source.jalview.org Git - jalview.git/commit

git://source.jalview.org / jalview.git / commit

author	Jim Procter <jprocter@dundee.ac.uk>
	Fri, 6 Jun 2014 09:04:38 +0000 (10:04 +0100)
committer	Jim Procter <jprocter@dundee.ac.uk>
	Fri, 6 Jun 2014 09:04:38 +0000 (10:04 +0100)
commit	7ab5d6b0ba5fec1ea4a4239e79c476d841622485
tree	ece75b1e32170aa110efa141eb81c7f82b3ae75a	tree \| snapshot
parent	1889827c44c51f6353fe8619e5d44b421158af23	commit \| diff

JAL-1517 source formatting

219 files changed:

src/MCview/AppletPDBCanvas.java		diff \| blob \| history
src/MCview/AppletPDBViewer.java		diff \| blob \| history
src/MCview/PDBViewer.java		diff \| blob \| history
src/MCview/PDBfile.java		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/Dna.java		diff \| blob \| history
src/jalview/analysis/NJTree.java		diff \| blob \| history
src/jalview/analysis/PCA.java		diff \| blob \| history
src/jalview/analysis/Rna.java		diff \| blob \| history
src/jalview/analysis/SecStrConsensus.java		diff \| blob \| history
src/jalview/analysis/StructureFrequency.java		diff \| blob \| history
src/jalview/analysis/scoremodels/SWScoreModel.java		diff \| blob \| history
src/jalview/api/AlignViewControllerGuiI.java		diff \| blob \| history
src/jalview/api/AlignViewControllerI.java		diff \| blob \| history
src/jalview/api/AlignViewportI.java		diff \| blob \| history
src/jalview/appletgui/APopupMenu.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/appletgui/AnnotationLabels.java		diff \| blob \| history
src/jalview/appletgui/AnnotationPanel.java		diff \| blob \| history
src/jalview/appletgui/AppletJmol.java		diff \| blob \| history
src/jalview/appletgui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/appletgui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/Finder.java		diff \| blob \| history
src/jalview/appletgui/FontChooser.java		diff \| blob \| history
src/jalview/appletgui/PCAPanel.java		diff \| blob \| history
src/jalview/appletgui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/appletgui/RedundancyPanel.java		diff \| blob \| history
src/jalview/appletgui/RotatableCanvas.java		diff \| blob \| history
src/jalview/appletgui/ScalePanel.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/appletgui/SliderPanel.java		diff \| blob \| history
src/jalview/appletgui/TreePanel.java		diff \| blob \| history
src/jalview/appletgui/UserDefinedColours.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/controller/AlignViewController.java		diff \| blob \| history
src/jalview/datamodel/AlignedCodonFrame.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AlignmentI.java		diff \| blob \| history
src/jalview/datamodel/AlignmentView.java		diff \| blob \| history
src/jalview/datamodel/AnnotatedCollectionI.java		diff \| blob \| history
src/jalview/datamodel/Annotation.java		diff \| blob \| history
src/jalview/datamodel/GraphLine.java		diff \| blob \| history
src/jalview/datamodel/SecondaryStructureAnnotation.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceCollectionI.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/jmol/PDBFileWithJmol.java		diff \| blob \| history
src/jalview/ext/paradise/Annotate3D.java		diff \| blob \| history
src/jalview/ext/varna/JalviewVarnaBinding.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AlignmentPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationExporter.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/AppVarna.java		diff \| blob \| history
src/jalview/gui/AppVarnaBinding.java		diff \| blob \| history
src/jalview/gui/AssociatePdbFileWithSeq.java		diff \| blob \| history
src/jalview/gui/BlogReader.java		diff \| blob \| history
src/jalview/gui/CutAndPasteHtmlTransfer.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/DasSourceBrowser.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/EPSOptions.java		diff \| blob \| history
src/jalview/gui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/gui/FeatureRenderer.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/Finder.java		diff \| blob \| history
src/jalview/gui/FontChooser.java		diff \| blob \| history
src/jalview/gui/JDatabaseTree.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/Jalview2XML_V1.java		diff \| blob \| history
src/jalview/gui/JvSwingUtils.java		diff \| blob \| history
src/jalview/gui/OptsAndParamsPage.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PaintRefresher.java		diff \| blob \| history
src/jalview/gui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/RedundancyPanel.java		diff \| blob \| history
src/jalview/gui/RestServiceEditorPane.java		diff \| blob \| history
src/jalview/gui/RotatableCanvas.java		diff \| blob \| history
src/jalview/gui/ScalePanel.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SliderPanel.java		diff \| blob \| history
src/jalview/gui/TreeCanvas.java		diff \| blob \| history
src/jalview/gui/TreePanel.java		diff \| blob \| history
src/jalview/gui/UserDefinedColours.java		diff \| blob \| history
src/jalview/gui/UserQuestionnaireCheck.java		diff \| blob \| history
src/jalview/gui/ViewSelectionMenu.java		diff \| blob \| history
src/jalview/gui/WebserviceInfo.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/gui/WsPreferences.java		diff \| blob \| history
src/jalview/io/AlignFile.java		diff \| blob \| history
src/jalview/io/AnnotationFile.java		diff \| blob \| history
src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
src/jalview/io/FastaFile.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/FileParse.java		diff \| blob \| history
src/jalview/io/FormatAdapter.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/InputStreamParser.java		diff \| blob \| history
src/jalview/io/JPredFile.java		diff \| blob \| history
src/jalview/io/JalviewFileView.java		diff \| blob \| history
src/jalview/io/NewickFile.java		diff \| blob \| history
src/jalview/io/PfamFile.java		diff \| blob \| history
src/jalview/io/PileUpfile.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/TCoffeeScoreFile.java		diff \| blob \| history
src/jalview/io/WSWUBlastClient.java		diff \| blob \| history
src/jalview/javascript/JsCallBack.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java		diff \| blob \| history
src/jalview/jbgui/GDasSourceBrowser.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GFontChooser.java		diff \| blob \| history
src/jalview/jbgui/GPCAPanel.java		diff \| blob \| history
src/jalview/jbgui/GPairwiseAlignPanel.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GRestInputParamEditDialog.java		diff \| blob \| history
src/jalview/jbgui/GRestServiceEditorPane.java		diff \| blob \| history
src/jalview/jbgui/GSliderPanel.java		diff \| blob \| history
src/jalview/jbgui/GStructureViewer.java		diff \| blob \| history
src/jalview/jbgui/GTreePanel.java		diff \| blob \| history
src/jalview/jbgui/GUserDefinedColours.java		diff \| blob \| history
src/jalview/jbgui/GWebserviceInfo.java		diff \| blob \| history
src/jalview/jbgui/GWsPreferences.java		diff \| blob \| history
src/jalview/math/Matrix.java		diff \| blob \| history
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/AwtRenderPanelI.java		diff \| blob \| history
src/jalview/schemes/AnnotationColourGradient.java		diff \| blob \| history
src/jalview/schemes/Blosum62ColourScheme.java		diff \| blob \| history
src/jalview/schemes/ClustalxColourScheme.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeI.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeProperty.java		diff \| blob \| history
src/jalview/schemes/FollowerColourScheme.java		diff \| blob \| history
src/jalview/schemes/RNAHelicesColour.java		diff \| blob \| history
src/jalview/schemes/RNAInteractionColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/schemes/ScoreMatrix.java		diff \| blob \| history
src/jalview/schemes/TCoffeeColourScheme.java		diff \| blob \| history
src/jalview/schemes/UserColourScheme.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/util/DBRefUtils.java		diff \| blob \| history
src/jalview/util/MessageManager.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/PCAModel.java		diff \| blob \| history
src/jalview/workers/ConsensusThread.java		diff \| blob \| history
src/jalview/workers/StrucConsensusThread.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/EnfinEnvision2OneWay.java		diff \| blob \| history
src/jalview/ws/HttpClientUtils.java		diff \| blob \| history
src/jalview/ws/JobStateSummary.java		diff \| blob \| history
src/jalview/ws/SequenceFetcher.java		diff \| blob \| history
src/jalview/ws/dbsources/GeneDbSource.java		diff \| blob \| history
src/jalview/ws/dbsources/Pdb.java		diff \| blob \| history
src/jalview/ws/dbsources/Pfam.java		diff \| blob \| history
src/jalview/ws/dbsources/PfamFull.java		diff \| blob \| history
src/jalview/ws/dbsources/das/api/jalviewSourceI.java		diff \| blob \| history
src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java		diff \| blob \| history
src/jalview/ws/dbsources/das/datamodel/JalviewSource.java		diff \| blob \| history
src/jalview/ws/ebi/EBIFetchClient.java		diff \| blob \| history
src/jalview/ws/jws1/Annotate3D.java		diff \| blob \| history
src/jalview/ws/jws2/AAConClient.java		diff \| blob \| history
src/jalview/ws/jws2/AADisorderClient.java		diff \| blob \| history
src/jalview/ws/jws2/JabaParamStore.java		diff \| blob \| history
src/jalview/ws/jws2/JabaWsServerQuery.java		diff \| blob \| history
src/jalview/ws/jws2/JabawsAlignCalcWorker.java		diff \| blob \| history
src/jalview/ws/jws2/JabawsCalcWorker.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Client.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Discoverer.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/jws2/RNAalifoldClient.java		diff \| blob \| history
src/jalview/ws/jws2/SequenceAnnotationWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/dm/JabaOption.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2Instance.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java		diff \| blob \| history
src/jalview/ws/params/ParamManager.java		diff \| blob \| history
src/jalview/ws/rest/RestClient.java		diff \| blob \| history
src/jalview/ws/rest/RestJob.java		diff \| blob \| history
src/jalview/ws/rest/params/SeqGroupIndexVector.java		diff \| blob \| history
src/jalview/ws/seqfetcher/ASequenceFetcher.java		diff \| blob \| history
src/jalview/ws/seqfetcher/DbSourceProxy.java		diff \| blob \| history
test/jalview/analysis/DnaTranslation.java		diff \| blob \| history
test/jalview/analysis/TestAlignSeq.java		diff \| blob \| history
test/jalview/bin/CommandLineOperations.java		diff \| blob \| history
test/jalview/ext/jmol/PDBFileWithJmolTest.java		diff \| blob \| history
test/jalview/ext/paradise/TestAnnotate3D.java		diff \| blob \| history
test/jalview/gui/JAL1353bugdemo.java		diff \| blob \| history
test/jalview/io/AnnotationFileIOTest.java		diff \| blob \| history
test/jalview/io/FileIOTester.java		diff \| blob \| history
test/jalview/io/Jalview2xmlTests.java		diff \| blob \| history
test/jalview/io/NewickFileTests.java		diff \| blob \| history
test/jalview/io/RNAMLfileTest.java		diff \| blob \| history
test/jalview/io/StockholmFileTest.java		diff \| blob \| history
test/jalview/io/TCoffeeScoreFileTest.java		diff \| blob \| history
test/jalview/schemes/DnaCodonTests.java		diff \| blob \| history
test/jalview/schemes/ScoreMatrixPrinter.java		diff \| blob \| history
test/jalview/ws/PDBSequenceFetcherTest.java		diff \| blob \| history
test/jalview/ws/gui/Jws2ParamView.java		diff \| blob \| history
test/jalview/ws/jabaws/DisorderAnnotExportImport.java		diff \| blob \| history
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java		diff \| blob \| history
test/jalview/ws/jabaws/RNAStructExportImport.java		diff \| blob \| history
test/jalview/ws/rest/ShmmrRSBSService.java		diff \| blob \| history
test/jalview/ws/seqfetcher/DbRefFetcherTest.java		diff \| blob \| history

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