader.java
src/jalview/io/FileParse.java
src/jalview/io/FormatAdapter.java
src/jalview/io/HTMLOutput.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JPredFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/JalviewFileFilter.java
src/jalview/io/JalviewFileView.java
src/jalview/io/JnetAnnotationMaker.java
src/jalview/io/MSFfile.java
src/jalview/io/ModellerDescription.java
src/jalview/io/NewickFile.java
src/jalview/io/PIRFile.java
src/jalview/io/PfamFile.java
src/jalview/io/PileUpfile.java
src/jalview/io/StockholmFile.java
src/jalview/io/VamsasDatastore.java
src/jalview/io/WSWUBlastClient.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GAlignmentPanel.java
src/jalview/jbgui/GCutAndPasteTransfer.java
src/jalview/jbgui/GDasSourceBrowser.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GFinder.java
src/jalview/jbgui/GFontChooser.java
src/jalview/jbgui/GPCAPanel.java
src/jalview/jbgui/GPairwiseAlignPanel.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GSequenceLink.java
src/jalview/jbgui/GSliderPanel.java
src/jalview/jbgui/GTreePanel.java
src/jalview/jbgui/GUserDefinedColours.java
src/jalview/jbgui/GWebserviceInfo.java
src/jalview/math/Matrix.java
src/jalview/math/RotatableMatrix.java
src/jalview/schemabinding/version2/Annotation.java
src/jalview/schemabinding/version2/AnnotationColours.java
src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
src/jalview/schemabinding/version2/AnnotationDescriptor.java
src/jalview/schemabinding/version2/AnnotationElement.java
src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
src/jalview/schemabinding/version2/Colour.java
src/jalview/schemabinding/version2/ColourDescriptor.java
src/jalview/schemabinding/version2/DBRef.java
src/jalview/schemabinding/version2/DBRefDescriptor.java
src/jalview/schemabinding/version2/Feature.java
src/jalview/schemabinding/version2/FeatureDescriptor.java
src/jalview/schemabinding/version2/FeatureSettings.java
src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
src/jalview/schemabinding/version2/Features.java
src/jalview/schemabinding/version2/FeaturesDescriptor.java
src/jalview/schemabinding/version2/HiddenColumns.java
src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
src/jalview/schemabinding/version2/JGroup.java
src/jalview/schemabinding/version2/JGroupDescriptor.java
src/jalview/schemabinding/version2/JSeq.java
src/jalview/schemabinding/version2/JSeqDescriptor.java
src/jalview/schemabinding/version2/JalviewModel.java
src/jalview/schemabinding/version2/JalviewModelDescriptor.java
src/jalview/schemabinding/version2/JalviewModelSequence.java
src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
src/jalview/schemabinding/version2/JalviewUserColours.java
src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
src/jalview/schemabinding/version2/OtherData.java
src/jalview/schemabinding/version2/OtherDataDescriptor.java
src/jalview/schemabinding/version2/Pdbentry.java
src/jalview/schemabinding/version2/PdbentryDescriptor.java
src/jalview/schemabinding/version2/PdbentryItem.java
src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
src/jalview/schemabinding/version2/Pdbids.java
src/jalview/schemabinding/version2/PdbidsDescriptor.java
src/jalview/schemabinding/version2/Property.java
src/jalview/schemabinding/version2/PropertyDescriptor.java
src/jalview/schemabinding/version2/Sequence.java
src/jalview/schemabinding/version2/SequenceDescriptor.java
src/jalview/schemabinding/version2/SequenceSet.java
src/jalview/schemabinding/version2/SequenceSetDescriptor.java
src/jalview/schemabinding/version2/SequenceType.java
src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
src/jalview/schemabinding/version2/Setting.java
src/jalview/schemabinding/version2/SettingDescriptor.java
src/jalview/schemabinding/version2/ThresholdLine.java
src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
src/jalview/schemabinding/version2/Tree.java
src/jalview/schemabinding/version2/TreeDescriptor.java
src/jalview/schemabinding/version2/UserColourScheme.java
src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
src/jalview/schemabinding/version2/UserColours.java
src/jalview/schemabinding/version2/UserColoursDescriptor.java
src/jalview/schemabinding/version2/VAMSAS.java
src/jalview/schemabinding/version2/VAMSASDescriptor.java
src/jalview/schemabinding/version2/VamsasModel.java
src/jalview/schemabinding/version2/VamsasModelDescriptor.java
src/jalview/schemabinding/version2/Viewport.java
src/jalview/schemabinding/version2/ViewportDescriptor.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/Blosum62ColourScheme.java
src/jalview/schemes/BuriedColourScheme.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/schemes/ColourSchemeI.java
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/Consensus.java
src/jalview/schemes/HelixColourScheme.java
src/jalview/schemes/HydrophobicColourScheme.java
src/jalview/schemes/NucleotideColourScheme.java
src/jalview/schemes/PIDColourScheme.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/ScoreColourScheme.java
src/jalview/schemes/ScoreMatrix.java
src/jalview/schemes/StrandColourScheme.java
src/jalview/schemes/TaylorColourScheme.java
src/jalview/schemes/TurnColourScheme.java
src/jalview/schemes/UserColourScheme.java
src/jalview/schemes/ZappoColourScheme.java
src/jalview/util/BrowserLauncher.java
src/jalview/util/Comparison.java
src/jalview/util/DBRefUtils.java
src/jalview/util/Format.java
src/jalview/util/ImageMaker.java
src/jalview/util/MapList.java
src/jalview/util/QuickSort.java
src/jalview/util/ShiftList.java
src/jalview/util/TableSorter.java
src/jalview/ws/Discoverer.java
src/jalview/ws/JPredClient.java
src/jalview/ws/JPredThread.java
src/jalview/ws/MsaWSClient.java
src/jalview/ws/MsaWSThread.java
src/jalview/ws/WSClient.java
src/jalview/ws/WSClientI.java
src/jalview/ws/WSThread.java
src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
src/org/biojava/dasobert/das/DAS_Feature_Handler.java
src/org/biojava/dasobert/das/FeatureThread.java
src/org/biojava/dasobert/das2/Das2Capability.java
src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
src/org/biojava/dasobert/das2/Das2Source.java
src/org/biojava/dasobert/das2/Das2SourceImpl.java
src/org/biojava/dasobert/das2/DasSourceConverter.java
src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
src/org/biojava/dasobert/das2/io/DasSourceReader.java
src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
src/org/biojava/dasobert/dasregistry/Das1Source.java
src/org/biojava/dasobert/dasregistry/Das2Validator.java
src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
src/org/biojava/dasobert/dasregistry/DasSource.java
src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
src/org/biojava/dasobert/eventmodel/FeatureEvent.java
src/org/biojava/dasobert/eventmodel/FeatureListener.java
src/org/biojava/dasobert/eventmodel/ObjectListener.java
src/org/biojava/dasobert/eventmodel/SequenceEvent.java
src/org/biojava/dasobert/eventmodel/SequenceListener.java
src/org/jibble/epsgraphics/EpsDocument.java
src/org/jibble/epsgraphics/EpsException.java
src/org/jibble/epsgraphics/EpsGraphics2D.java
src/uk/ac/ebi/www/Data.java
src/uk/ac/ebi/www/InputParams.java
src/uk/ac/ebi/www/WSFile.java
src/uk/ac/ebi/www/WSWUBlast.java
src/uk/ac/ebi/www/WSWUBlastService.java
src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
src/vamsas/IMsaWS.java
src/vamsas/objects/simple/Alignment.java
src/vamsas/objects/simple/Alignment_Helper.java
src/vamsas/objects/simple/JpredResult.java
src/vamsas/objects/simple/JpredResult_Helper.java
src/vamsas/objects/simple/MsaResult.java
src/vamsas/objects/simple/MsaResult_Helper.java
src/vamsas/objects/simple/Msfalignment.java
src/vamsas/objects/simple/Msfalignment_Helper.java
src/vamsas/objects/simple/Object.java
src/vamsas/objects/simple/Object_Helper.java
src/vamsas/objects/simple/Result.java
src/vamsas/objects/simple/Result_Helper.java
src/vamsas/objects/simple/Secstructpred.java
src/vamsas/objects/simple/Secstructpred_Helper.java
src/vamsas/objects/simple/Sequence.java
src/vamsas/objects/simple/SequenceSet.java
src/vamsas/objects/simple/SequenceSet_Helper.java
src/vamsas/objects/simple/Sequence_Helper.java
src/vamsas/objects/simple/WsJobId.java
src/vamsas/objects/simple/WsJobId_Helper.java