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

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

author	jprocter <Jim Procter>
	Thu, 17 Feb 2011 11:29:57 +0000 (11:29 +0000)
committer	jprocter <Jim Procter>
	Thu, 17 Feb 2011 11:29:57 +0000 (11:29 +0000)
commit	a95b88b05400d7e841f9523d4c4228c678307654
tree	08383266d3a13a5d2f37d7cc19bd4591df5bb2be	tree \| snapshot
parent	d2f229824ea8104aacccc8f72887d464a58e73d4	commit \| diff

fixes JAL-778 - flag to indicate binding between an alignment panel and Jmol view for colouring and optionally for superposition as well.

112 files changed:

schemas/jalview.xsd		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/schemabinding/version2/.castor.cdr		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/AnnotationColours.java		diff \| blob \| history
src/jalview/schemabinding/version2/AnnotationElement.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/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/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/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/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

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