Directory src/jalview/schemabinding/version2/

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jprocter 2010-09-06 17:37

new XML representation for web services parameters

439 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), WebServiceParameterSet.java (new 439)

jprocter 2010-04-30 10:29

jalview 2.5 release banner

618 lines of code changed in:

• src/jalview/schemabinding/version2: AlcodMap.java (changed), Alcodon.java (changed), AlcodonFrame.java (changed), Annotation.java (changed), AnnotationColours.java (changed), AnnotationElement.java (changed), Colour.java (changed), DBRef.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), Group.java (changed), HiddenColumns.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), MapListFrom.java (changed), MapListTo.java (changed), MapListType.java (changed), Mapping.java (changed), MappingChoice.java (changed), OtherData.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceSetProperties.java (+174 -162), SequenceType.java (changed), Setting.java (changed), StructureState.java (+444 -440), ThresholdLine.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2010-04-14 15:35

profile visualizations are now logos

0 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), JGroup.java (changed), SequenceSetProperties.java (changed), StructureState.java (changed), Viewport.java (changed)

jprocter 2010-04-05 16:34

extend XML model for graduated feature colours, group associated manual/auto annotation, consensus profile/histograms, annotation label formatting, viewport highlight follow/select message receive settings

0 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), Annotation.java (changed), JGroup.java (changed), SequenceSetProperties.java (changed), Setting.java (changed), StructureState.java (changed), Viewport.java (changed)

jprocter 2010-04-02 15:41

extended Colour element with additional optional attributes for graduated colour

4 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), AlcodMap.java (changed), Alcodon.java (changed), AlcodonFrame.java (changed), Annotation.java (changed), AnnotationColours.java (changed), AnnotationElement.java (changed), Colour.java (changed), DBRef.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), Group.java (changed), HiddenColumns.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), MapListFrom.java (changed), MapListTo.java (changed), MapListType.java (changed), Mapping.java (changed), MappingChoice.java (changed), OtherData.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceSetProperties.java (+2 -2), SequenceType.java (changed), Setting.java (changed), StructureState.java (+2 -2), ThresholdLine.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2009-06-08 11:46

apply gpl development license

34 lines of code changed in:

• src/jalview/schemabinding/version2: AlcodMap.java (changed), Alcodon.java (changed), AlcodonFrame.java (changed), Annotation.java (changed), AnnotationColours.java (changed), AnnotationElement.java (changed), Colour.java (changed), DBRef.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), Group.java (changed), HiddenColumns.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), MapListFrom.java (changed), MapListTo.java (changed), MapListType.java (changed), Mapping.java (changed), MappingChoice.java (changed), OtherData.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceSetProperties.java (+17 -6), SequenceType.java (changed), Setting.java (changed), StructureState.java (+17 -6), ThresholdLine.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2009-03-31 17:38

prototype for store/restore of feature colour gradient settings

0 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), SequenceSetProperties.java (changed), Setting.java (changed), StructureState.java (changed)

jprocter 2009-02-06 14:51

added showUnconserved property to group and view attributes

0 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), JGroup.java (changed), SequenceSetProperties.java (changed), StructureState.java (changed), Viewport.java (changed)

jprocter 2008-12-15 10:31

structureState element to structure view Id is a many to one relationship - so viewId cannot be an XML element ID.

28 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), StructureState.java (+28 -3)

jprocter 2008-11-12 11:18

jalview XML schema update for 2.4.1 (or 2.5?) introducing IDs for views and treepanels and proper reconstruction of dataset/Alignment relationships

563 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), AlcodMap.java (changed), Alcodon.java (changed), AlcodonFrame.java (changed), Annotation.java (changed), AnnotationColours.java (changed), AnnotationElement.java (changed), Colour.java (changed), DBRef.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), Group.java (changed), HiddenColumns.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), MapListFrom.java (changed), MapListTo.java (changed), MapListType.java (changed), Mapping.java (changed), MappingChoice.java (changed), OtherData.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceSetProperties.java (+155 -183), SequenceType.java (changed), Setting.java (changed), StructureState.java (+408 -413), ThresholdLine.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2008-09-04 14:33

merge from 2_4_Release branch

596 lines of code changed in:

• src/jalview/schemabinding/version2: AlcodMap.java (changed), Alcodon.java (changed), AlcodonFrame.java (changed), Annotation.java (changed), AnnotationColours.java (changed), AnnotationElement.java (changed), Colour.java (changed), DBRef.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), Group.java (changed), HiddenColumns.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), MapListFrom.java (changed), MapListTo.java (changed), MapListType.java (changed), Mapping.java (changed), MappingChoice.java (changed), OtherData.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceSetProperties.java (+183 -155), SequenceType.java (changed), Setting.java (changed), StructureState.java (+413 -383), ThresholdLine.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2008-02-24 20:08

sequenceId is a string, not an integer - allows generation of unlimited unique sequential sequence Ids

0 lines of code changed in:

• src/jalview/schemabinding/version2: SequenceSetProperties.java (changed), StructureState.java (changed)

jprocter 2008-02-22 16:32

sequenceId is a string, not an integer - allows generation of unlimited unique sequential sequence Ids

0 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), JGroup.java (changed), JSeq.java (changed)

jprocter 2007-08-30 12:38

added aligned codon frames, and dataset reference ids for sequenceSet and sequences to project xml

0 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), AlcodMap.java (new), Alcodon.java (new), AlcodonFrame.java (new), DBRef.java (changed), MapListFrom.java (new), MapListTo.java (new), MapListType.java (new), Mapping.java (new), MappingChoice.java (new), Sequence.java (changed), SequenceSet.java (changed), SequenceSetProperties.java (changed), StructureState.java (changed)

jprocter 2007-07-13 15:54

moved to castor-1.1-cycle - a specially patched version of castor relating to jira bugs : http://jira.codehaus.org/browse/CASTOR-2027 http://jira.codehaus.org/browse/CASTOR-2012 http://jira.codehaus.org/browse/CASTOR-2011

0 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), SequenceSetProperties.java (changed), StructureState.java (changed)

jprocter 2007-05-24 16:20

castor-1.1 classes (descriptors moved to subpackage)

0 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (changed), AnnotationColoursDescriptor.java (del), AnnotationDescriptor.java (del), AnnotationElementDescriptor.java (del), ColourDescriptor.java (del), DBRefDescriptor.java (del), FeatureDescriptor.java (del), FeatureSettingsDescriptor.java (del), FeaturesDescriptor.java (del), GroupDescriptor.java (del), HiddenColumnsDescriptor.java (del), JGroupDescriptor.java (del), JSeqDescriptor.java (del), JalviewModelDescriptor.java (del), JalviewModelSequenceDescriptor.java (del), JalviewUserColoursDescriptor.java (del), OtherDataDescriptor.java (del), PdbentryDescriptor.java (del), PdbentryItemDescriptor.java (del), PdbidsDescriptor.java (del), PropertyDescriptor.java (del), SequenceDescriptor.java (del), SequenceSetDescriptor.java (del), SequenceSetProperties.java (changed), SequenceSetPropertiesDescriptor.java (del), SequenceTypeDescriptor.java (del), SettingDescriptor.java (del), StructureState.java (changed), StructureStateDescriptor.java (del), ThresholdLineDescriptor.java (del), TreeDescriptor.java (del), UserColourSchemeDescriptor.java (del), UserColoursDescriptor.java (del), VAMSASDescriptor.java (del), VamsasModelDescriptor.java (del), ViewportDescriptor.java (del)

jprocter 2007-05-17 18:06

modified castor-1.1 library and refactored uk.ac.vamsas

313 lines of code changed in:

• src/jalview/schemabinding/version2: .castor.cdr (new), Annotation.java (changed), AnnotationColours.java (changed), AnnotationElement.java (changed), Colour.java (changed), DBRef.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), Group.java (changed), HiddenColumns.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), OtherData.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceSetProperties.java (+170 -173), SequenceType.java (changed), Setting.java (changed), StructureState.java (+143 -160), ThresholdLine.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

andrew 2007-05-10 08:12

save visible state of annotation

0 lines of code changed in:

• src/jalview/schemabinding/version2: Annotation.java (changed), AnnotationDescriptor.java (changed), SequenceSetProperties.java (changed), SequenceSetPropertiesDescriptor.java (changed)

andrew 2007-05-01 11:04

Save seqset properties

173 lines of code changed in:

• src/jalview/schemabinding/version2: SequenceSet.java (changed), SequenceSetDescriptor.java (changed), SequenceSetProperties.java (new 173), SequenceSetPropertiesDescriptor.java (new)

jprocter 2007-04-26 18:10

total annotation score is a double for maximum precision.

0 lines of code changed in:

• src/jalview/schemabinding/version2: Annotation.java (changed), AnnotationDescriptor.java (changed), PdbidsItem.java (del), PdbidsItemDescriptor.java (del), StructureState.java (changed), StructureStateDescriptor.java (changed)

(19 more)