apply jalview code style
authorjprocter <Jim Procter>
Thu, 23 Sep 2010 07:06:55 +0000 (07:06 +0000)
committerjprocter <Jim Procter>
Thu, 23 Sep 2010 07:06:55 +0000 (07:06 +0000)
commit8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb
tree42dd9d8ea258853b75844d34d9f789571ce8d6f6
parent153dd62dc91da13ae732600e6ea55ddbe15eab39
apply jalview code style
185 files changed:
src/MCview/AppletPDBCanvas.java
src/MCview/PDBCanvas.java
src/MCview/PDBChain.java
src/MCview/PDBViewer.java
src/ext/vamsas/JpredSoapBindingStub.java
src/ext/vamsas/MuscleWSSoapBindingStub.java
src/ext/vamsas/RegistryServiceSoapBindingStub.java
src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/analysis/NJTree.java
src/jalview/analysis/PCA.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/api/FeatureRenderer.java
src/jalview/api/SequenceStructureBinding.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/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/ExtJmol.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/RotatableCanvas.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.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/EditCommand.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/SeqCigar.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/xdb/embl/EmblEntry.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/AppJmol.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/Console.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/EditNameDialog.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/FontChooser.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OOMWarning.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/RotatableCanvas.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceRenderer.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/TextColourChooser.java
src/jalview/gui/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/UserQuestionnaireCheck.java
src/jalview/gui/VamsasApplication.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/WsPreferences.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/ClustalFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FormatAdapter.java
src/jalview/io/HTMLOutput.java
src/jalview/io/JPredFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/JnetAnnotationMaker.java
src/jalview/io/NewickFile.java
src/jalview/io/PIRFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/WSWUBlastClient.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/io/vamsas/DatastoreItem.java
src/jalview/io/vamsas/Dbref.java
src/jalview/io/vamsas/Sequencefeature.java
src/jalview/io/vamsas/Sequencemapping.java
src/jalview/io/vamsas/Tree.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GPCAPanel.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/jbgui/GUserDefinedColours.java
src/jalview/jbgui/GWsPreferences.java
src/jalview/schemabinding/version2/WebServiceParameterSet.java
src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/util/AWTConsole.java
src/jalview/util/DBRefUtils.java
src/jalview/util/Format.java
src/jalview/util/ImageMaker.java
src/jalview/util/TableSorter.java
src/jalview/ws/AWSThread.java
src/jalview/ws/AWsJob.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/DasSequenceFeatureFetcher.java
src/jalview/ws/EnfinEnvision2OneWay.java
src/jalview/ws/JobStateSummary.java
src/jalview/ws/WSClient.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/dbsources/GeneDbSource.java
src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
src/jalview/ws/ebi/EBIFetchClient.java
src/jalview/ws/jws1/Discoverer.java
src/jalview/ws/jws1/JPredClient.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws1/JWS1Thread.java
src/jalview/ws/jws1/MsaWSClient.java
src/jalview/ws/jws1/MsaWSThread.java
src/jalview/ws/jws1/SeqSearchWSClient.java
src/jalview/ws/jws1/SeqSearchWSThread.java
src/jalview/ws/jws1/WS1Client.java
src/jalview/ws/jws1/WSJob.java
src/jalview/ws/jws2/JWs2Job.java
src/jalview/ws/jws2/JabaPreset.java
src/jalview/ws/jws2/Jws2Client.java
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/jws2/ParameterUtils.java
src/jalview/ws/jws2/dm/JabaOption.java
src/jalview/ws/jws2/dm/JabaParameter.java
src/jalview/ws/jws2/dm/JabaValueConstrain.java
src/jalview/ws/params/ArgumentI.java
src/jalview/ws/params/OptionI.java
src/jalview/ws/params/ParamDatastoreI.java
src/jalview/ws/params/ParamManager.java
src/jalview/ws/params/ParameterI.java
src/jalview/ws/params/ValueConstrainI.java
src/jalview/ws/params/WsParamSetI.java
src/uk/ac/ebi/picr/model/UPEntry.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java