Directory src/jalview/schemabinding/version2/descriptors/

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jprocter 2010-09-06 17:37

new XML representation for web services parameters

354 lines of code changed in:

• src/jalview/schemabinding/version2/descriptors: WebServiceParameterSetDescriptor.java (new 354)

jprocter 2010-04-30 10:29

jalview 2.5 release banner

0 lines of code changed in:

• src/jalview/schemabinding/version2/descriptors: AlcodMapDescriptor.java (changed), AlcodonDescriptor.java (changed), AlcodonFrameDescriptor.java (changed), AnnotationColoursDescriptor.java (changed), AnnotationDescriptor.java (changed), AnnotationElementDescriptor.java (changed), ColourDescriptor.java (changed), DBRefDescriptor.java (changed), FeatureDescriptor.java (changed), FeatureSettingsDescriptor.java (changed), FeaturesDescriptor.java (changed), GroupDescriptor.java (changed), HiddenColumnsDescriptor.java (changed), JGroupDescriptor.java (changed), JSeqDescriptor.java (changed), JalviewModelDescriptor.java (changed), JalviewModelSequenceDescriptor.java (changed), JalviewUserColoursDescriptor.java (changed), MapListFromDescriptor.java (changed), MapListToDescriptor.java (changed), MapListTypeDescriptor.java (changed), MappingChoiceDescriptor.java (changed), MappingDescriptor.java (changed), OtherDataDescriptor.java (changed), PdbentryDescriptor.java (changed), PdbentryItemDescriptor.java (changed), PdbidsDescriptor.java (changed), PropertyDescriptor.java (changed), SequenceDescriptor.java (changed), SequenceSetDescriptor.java (changed), SequenceSetPropertiesDescriptor.java (changed), SequenceTypeDescriptor.java (changed), SettingDescriptor.java (changed), StructureStateDescriptor.java (changed), ThresholdLineDescriptor.java (changed), TreeDescriptor.java (changed), UserColourSchemeDescriptor.java (changed), UserColoursDescriptor.java (changed), VAMSASDescriptor.java (changed), VamsasModelDescriptor.java (changed), ViewportDescriptor.java (changed)

jprocter 2010-04-14 15:35

profile visualizations are now logos

0 lines of code changed in:

• src/jalview/schemabinding/version2/descriptors: JGroupDescriptor.java (changed), ViewportDescriptor.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/descriptors: AnnotationDescriptor.java (changed), JGroupDescriptor.java (changed), SettingDescriptor.java (changed), ViewportDescriptor.java (changed)

jprocter 2010-04-02 15:41

extended Colour element with additional optional attributes for graduated colour

0 lines of code changed in:

• src/jalview/schemabinding/version2/descriptors: AlcodMapDescriptor.java (changed), AlcodonDescriptor.java (changed), AlcodonFrameDescriptor.java (changed), AnnotationColoursDescriptor.java (changed), AnnotationDescriptor.java (changed), AnnotationElementDescriptor.java (changed), ColourDescriptor.java (changed), DBRefDescriptor.java (changed), FeatureDescriptor.java (changed), FeatureSettingsDescriptor.java (changed), FeaturesDescriptor.java (changed), GroupDescriptor.java (changed), HiddenColumnsDescriptor.java (changed), JGroupDescriptor.java (changed), JSeqDescriptor.java (changed), JalviewModelDescriptor.java (changed), JalviewModelSequenceDescriptor.java (changed), JalviewUserColoursDescriptor.java (changed), MapListFromDescriptor.java (changed), MapListToDescriptor.java (changed), MapListTypeDescriptor.java (changed), MappingChoiceDescriptor.java (changed), MappingDescriptor.java (changed), OtherDataDescriptor.java (changed), PdbentryDescriptor.java (changed), PdbentryItemDescriptor.java (changed), PdbidsDescriptor.java (changed), PropertyDescriptor.java (changed), SequenceDescriptor.java (changed), SequenceSetDescriptor.java (changed), SequenceSetPropertiesDescriptor.java (changed), SequenceTypeDescriptor.java (changed), SettingDescriptor.java (changed), StructureStateDescriptor.java (changed), ThresholdLineDescriptor.java (changed), TreeDescriptor.java (changed), UserColourSchemeDescriptor.java (changed), UserColoursDescriptor.java (changed), VAMSASDescriptor.java (changed), VamsasModelDescriptor.java (changed), ViewportDescriptor.java (changed)

jprocter 2009-06-08 11:46

apply gpl development license

0 lines of code changed in:

• src/jalview/schemabinding/version2/descriptors: AlcodMapDescriptor.java (changed), AlcodonDescriptor.java (changed), AlcodonFrameDescriptor.java (changed), AnnotationColoursDescriptor.java (changed), AnnotationDescriptor.java (changed), AnnotationElementDescriptor.java (changed), ColourDescriptor.java (changed), DBRefDescriptor.java (changed), FeatureDescriptor.java (changed), FeatureSettingsDescriptor.java (changed), FeaturesDescriptor.java (changed), GroupDescriptor.java (changed), HiddenColumnsDescriptor.java (changed), JGroupDescriptor.java (changed), JSeqDescriptor.java (changed), JalviewModelDescriptor.java (changed), JalviewModelSequenceDescriptor.java (changed), JalviewUserColoursDescriptor.java (changed), MapListFromDescriptor.java (changed), MapListToDescriptor.java (changed), MapListTypeDescriptor.java (changed), MappingChoiceDescriptor.java (changed), MappingDescriptor.java (changed), OtherDataDescriptor.java (changed), PdbentryDescriptor.java (changed), PdbentryItemDescriptor.java (changed), PdbidsDescriptor.java (changed), PropertyDescriptor.java (changed), SequenceDescriptor.java (changed), SequenceSetDescriptor.java (changed), SequenceSetPropertiesDescriptor.java (changed), SequenceTypeDescriptor.java (changed), SettingDescriptor.java (changed), StructureStateDescriptor.java (changed), ThresholdLineDescriptor.java (changed), TreeDescriptor.java (changed), UserColourSchemeDescriptor.java (changed), UserColoursDescriptor.java (changed), VAMSASDescriptor.java (changed), VamsasModelDescriptor.java (changed), ViewportDescriptor.java (changed)

jprocter 2009-03-31 17:39

prototype for store/restore of feature colour gradient settings

0 lines of code changed in:

• src/jalview/schemabinding/version2/descriptors: SettingDescriptor.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/descriptors: JGroupDescriptor.java (changed), ViewportDescriptor.java (changed)

jprocter 2009-01-08 16:00

structure ids are not IDs, but simply references

0 lines of code changed in:

• src/jalview/schemabinding/version2/descriptors: StructureStateDescriptor.java (changed)

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

0 lines of code changed in:

• src/jalview/schemabinding/version2/descriptors: AlcodMapDescriptor.java (changed), AlcodonDescriptor.java (changed), AlcodonFrameDescriptor.java (changed), AnnotationColoursDescriptor.java (changed), AnnotationDescriptor.java (changed), AnnotationElementDescriptor.java (changed), ColourDescriptor.java (changed), DBRefDescriptor.java (changed), FeatureDescriptor.java (changed), FeatureSettingsDescriptor.java (changed), FeaturesDescriptor.java (changed), GroupDescriptor.java (changed), HiddenColumnsDescriptor.java (changed), JGroupDescriptor.java (changed), JSeqDescriptor.java (changed), JalviewModelDescriptor.java (changed), JalviewModelSequenceDescriptor.java (changed), JalviewUserColoursDescriptor.java (changed), MapListFromDescriptor.java (changed), MapListToDescriptor.java (changed), MapListTypeDescriptor.java (changed), MappingChoiceDescriptor.java (changed), MappingDescriptor.java (changed), OtherDataDescriptor.java (changed), PdbentryDescriptor.java (changed), PdbentryItemDescriptor.java (changed), PdbidsDescriptor.java (changed), PropertyDescriptor.java (changed), SequenceDescriptor.java (changed), SequenceSetDescriptor.java (changed), SequenceSetPropertiesDescriptor.java (changed), SequenceTypeDescriptor.java (changed), SettingDescriptor.java (changed), StructureStateDescriptor.java (changed), ThresholdLineDescriptor.java (changed), TreeDescriptor.java (changed), UserColourSchemeDescriptor.java (changed), UserColoursDescriptor.java (changed), VAMSASDescriptor.java (changed), VamsasModelDescriptor.java (changed), ViewportDescriptor.java (changed)

jprocter 2008-09-04 14:33

merge from 2_4_Release branch

0 lines of code changed in:

• src/jalview/schemabinding/version2/descriptors: AlcodMapDescriptor.java (changed), AlcodonDescriptor.java (changed), AlcodonFrameDescriptor.java (changed), AnnotationColoursDescriptor.java (changed), AnnotationDescriptor.java (changed), AnnotationElementDescriptor.java (changed), ColourDescriptor.java (changed), DBRefDescriptor.java (changed), FeatureDescriptor.java (changed), FeatureSettingsDescriptor.java (changed), FeaturesDescriptor.java (changed), GroupDescriptor.java (changed), HiddenColumnsDescriptor.java (changed), JGroupDescriptor.java (changed), JSeqDescriptor.java (changed), JalviewModelDescriptor.java (changed), JalviewModelSequenceDescriptor.java (changed), JalviewUserColoursDescriptor.java (changed), MapListFromDescriptor.java (changed), MapListToDescriptor.java (changed), MapListTypeDescriptor.java (changed), MappingChoiceDescriptor.java (changed), MappingDescriptor.java (changed), OtherDataDescriptor.java (changed), PdbentryDescriptor.java (changed), PdbentryItemDescriptor.java (changed), PdbidsDescriptor.java (changed), PropertyDescriptor.java (changed), SequenceDescriptor.java (changed), SequenceSetDescriptor.java (changed), SequenceSetPropertiesDescriptor.java (changed), SequenceTypeDescriptor.java (changed), SettingDescriptor.java (changed), StructureStateDescriptor.java (changed), ThresholdLineDescriptor.java (changed), TreeDescriptor.java (changed), UserColourSchemeDescriptor.java (changed), UserColoursDescriptor.java (changed), VAMSASDescriptor.java (changed), VamsasModelDescriptor.java (changed), ViewportDescriptor.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/descriptors: JSeqDescriptor.java (changed)

jprocter 2008-02-24 19:52

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/descriptors: JGroupDescriptor.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/descriptors: AlcodMapDescriptor.java (new), AlcodonDescriptor.java (new), AlcodonFrameDescriptor.java (new), DBRefDescriptor.java (changed), MapListFromDescriptor.java (new), MapListToDescriptor.java (new), MapListTypeDescriptor.java (new), MappingChoiceDescriptor.java (new), MappingDescriptor.java (new), SequenceDescriptor.java (changed), SequenceSetDescriptor.java (changed)

jprocter 2007-07-13 15:53

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/descriptors: AnnotationColoursDescriptor.java (changed), AnnotationDescriptor.java (changed), AnnotationElementDescriptor.java (changed), ColourDescriptor.java (changed), DBRefDescriptor.java (changed), FeatureDescriptor.java (changed), FeatureSettingsDescriptor.java (changed), FeaturesDescriptor.java (changed), GroupDescriptor.java (changed), HiddenColumnsDescriptor.java (changed), JGroupDescriptor.java (changed), JSeqDescriptor.java (changed), JalviewModelDescriptor.java (changed), JalviewModelSequenceDescriptor.java (changed), JalviewUserColoursDescriptor.java (changed), OtherDataDescriptor.java (changed), PdbentryDescriptor.java (changed), PdbentryItemDescriptor.java (changed), PdbidsDescriptor.java (changed), PropertyDescriptor.java (changed), SequenceDescriptor.java (changed), SequenceSetDescriptor.java (changed), SequenceSetPropertiesDescriptor.java (changed), SequenceTypeDescriptor.java (changed), SettingDescriptor.java (changed), StructureStateDescriptor.java (changed), ThresholdLineDescriptor.java (changed), TreeDescriptor.java (changed), UserColourSchemeDescriptor.java (changed), UserColoursDescriptor.java (changed), VAMSASDescriptor.java (changed), VamsasModelDescriptor.java (changed), ViewportDescriptor.java (changed)

jprocter 2007-05-17 18:06

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

0 lines of code changed in:

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