Directory src/jalview/binding/

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jprocter 2010-04-30 10:29

jalview 2.5 release banner

10172 lines of code changed in:

• src/jalview/binding: Alignment.java (+171 -161), Annotation.java (+450 -424), AnnotationElement.java (+296 -283), Colour.java (+489 -475), Feature.java (+295 -282), FeatureSettings.java (+280 -267), Features.java (+114 -107), JGroup.java (+751 -731), JSeq.java (+636 -615), JalviewModel.java (+224 -212), JalviewModelSequence.java (+946 -914), JalviewUserColours.java (+335 -322), Pdbentry.java (+335 -318), PdbentryItem.java (+191 -188), Pdbids.java (+114 -107), Property.java (+171 -161), Sequence.java (+114 -107), SequenceSet.java (+529 -506), SequenceType.java (+197 -186), Setting.java (+253 -242), Tree.java (+834 -812), UserColourScheme.java (+115 -107), UserColours.java (+172 -161), VAMSAS.java (+593 -573), VamsasModel.java (+113 -107), Viewport.java (+1454 -1424)

jprocter 2010-04-14 15:35

profile visualizations are now logos

0 lines of code changed in:

• src/jalview/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Colour.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2010-04-05 16:39

regenerated binding for extensions to XML for 2.5

0 lines of code changed in:

• src/jalview/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Colour.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2010-04-02 15:41

extended Colour element with additional optional attributes for graduated colour

398 lines of code changed in:

• src/jalview/binding: Alignment.java (+2 -2), Annotation.java (+2 -2), AnnotationElement.java (+2 -2), Colour.java (+316 -2), Feature.java (+2 -2), FeatureSettings.java (+2 -2), Features.java (+2 -2), JGroup.java (+2 -2), JSeq.java (+2 -2), JalviewModel.java (+2 -2), JalviewModelSequence.java (+2 -2), JalviewUserColours.java (+34 -2), Pdbentry.java (+2 -2), PdbentryItem.java (+2 -2), Pdbids.java (+2 -2), Property.java (+2 -2), Sequence.java (+2 -2), SequenceSet.java (+2 -2), SequenceType.java (+2 -2), Setting.java (+2 -2), Tree.java (+2 -2), UserColourScheme.java (+2 -2), UserColours.java (+2 -2), VAMSAS.java (+2 -2), VamsasModel.java (+2 -2), Viewport.java (+2 -2)

jprocter 2009-06-08 11:36

apply gpl development license

442 lines of code changed in:

• src/jalview/binding: Alignment.java (+17 -6), Annotation.java (+17 -6), AnnotationElement.java (+17 -6), Colour.java (+17 -6), Feature.java (+17 -6), FeatureSettings.java (+17 -6), Features.java (+17 -6), JGroup.java (+17 -6), JSeq.java (+17 -6), JalviewModel.java (+17 -6), JalviewModelSequence.java (+17 -6), JalviewUserColours.java (+17 -6), Pdbentry.java (+17 -6), PdbentryItem.java (+17 -6), Pdbids.java (+17 -6), Property.java (+17 -6), Sequence.java (+17 -6), SequenceSet.java (+17 -6), SequenceType.java (+17 -6), Setting.java (+17 -6), Tree.java (+17 -6), UserColourScheme.java (+17 -6), UserColours.java (+17 -6), VAMSAS.java (+17 -6), VamsasModel.java (+17 -6), Viewport.java (+17 -6)

jprocter 2009-03-31 17:39

prototype for store/restore of feature colour gradient settings

0 lines of code changed in:

• src/jalview/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Colour.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2009-02-06 14:56

updated binding

0 lines of code changed in:

• src/jalview/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Colour.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.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

9263 lines of code changed in:

• src/jalview/binding: Alignment.java (+154 -180), Annotation.java (+417 -459), AnnotationElement.java (+276 -305), Colour.java (+154 -179), Feature.java (+275 -304), FeatureSettings.java (+260 -289), Features.java (+100 -123), JGroup.java (+724 -760), JSeq.java (+608 -645), JalviewModel.java (+205 -233), JalviewModelSequence.java (+907 -955), JalviewUserColours.java (+283 -313), Pdbentry.java (+311 -344), PdbentryItem.java (+180 -195), Pdbids.java (+100 -123), Property.java (+154 -180), Sequence.java (+100 -123), SequenceSet.java (+499 -538), SequenceType.java (+179 -206), Setting.java (+235 -262), Tree.java (+805 -843), UserColourScheme.java (+100 -124), UserColours.java (+154 -181), VAMSAS.java (+566 -602), VamsasModel.java (+100 -122), Viewport.java (+1417 -1463)

jprocter 2008-09-04 14:33

merge from 2_4_Release branch

10051 lines of code changed in:

• src/jalview/binding: Alignment.java (+180 -154), Annotation.java (+459 -417), AnnotationElement.java (+305 -276), Colour.java (+179 -154), Feature.java (+304 -275), FeatureSettings.java (+289 -260), Features.java (+123 -100), JGroup.java (+760 -724), JSeq.java (+645 -608), JalviewModel.java (+233 -205), JalviewModelSequence.java (+955 -907), JalviewUserColours.java (+313 -283), Pdbentry.java (+344 -311), PdbentryItem.java (+195 -180), Pdbids.java (+123 -100), Property.java (+180 -154), Sequence.java (+123 -100), SequenceSet.java (+538 -499), SequenceType.java (+206 -179), Setting.java (+262 -235), Tree.java (+843 -805), UserColourScheme.java (+124 -100), UserColours.java (+181 -154), VAMSAS.java (+602 -566), VamsasModel.java (+122 -100), Viewport.java (+1463 -1417)

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/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Colour.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2007-08-30 12:39

updated source generation for castor-1.1-cycle patched

0 lines of code changed in:

• src/jalview/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Colour.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.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/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Colour.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2007-05-24 16:19

castor-1.1 compatible classes from ant task

0 lines of code changed in:

• src/jalview/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Colour.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), JalviewUserColoursItem.java (del), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Residue.java (del), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (changed), Tree.java (changed), UserColour.java (del), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)

jprocter 2007-05-24 16:16

jalview 2.0 XML schema versions for backwards compatibility in future castor upgrades

9655 lines of code changed in:

• src/jalview/binding: Alignment.java (+169 -173), Annotation.java (+432 -432), AnnotationElement.java (+291 -306), Colour.java (+169 -173), Feature.java (+290 -331), FeatureSettings.java (+275 -274), Features.java (+116 -118), JGroup.java (+739 -750), JSeq.java (+623 -637), JalviewModel.java (+220 -227), JalviewModelSequence.java (+922 -904), JalviewUserColours.java (+298 -300), Pdbentry.java (+326 -326), PdbentryItem.java (+192 -197), Pdbids.java (+116 -118), Property.java (+169 -173), Sequence.java (+116 -118), SequenceSet.java (+514 -504), SequenceType.java (+194 -225), Setting.java (+250 -253), Tree.java (+820 -835), UserColourScheme.java (+116 -118), UserColours.java (+169 -173), VAMSAS.java (+581 -576), VamsasModel.java (+116 -118), Viewport.java (+1432 -1420)

andrew 2006-02-16 15:44

Allows saving of sequence description

60 lines of code changed in:

• src/jalview/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Feature.java (+28 -2), FeatureSettings.java (+2 -2), Features.java (+2 -2), JGroup.java (+2 -2), JSeq.java (+2 -2), JalviewModel.java (+2 -2), JalviewModelSequence.java (+2 -2), Pdbentry.java (+2 -2), PdbentryItem.java (+2 -2), Pdbids.java (+2 -2), Property.java (+2 -2), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (+2 -2), Tree.java (+2 -2), UserColourScheme.java (+2 -2), UserColours.java (+2 -2), VAMSAS.java (changed), VamsasModel.java (+2 -2), Viewport.java (+2 -2)

andrew 2006-02-15 15:19

Save sequence description in VAMSAS sequence

26 lines of code changed in:

• src/jalview/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (+26), VAMSAS.java (changed)

andrew 2006-02-03 17:52

Added graphtype

53 lines of code changed in:

• src/jalview/binding: Alignment.java (changed), Annotation.java (+53), AnnotationElement.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), VAMSAS.java (changed)

andrew 2005-12-06 11:43

after merge

2112 lines of code changed in:

• src/jalview/binding: Feature.java (new 305), FeatureSettings.java (new 274), Features.java (new 118), JGroup.java (+2 -2), JSeq.java (+306 -2), JalviewModel.java (+2 -2), JalviewModelSequence.java (+28 -2), JalviewModelSequence2.java (del), JalviewModelSequence2Item.java (del), Pdbentry.java (new 326), PdbentryItem.java (new 197), Pdbids.java (new 118), Property.java (new 173), Setting.java (new 253), Tree.java (+2 -2), UserColourScheme.java (+2 -2), UserColours.java (+2 -2), VamsasModel.java (+2 -2), Viewport.java (+2 -2)

andrew 2005-09-14 12:19

TreeFont added, binding rebuilt

79 lines of code changed in:

• src/jalview/binding: JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), Tree.java (+79), UserColourScheme.java (changed), UserColours.java (changed), VamsasModel.java (changed), Viewport.java (changed)

andrew 2005-08-17 10:12

Rebuilt with new schema

4901 lines of code changed in:

• src/jalview/binding: Alignment.java (+66 -83), Annotation.java (+364 -376), AnnotationElement.java (+90 -127), Colour.java (+66 -83), JGroup.java (+203 -313), JSeq.java (+100 -141), JalviewModel.java (+75 -102), JalviewModelSequence.java (+863 -885), JalviewUserColours.java (+124 -138), Sequence.java (+99 -97), SequenceSet.java (+158 -239), SequenceType.java (+184 -183), Tree.java (+231 -336), UserColourScheme.java (+99 -97), UserColours.java (+158 -158), VAMSAS.java (+561 -576), VamsasModel.java (+55 -62), Viewport.java (+1405 -1404)

(7 more)