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

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

author	Jim Procter <jprocter@issues.jalview.org>
	Wed, 5 Oct 2016 15:28:14 +0000 (16:28 +0100)
committer	Jim Procter <jprocter@issues.jalview.org>
	Wed, 5 Oct 2016 15:28:14 +0000 (16:28 +0100)
commit	853624fb32058cccc544ae7d13af6ad4b0800b6c
tree	9c82e5423742a61fff0c172fc8e532b6dacffdb0	tree \| snapshot
parent	02d6aa2077a261d41db77a0158f2b4b779a36398	commit \| diff

JAL-2189 source formatting

134 files changed:

src/MCview/AppletPDBCanvas.java		diff \| blob \| history
src/MCview/Atom.java		diff \| blob \| history
src/MCview/PDBCanvas.java		diff \| blob \| history
src/MCview/PDBChain.java		diff \| blob \| history
src/MCview/PDBViewer.java		diff \| blob \| history
src/MCview/PDBfile.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentSorter.java		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/Conservation.java		diff \| blob \| history
src/jalview/analysis/CrossRef.java		diff \| blob \| history
src/jalview/analysis/Dna.java		diff \| blob \| history
src/jalview/analysis/NJTree.java		diff \| blob \| history
src/jalview/analysis/Rna.java		diff \| blob \| history
src/jalview/analysis/SeqsetUtils.java		diff \| blob \| history
src/jalview/analysis/StructureFrequency.java		diff \| blob \| history
src/jalview/api/AlignViewportI.java		diff \| blob \| history
src/jalview/api/SiftsClientI.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/IdPanel.java		diff \| blob \| history
src/jalview/appletgui/ScalePanel.java		diff \| blob \| history
src/jalview/appletgui/SeqCanvas.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/appletgui/SliderPanel.java		diff \| blob \| history
src/jalview/appletgui/TreeCanvas.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/commands/TrimRegionCommand.java		diff \| blob \| history
src/jalview/datamodel/AlignedCodonFrame.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/ColumnSelection.java		diff \| blob \| history
src/jalview/datamodel/HiddenSequences.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblEntry.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblCdna.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblFeatures.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblGene.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblGenomes.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblLookup.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblRestClient.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSeqProxy.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSymbol.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblXref.java		diff \| blob \| history
src/jalview/ext/htsjdk/HtsContigDb.java		diff \| blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/jmol/JmolParser.java		diff \| blob \| history
src/jalview/ext/so/SequenceOntology.java		diff \| blob \| history
src/jalview/fts/api/FTSRestClientI.java		diff \| blob \| history
src/jalview/fts/core/FTSDataColumnPreferences.java		diff \| blob \| history
src/jalview/fts/core/FTSRestClient.java		diff \| blob \| history
src/jalview/fts/core/FTSRestRequest.java		diff \| blob \| history
src/jalview/fts/core/FTSRestResponse.java		diff \| blob \| history
src/jalview/fts/core/GFTSPanel.java		diff \| blob \| history
src/jalview/fts/service/pdb/PDBFTSPanel.java		diff \| blob \| history
src/jalview/fts/service/pdb/PDBFTSRestClient.java		diff \| blob \| history
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java		diff \| blob \| history
src/jalview/fts/service/uniprot/UniprotFTSPanel.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/AnnotationExporter.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationRowFilter.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/Help.java		diff \| blob \| history
src/jalview/gui/IdPanel.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/OptsAndParamsPage.java		diff \| blob \| history
src/jalview/gui/OverviewPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.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/SplitFrame.java		diff \| blob \| history
src/jalview/gui/StructureChooser.java		diff \| blob \| history
src/jalview/gui/TreeCanvas.java		diff \| blob \| history
src/jalview/io/FastaFile.java		diff \| blob \| history
src/jalview/io/FeaturesFile.java		diff \| blob \| history
src/jalview/io/HtmlSvgOutput.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/MSFfile.java		diff \| blob \| history
src/jalview/io/PDBFeatureSettings.java		diff \| blob \| history
src/jalview/io/PfamFile.java		diff \| blob \| history
src/jalview/io/SequenceAnnotationReport.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/StructureFile.java		diff \| blob \| history
src/jalview/io/gff/ExonerateHelper.java		diff \| blob \| history
src/jalview/io/gff/Gff3Helper.java		diff \| blob \| history
src/jalview/io/gff/GffHelperBase.java		diff \| blob \| history
src/jalview/io/gff/GffHelperFactory.java		diff \| blob \| history
src/jalview/io/gff/GffHelperI.java		diff \| blob \| history
src/jalview/io/gff/SequenceOntologyFactory.java		diff \| blob \| history
src/jalview/io/gff/SequenceOntologyLite.java		diff \| blob \| history
src/jalview/io/packed/JalviewDataset.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GStructureChooser.java		diff \| blob \| history
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/ScaleRenderer.java		diff \| blob \| history
src/jalview/schemes/FeatureColour.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/structure/StructureImportSettings.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/util/ImageMaker.java		diff \| blob \| history
src/jalview/util/MapList.java		diff \| blob \| history
src/jalview/util/MappingUtils.java		diff \| blob \| history
src/jalview/util/QuickSort.java		diff \| blob \| history
src/jalview/util/StringUtils.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java		diff \| blob \| history
src/jalview/workers/AlignCalcWorker.java		diff \| blob \| history
src/jalview/workers/AlignmentAnnotationFactory.java		diff \| blob \| history
src/jalview/workers/ColumnCounterWorker.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/DasSequenceFeatureFetcher.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/PfamSeed.java		diff \| blob \| history
src/jalview/ws/dbsources/RfamFull.java		diff \| blob \| history
src/jalview/ws/dbsources/RfamSeed.java		diff \| blob \| history
src/jalview/ws/dbsources/Uniprot.java		diff \| blob \| history
src/jalview/ws/dbsources/Xfam.java		diff \| blob \| history
src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java		diff \| blob \| history
src/jalview/ws/ebi/EBIFetchClient.java		diff \| blob \| history
src/jalview/ws/jws1/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/jws1/SeqSearchWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/seqfetcher/ASequenceFetcher.java		diff \| blob \| history
src/jalview/ws/sifts/MappingOutputPojo.java		diff \| blob \| history
src/jalview/ws/sifts/SiftsClient.java		diff \| blob \| history

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