JAL-1551 spotlessApply
authorJames Procter <j.procter@dundee.ac.uk>
Fri, 19 May 2023 16:11:26 +0000 (17:11 +0100)
committerJames Procter <j.procter@dundee.ac.uk>
Fri, 19 May 2023 16:11:26 +0000 (17:11 +0100)
commit80b889f0cca49103e1b20ed806755a0719789906
tree36f4d99caeaaa27d8bc610c70e43e7926a12e81c
parent8288438dd58cfc2d1fe18a060afda0d647b85c32
JAL-1551 spotlessApply
139 files changed:
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/AnnotationSorter.java
src/jalview/analysis/AverageDistanceEngine.java
src/jalview/analysis/TreeModel.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/bin/Cache.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/BinaryNode.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/ContactListI.java
src/jalview/datamodel/ContactListImpl.java
src/jalview/datamodel/ContactListProviderI.java
src/jalview/datamodel/ContactMapHolder.java
src/jalview/datamodel/ContactMatrix.java
src/jalview/datamodel/ContactMatrixI.java
src/jalview/datamodel/ContactRange.java
src/jalview/datamodel/GroupSet.java
src/jalview/datamodel/SeqDistanceContactMatrix.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceNode.java
src/jalview/datamodel/annotations/AnnotationRowBuilder.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/Desktop.java
src/jalview/gui/OverviewCanvas.java
src/jalview/gui/QuitHandler.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreePanel.java
src/jalview/gui/WebserviceInfo.java
src/jalview/io/FileParse.java
src/jalview/io/NewickFile.java
src/jalview/io/PContactPredictionFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/vamsas/Tree.java
src/jalview/jbgui/GStructureChooser.java
src/jalview/project/Jalview2XML.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/AnnotationRendererFactory.java
src/jalview/renderer/ContactGeometry.java
src/jalview/renderer/ContactMapRenderer.java
src/jalview/renderer/OverviewResColourFinder.java
src/jalview/renderer/api/AnnotationRowRendererI.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/datamodel/MappableContactMatrixI.java
src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
src/jalview/ws/dbsources/EBIAlfaFold.java
src/jalview/xml/binding/embl/EntrySetType.java
src/jalview/xml/binding/embl/EntryType.java
src/jalview/xml/binding/embl/ObjectFactory.java
src/jalview/xml/binding/embl/ROOT.java
src/jalview/xml/binding/embl/XrefType.java
src/jalview/xml/binding/jalview/AlcodonFrame.java
src/jalview/xml/binding/jalview/Annotation.java
src/jalview/xml/binding/jalview/AnnotationColourScheme.java
src/jalview/xml/binding/jalview/AnnotationElement.java
src/jalview/xml/binding/jalview/DoubleMatrix.java
src/jalview/xml/binding/jalview/DoubleVector.java
src/jalview/xml/binding/jalview/Feature.java
src/jalview/xml/binding/jalview/FeatureMatcher.java
src/jalview/xml/binding/jalview/FeatureMatcherSet.java
src/jalview/xml/binding/jalview/FilterBy.java
src/jalview/xml/binding/jalview/JalviewModel.java
src/jalview/xml/binding/jalview/JalviewUserColours.java
src/jalview/xml/binding/jalview/MapListType.java
src/jalview/xml/binding/jalview/Mapping.java
src/jalview/xml/binding/jalview/MatrixType.java
src/jalview/xml/binding/jalview/NoValueColour.java
src/jalview/xml/binding/jalview/ObjectFactory.java
src/jalview/xml/binding/jalview/PcaDataType.java
src/jalview/xml/binding/jalview/Pdbentry.java
src/jalview/xml/binding/jalview/Property.java
src/jalview/xml/binding/jalview/Sequence.java
src/jalview/xml/binding/jalview/SequenceSet.java
src/jalview/xml/binding/jalview/SequenceType.java
src/jalview/xml/binding/jalview/ThresholdType.java
src/jalview/xml/binding/jalview/VAMSAS.java
src/jalview/xml/binding/jalview/WebServiceParameterSet.java
src/jalview/xml/binding/jalview/package-info.java
src/jalview/xml/binding/uniprot/CitationType.java
src/jalview/xml/binding/uniprot/CofactorType.java
src/jalview/xml/binding/uniprot/CommentType.java
src/jalview/xml/binding/uniprot/ConsortiumType.java
src/jalview/xml/binding/uniprot/DbReferenceType.java
src/jalview/xml/binding/uniprot/Entry.java
src/jalview/xml/binding/uniprot/EventType.java
src/jalview/xml/binding/uniprot/EvidenceType.java
src/jalview/xml/binding/uniprot/EvidencedStringType.java
src/jalview/xml/binding/uniprot/FeatureType.java
src/jalview/xml/binding/uniprot/GeneLocationType.java
src/jalview/xml/binding/uniprot/GeneNameType.java
src/jalview/xml/binding/uniprot/GeneType.java
src/jalview/xml/binding/uniprot/ImportedFromType.java
src/jalview/xml/binding/uniprot/InteractantType.java
src/jalview/xml/binding/uniprot/IsoformType.java
src/jalview/xml/binding/uniprot/KeywordType.java
src/jalview/xml/binding/uniprot/LocationType.java
src/jalview/xml/binding/uniprot/MoleculeType.java
src/jalview/xml/binding/uniprot/NameListType.java
src/jalview/xml/binding/uniprot/ObjectFactory.java
src/jalview/xml/binding/uniprot/OrganismNameType.java
src/jalview/xml/binding/uniprot/OrganismType.java
src/jalview/xml/binding/uniprot/PersonType.java
src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
src/jalview/xml/binding/uniprot/PositionType.java
src/jalview/xml/binding/uniprot/PropertyType.java
src/jalview/xml/binding/uniprot/ProteinExistenceType.java
src/jalview/xml/binding/uniprot/ProteinType.java
src/jalview/xml/binding/uniprot/ReactionType.java
src/jalview/xml/binding/uniprot/ReferenceType.java
src/jalview/xml/binding/uniprot/SequenceType.java
src/jalview/xml/binding/uniprot/SourceDataType.java
src/jalview/xml/binding/uniprot/SourceType.java
src/jalview/xml/binding/uniprot/StatusType.java
src/jalview/xml/binding/uniprot/SubcellularLocationType.java
src/jalview/xml/binding/uniprot/Uniprot.java
src/jalview/xml/binding/uniprot/package-info.java
src/mc_view/PDBChain.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/AverageDistanceEngineTest.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/datamodel/ContactRangeTest.java
test/jalview/datamodel/PAEContactMatrixTest.java
test/jalview/gui/AlignmentPanelTest.java
test/jalview/gui/SeqPanelTest.java
test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
test/jalview/project/Jalview2xmlTests.java
test/jalview/renderer/OverviewRendererTest.java
test/jalview/renderer/OverviewResColourFinderTest.java
test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java