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

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

author	kjvdheide <kjvanderheide@dundee.ac.uk>
	Tue, 3 Oct 2017 12:17:52 +0000 (13:17 +0100)
committer	kjvdheide <kjvanderheide@dundee.ac.uk>
	Tue, 3 Oct 2017 12:17:52 +0000 (13:17 +0100)
commit	667fe9aec1360b33800b3d49ec53401cc8fe0e5d
tree	258017ebff6c32d3bfcdab0fdbb4d0e4188601ba	tree \| snapshot
parent	8dbf6e85ebb3dbcd84635f194457cd4dc65010cf	commit \| diff

Kept copyright test to just the new classes

234 files changed:

src/com/github/reinert/jjschema/Attributes.java		diff \| blob \| history
src/com/stevesoft/pat/AmpersandRule.java		diff \| blob \| history
src/com/stevesoft/pat/Any.java		diff \| blob \| history
src/com/stevesoft/pat/BackG.java		diff \| blob \| history
src/com/stevesoft/pat/BackMatch.java		diff \| blob \| history
src/com/stevesoft/pat/BackRefRule.java		diff \| blob \| history
src/com/stevesoft/pat/Backup.java		diff \| blob \| history
src/com/stevesoft/pat/BasicStringBufferLike.java		diff \| blob \| history
src/com/stevesoft/pat/Bits.java		diff \| blob \| history
src/com/stevesoft/pat/Boundary.java		diff \| blob \| history
src/com/stevesoft/pat/Bracket.java		diff \| blob \| history
src/com/stevesoft/pat/CaseMgr.java		diff \| blob \| history
src/com/stevesoft/pat/ChangeRule.java		diff \| blob \| history
src/com/stevesoft/pat/CodeRule.java		diff \| blob \| history
src/com/stevesoft/pat/Ctrl.java		diff \| blob \| history
src/com/stevesoft/pat/Custom.java		diff \| blob \| history
src/com/stevesoft/pat/CustomEndpoint.java		diff \| blob \| history
src/com/stevesoft/pat/DirFileRegex.java		diff \| blob \| history
src/com/stevesoft/pat/DotMulti.java		diff \| blob \| history
src/com/stevesoft/pat/End.java		diff \| blob \| history
src/com/stevesoft/pat/FastBracket.java		diff \| blob \| history
src/com/stevesoft/pat/FastMulti.java		diff \| blob \| history
src/com/stevesoft/pat/FileRegex.java		diff \| blob \| history
src/com/stevesoft/pat/Group.java		diff \| blob \| history
src/com/stevesoft/pat/LeftRule.java		diff \| blob \| history
src/com/stevesoft/pat/Multi.java		diff \| blob \| history
src/com/stevesoft/pat/MultiMin.java		diff \| blob \| history
src/com/stevesoft/pat/Multi_stage2.java		diff \| blob \| history
src/com/stevesoft/pat/NoPattern.java		diff \| blob \| history
src/com/stevesoft/pat/NonDirFileRegex.java		diff \| blob \| history
src/com/stevesoft/pat/NotImplementedError.java		diff \| blob \| history
src/com/stevesoft/pat/NullPattern.java		diff \| blob \| history
src/com/stevesoft/pat/NullRule.java		diff \| blob \| history
src/com/stevesoft/pat/Or.java		diff \| blob \| history
src/com/stevesoft/pat/OrMark.java		diff \| blob \| history
src/com/stevesoft/pat/PartialBuffer.java		diff \| blob \| history
src/com/stevesoft/pat/Pattern.java		diff \| blob \| history
src/com/stevesoft/pat/PatternSub.java		diff \| blob \| history
src/com/stevesoft/pat/PopRule.java		diff \| blob \| history
src/com/stevesoft/pat/Prop.java		diff \| blob \| history
src/com/stevesoft/pat/Pthings.java		diff \| blob \| history
src/com/stevesoft/pat/PushRule.java		diff \| blob \| history
src/com/stevesoft/pat/RBuffer.java		diff \| blob \| history
src/com/stevesoft/pat/Range.java		diff \| blob \| history
src/com/stevesoft/pat/RegOpt.java		diff \| blob \| history
src/com/stevesoft/pat/RegRes.java		diff \| blob \| history
src/com/stevesoft/pat/RegSyntax.java		diff \| blob \| history
src/com/stevesoft/pat/RegSyntaxError.java		diff \| blob \| history
src/com/stevesoft/pat/Regex.java		diff \| blob \| history
src/com/stevesoft/pat/RegexReader.java		diff \| blob \| history
src/com/stevesoft/pat/RegexTokenizer.java		diff \| blob \| history
src/com/stevesoft/pat/RegexWriter.java		diff \| blob \| history
src/com/stevesoft/pat/ReplaceRule.java		diff \| blob \| history
src/com/stevesoft/pat/Replacer.java		diff \| blob \| history
src/com/stevesoft/pat/RightRule.java		diff \| blob \| history
src/com/stevesoft/pat/Rthings.java		diff \| blob \| history
src/com/stevesoft/pat/RuleHolder.java		diff \| blob \| history
src/com/stevesoft/pat/Skip.java		diff \| blob \| history
src/com/stevesoft/pat/Skip2.java		diff \| blob \| history
src/com/stevesoft/pat/SkipBMH.java		diff \| blob \| history
src/com/stevesoft/pat/Skipped.java		diff \| blob \| history
src/com/stevesoft/pat/SpecialRule.java		diff \| blob \| history
src/com/stevesoft/pat/Start.java		diff \| blob \| history
src/com/stevesoft/pat/StrPos.java		diff \| blob \| history
src/com/stevesoft/pat/StringBufferLike.java		diff \| blob \| history
src/com/stevesoft/pat/StringLike.java		diff \| blob \| history
src/com/stevesoft/pat/StringRule.java		diff \| blob \| history
src/com/stevesoft/pat/SubMark.java		diff \| blob \| history
src/com/stevesoft/pat/TransPat.java		diff \| blob \| history
src/com/stevesoft/pat/Transformer.java		diff \| blob \| history
src/com/stevesoft/pat/UniValidator.java		diff \| blob \| history
src/com/stevesoft/pat/Validator.java		diff \| blob \| history
src/com/stevesoft/pat/WantMoreTextReplaceRule.java		diff \| blob \| history
src/com/stevesoft/pat/lookAhead.java		diff \| blob \| history
src/com/stevesoft/pat/oneChar.java		diff \| blob \| history
src/com/stevesoft/pat/parsePerl.java		diff \| blob \| history
src/com/stevesoft/pat/patInf.java		diff \| blob \| history
src/com/stevesoft/pat/patInt.java		diff \| blob \| history
src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java		diff \| blob \| history
src/com/stevesoft/pat/wrap/CharArrayWrap.java		diff \| blob \| history
src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java		diff \| blob \| history
src/com/stevesoft/pat/wrap/StringBufferWrap.java		diff \| blob \| history
src/com/stevesoft/pat/wrap/StringWrap.java		diff \| blob \| history
src/com/stevesoft/pat/wrap/WriterWrap.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java		diff \| blob \| history
src/jalview/binding/Alignment.java		diff \| blob \| history
src/jalview/binding/Annotation.java		diff \| blob \| history
src/jalview/binding/AnnotationElement.java		diff \| blob \| history
src/jalview/binding/Colour.java		diff \| blob \| history
src/jalview/binding/Feature.java		diff \| blob \| history
src/jalview/binding/FeatureSettings.java		diff \| blob \| history
src/jalview/binding/Features.java		diff \| blob \| history
src/jalview/binding/JGroup.java		diff \| blob \| history
src/jalview/binding/JSeq.java		diff \| blob \| history
src/jalview/binding/JalviewModel.java		diff \| blob \| history
src/jalview/binding/JalviewModelSequence.java		diff \| blob \| history
src/jalview/binding/JalviewUserColours.java		diff \| blob \| history
src/jalview/binding/Pdbentry.java		diff \| blob \| history
src/jalview/binding/PdbentryItem.java		diff \| blob \| history
src/jalview/binding/Pdbids.java		diff \| blob \| history
src/jalview/binding/Property.java		diff \| blob \| history
src/jalview/binding/Sequence.java		diff \| blob \| history
src/jalview/binding/SequenceSet.java		diff \| blob \| history
src/jalview/binding/SequenceType.java		diff \| blob \| history
src/jalview/binding/Setting.java		diff \| blob \| history
src/jalview/binding/Tree.java		diff \| blob \| history
src/jalview/binding/UserColourScheme.java		diff \| blob \| history
src/jalview/binding/UserColours.java		diff \| blob \| history
src/jalview/binding/VAMSAS.java		diff \| blob \| history
src/jalview/binding/VamsasModel.java		diff \| blob \| history
src/jalview/binding/Viewport.java		diff \| blob \| history
src/jalview/datamodel/ContiguousI.java		diff \| blob \| history
src/jalview/datamodel/Range.java		diff \| blob \| history
src/jalview/datamodel/SequenceCursor.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureLocationI.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureStore.java		diff \| blob \| history
src/jalview/datamodel/features/NCList.java		diff \| blob \| history
src/jalview/datamodel/features/NCNode.java		diff \| blob \| history
src/jalview/datamodel/features/RangeComparator.java		diff \| blob \| history
src/jalview/datamodel/features/SequenceFeatures.java		diff \| blob \| history
src/jalview/datamodel/features/SequenceFeaturesI.java		diff \| blob \| history
src/jalview/datamodel/xdb/uniprot/UniprotFeature.java		diff \| blob \| history
src/jalview/ext/android/ContainerHelpers.java		diff \| blob \| history
src/jalview/ext/android/SparseDoubleArray.java		diff \| blob \| history
src/jalview/ext/android/SparseIntArray.java		diff \| blob \| history
src/jalview/ext/android/SparseShortArray.java		diff \| blob \| history
src/jalview/jbgui/GStructureChooser.java		diff \| blob \| history
src/jalview/schemabinding/version2/AlcodMap.java		diff \| blob \| history
src/jalview/schemabinding/version2/Alcodon.java		diff \| blob \| history
src/jalview/schemabinding/version2/AlcodonFrame.java		diff \| blob \| history
src/jalview/schemabinding/version2/Annotation.java		diff \| blob \| history
src/jalview/schemabinding/version2/AnnotationColourScheme.java		diff \| blob \| history
src/jalview/schemabinding/version2/AnnotationColours.java		diff \| blob \| history
src/jalview/schemabinding/version2/AnnotationElement.java		diff \| blob \| history
src/jalview/schemabinding/version2/CalcIdParam.java		diff \| blob \| history
src/jalview/schemabinding/version2/Colour.java		diff \| blob \| history
src/jalview/schemabinding/version2/DBRef.java		diff \| blob \| history
src/jalview/schemabinding/version2/Feature.java		diff \| blob \| history
src/jalview/schemabinding/version2/FeatureSettings.java		diff \| blob \| history
src/jalview/schemabinding/version2/Features.java		diff \| blob \| history
src/jalview/schemabinding/version2/Group.java		diff \| blob \| history
src/jalview/schemabinding/version2/HiddenColumns.java		diff \| blob \| history
src/jalview/schemabinding/version2/JGroup.java		diff \| blob \| history
src/jalview/schemabinding/version2/JSeq.java		diff \| blob \| history
src/jalview/schemabinding/version2/JalviewModel.java		diff \| blob \| history
src/jalview/schemabinding/version2/JalviewModelSequence.java		diff \| blob \| history
src/jalview/schemabinding/version2/JalviewUserColours.java		diff \| blob \| history
src/jalview/schemabinding/version2/MapListFrom.java		diff \| blob \| history
src/jalview/schemabinding/version2/MapListTo.java		diff \| blob \| history
src/jalview/schemabinding/version2/MapListType.java		diff \| blob \| history
src/jalview/schemabinding/version2/Mapping.java		diff \| blob \| history
src/jalview/schemabinding/version2/MappingChoice.java		diff \| blob \| history
src/jalview/schemabinding/version2/OtherData.java		diff \| blob \| history
src/jalview/schemabinding/version2/Pdbentry.java		diff \| blob \| history
src/jalview/schemabinding/version2/PdbentryItem.java		diff \| blob \| history
src/jalview/schemabinding/version2/Pdbids.java		diff \| blob \| history
src/jalview/schemabinding/version2/Property.java		diff \| blob \| history
src/jalview/schemabinding/version2/RnaViewer.java		diff \| blob \| history
src/jalview/schemabinding/version2/SecondaryStructure.java		diff \| blob \| history
src/jalview/schemabinding/version2/Sequence.java		diff \| blob \| history
src/jalview/schemabinding/version2/SequenceSet.java		diff \| blob \| history
src/jalview/schemabinding/version2/SequenceSetProperties.java		diff \| blob \| history
src/jalview/schemabinding/version2/SequenceType.java		diff \| blob \| history
src/jalview/schemabinding/version2/Setting.java		diff \| blob \| history
src/jalview/schemabinding/version2/StructureState.java		diff \| blob \| history
src/jalview/schemabinding/version2/ThresholdLine.java		diff \| blob \| history
src/jalview/schemabinding/version2/Tree.java		diff \| blob \| history
src/jalview/schemabinding/version2/UserColourScheme.java		diff \| blob \| history
src/jalview/schemabinding/version2/UserColours.java		diff \| blob \| history
src/jalview/schemabinding/version2/VAMSAS.java		diff \| blob \| history
src/jalview/schemabinding/version2/VamsasModel.java		diff \| blob \| history
src/jalview/schemabinding/version2/Viewport.java		diff \| blob \| history
src/jalview/schemabinding/version2/WebServiceParameterSet.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java		diff \| blob \| history
src/jalview/util/IntRangeComparator.java		diff \| blob \| history
src/jalview/xml/binding/sifts/Alignment.java		diff \| blob \| history
src/jalview/xml/binding/sifts/EntityType.java		diff \| blob \| history
src/jalview/xml/binding/sifts/Entry.java		diff \| blob \| history
src/jalview/xml/binding/sifts/ObjectFactory.java		diff \| blob \| history
src/jalview/xml/binding/sifts/package-info.java		diff \| blob \| history

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