JAL-1517 source formatting
authorJim Procter <jprocter@dundee.ac.uk>
Fri, 6 Jun 2014 09:04:38 +0000 (10:04 +0100)
committerJim Procter <jprocter@dundee.ac.uk>
Fri, 6 Jun 2014 09:04:38 +0000 (10:04 +0100)
commit7ab5d6b0ba5fec1ea4a4239e79c476d841622485
treeece75b1e32170aa110efa141eb81c7f82b3ae75a
parent1889827c44c51f6353fe8619e5d44b421158af23
JAL-1517 source formatting
219 files changed:
src/MCview/AppletPDBCanvas.java
src/MCview/AppletPDBViewer.java
src/MCview/PDBViewer.java
src/MCview/PDBfile.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Dna.java
src/jalview/analysis/NJTree.java
src/jalview/analysis/PCA.java
src/jalview/analysis/Rna.java
src/jalview/analysis/SecStrConsensus.java
src/jalview/analysis/StructureFrequency.java
src/jalview/analysis/scoremodels/SWScoreModel.java
src/jalview/api/AlignViewControllerGuiI.java
src/jalview/api/AlignViewControllerI.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.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/CutAndPasteTransfer.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/FontChooser.java
src/jalview/appletgui/PCAPanel.java
src/jalview/appletgui/PairwiseAlignPanel.java
src/jalview/appletgui/RedundancyPanel.java
src/jalview/appletgui/RotatableCanvas.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/TreePanel.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/AnnotatedCollectionI.java
src/jalview/datamodel/Annotation.java
src/jalview/datamodel/GraphLine.java
src/jalview/datamodel/SecondaryStructureAnnotation.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceCollectionI.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/PDBFileWithJmol.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/ext/varna/JalviewVarnaBinding.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/AppVarna.java
src/jalview/gui/AppVarnaBinding.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/BlogReader.java
src/jalview/gui/CutAndPasteHtmlTransfer.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/EPSOptions.java
src/jalview/gui/FeatureColourChooser.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/FontChooser.java
src/jalview/gui/JDatabaseTree.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OptsAndParamsPage.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/RestServiceEditorPane.java
src/jalview/gui/RotatableCanvas.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/UserQuestionnaireCheck.java
src/jalview/gui/ViewSelectionMenu.java
src/jalview/gui/WebserviceInfo.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/WsPreferences.java
src/jalview/io/AlignFile.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/FastaFile.java
src/jalview/io/FileLoader.java
src/jalview/io/FileParse.java
src/jalview/io/FormatAdapter.java
src/jalview/io/IdentifyFile.java
src/jalview/io/InputStreamParser.java
src/jalview/io/JPredFile.java
src/jalview/io/JalviewFileView.java
src/jalview/io/NewickFile.java
src/jalview/io/PfamFile.java
src/jalview/io/PileUpfile.java
src/jalview/io/StockholmFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/io/WSWUBlastClient.java
src/jalview/javascript/JsCallBack.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
src/jalview/jbgui/GDasSourceBrowser.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GFontChooser.java
src/jalview/jbgui/GPCAPanel.java
src/jalview/jbgui/GPairwiseAlignPanel.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GRestInputParamEditDialog.java
src/jalview/jbgui/GRestServiceEditorPane.java
src/jalview/jbgui/GSliderPanel.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/jbgui/GTreePanel.java
src/jalview/jbgui/GUserDefinedColours.java
src/jalview/jbgui/GWebserviceInfo.java
src/jalview/jbgui/GWsPreferences.java
src/jalview/math/Matrix.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/AwtRenderPanelI.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/Blosum62ColourScheme.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/schemes/ColourSchemeI.java
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/FollowerColourScheme.java
src/jalview/schemes/RNAHelicesColour.java
src/jalview/schemes/RNAInteractionColourScheme.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/ScoreMatrix.java
src/jalview/schemes/TCoffeeColourScheme.java
src/jalview/schemes/UserColourScheme.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/util/DBRefUtils.java
src/jalview/util/MessageManager.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/PCAModel.java
src/jalview/workers/ConsensusThread.java
src/jalview/workers/StrucConsensusThread.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/EnfinEnvision2OneWay.java
src/jalview/ws/HttpClientUtils.java
src/jalview/ws/JobStateSummary.java
src/jalview/ws/SequenceFetcher.java
src/jalview/ws/dbsources/GeneDbSource.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/dbsources/Pfam.java
src/jalview/ws/dbsources/PfamFull.java
src/jalview/ws/dbsources/das/api/jalviewSourceI.java
src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
src/jalview/ws/ebi/EBIFetchClient.java
src/jalview/ws/jws1/Annotate3D.java
src/jalview/ws/jws2/AAConClient.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/jws2/JabaParamStore.java
src/jalview/ws/jws2/JabaWsServerQuery.java
src/jalview/ws/jws2/JabawsAlignCalcWorker.java
src/jalview/ws/jws2/JabawsCalcWorker.java
src/jalview/ws/jws2/Jws2Client.java
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/jws2/MsaWSThread.java
src/jalview/ws/jws2/RNAalifoldClient.java
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
src/jalview/ws/jws2/dm/JabaOption.java
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
src/jalview/ws/params/ParamManager.java
src/jalview/ws/rest/RestClient.java
src/jalview/ws/rest/RestJob.java
src/jalview/ws/rest/params/SeqGroupIndexVector.java
src/jalview/ws/seqfetcher/ASequenceFetcher.java
src/jalview/ws/seqfetcher/DbSourceProxy.java
test/jalview/analysis/DnaTranslation.java
test/jalview/analysis/TestAlignSeq.java
test/jalview/bin/CommandLineOperations.java
test/jalview/ext/jmol/PDBFileWithJmolTest.java
test/jalview/ext/paradise/TestAnnotate3D.java
test/jalview/gui/JAL1353bugdemo.java
test/jalview/io/AnnotationFileIOTest.java
test/jalview/io/FileIOTester.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/NewickFileTests.java
test/jalview/io/RNAMLfileTest.java
test/jalview/io/StockholmFileTest.java
test/jalview/io/TCoffeeScoreFileTest.java
test/jalview/schemes/DnaCodonTests.java
test/jalview/schemes/ScoreMatrixPrinter.java
test/jalview/ws/PDBSequenceFetcherTest.java
test/jalview/ws/gui/Jws2ParamView.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/rest/ShmmrRSBSService.java
test/jalview/ws/seqfetcher/DbRefFetcherTest.java