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[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff
2016-08-16	gmungoc	JAL-2171 matching bracket default character for rna...	blob \| commitdiff \| diff to current
2016-08-12	gmungoc	JAL-1841 bug fixes / code tidy for rna SS rendering...	blob \| commitdiff \| diff to current
2015-11-16	tcofoegbu	JAL-1967 JAL-1479 refactored sequence<->structure mappi...	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	Merge branch 'develop' into Release_2_9_0b1_Branch	blob \| commitdiff \| diff to current
2015-10-07	Jim Procter	JAL-1912 formatting	blob \| commitdiff \| diff to current
2015-10-07	Jim Procter	JAL-1912 javadoc for adjustForAlignment stating current...	blob \| commitdiff \| diff to current
2015-10-07	Jim Procter	JAL-1912 efficiency: look up sequenceMapping once per...	blob \| commitdiff \| diff to current
2015-10-05	tcofoegbu	JAL-1912 added null check for SequenceMapping variable...	blob \| commitdiff \| diff to current
2015-10-01	tcofoegbu	JAL-1912 Double.NaN breaks JSON serialization - added...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-06-18	gmungoc	JAL-1781 annotation.sequenceRef now sequence id not... features/JAL-1781annotationXmlIds	blob \| commitdiff \| diff to current
2015-06-15	Jim Procter	JAL-1775 patch for regression from Anne Menard’s pseudo...	blob \| commitdiff \| diff to current
2015-06-15	Jim Procter	JAL-1775 patch for regression from Anne Menard’s pseudo...	blob \| commitdiff \| diff to current
2015-06-15	Jim Procter	JAL-1775 patch regression bug when displayChar is null...	blob \| commitdiff \| diff to current
2015-06-15	Jim Procter	fix for JAL-1775 (and reorganise imports)	blob \| commitdiff \| diff to current
2015-06-15	Jim Procter	JAL-1775 patch regression bug when displayChar is null...	blob \| commitdiff \| diff to current
2015-06-15	Jim Procter	fix for JAL-1775 (and reorganise imports)	blob \| commitdiff \| diff to current
2015-05-12	gmungoc	JAL-1712 fixes/tests for Castor binding and 'show flank...	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-11-24	Jim Procter	JAL-1595 annotation score is total number of rna helices	blob \| commitdiff \| diff to current
2014-11-21	Jim Procter	JAL-1489 change initial value to distinguish non-rna...	blob \| commitdiff \| diff to current
2014-11-20	Jim Procter	JAL-1569 rna pair code in secondary structure character...	blob \| commitdiff \| diff to current
2014-11-20	Jim Procter	JAL-674 JAL-1569 mark RNA helix number in the value...	blob \| commitdiff \| diff to current
2014-11-03	Jim Procter	JAL-1578 formatting and imports	blob \| commitdiff \| diff to current
2014-11-03	Jim Procter	JAL-1551 formatting	blob \| commitdiff \| diff to current
2014-11-03	Jim Procter	JAL-674 JAL-961 JAL-1578 accessors and copy constructor...	blob \| commitdiff \| diff to current
2014-11-03	Jim Procter	javadoc	blob \| commitdiff \| diff to current
2014-10-31	Jim Procter	JAL-674 JAL-961 properties to stash additional informat...	blob \| commitdiff \| diff to current
2014-10-30	Jim Procter	JAL-674 helpful javadoc for remap method	blob \| commitdiff \| diff to current
2014-10-29	Jim Procter	JAL-674 JAL-1264 remap method to allow annotation posit...	blob \| commitdiff \| diff to current
2014-10-21	Jim Procter	JAL-1551 source formatting	blob \| commitdiff \| diff to current
2014-10-15	Jim Procter	JAL-348 JAL-674 JAL-1564 TODO and implementation error...	blob \| commitdiff \| diff to current
2014-10-15	Jim Procter	JAL-674 patch logic to test whether old and new sequenc...	blob \| commitdiff \| diff to current
2014-10-15	Jim Procter	JAL-674 JAL-1305 JAL-348 new liftOver method and test...	blob \| commitdiff \| diff to current
2014-07-18	j.procter@dundee...	JAL-1520 switch between Protein and non-canonical RNA...	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1520 fix unicode translation errors.	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-02-18	Jim Procter	Merge branch 'JAL-1445' into develop	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2012-12-07	jprocter	revised renderer and annotation model to support differ...	blob \| commitdiff \| diff to current
2012-12-07	jprocter	convenience function to get the RNA model for an annota...	blob \| commitdiff \| diff to current
2012-12-07	jprocter	use new secstructure process algorithm	blob \| commitdiff \| diff to current
2012-11-15	jprocter	Merge branch 'develop' into menard	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-09-03	jprocter	JAL-1153 ensure _linecolour is copied in copy constructor	blob \| commitdiff \| diff to current
2012-08-31	jprocter	Merge branch 'develop' into menard	blob \| commitdiff \| diff to current
2012-08-29	jprocter	JAL-1153 new runtime property set to first non-null...	blob \| commitdiff \| diff to current
2012-08-14	Anne Menard	last version stay many bugs ..	blob \| commitdiff \| diff to current
2012-07-10	Anne Menard	v2	blob \| commitdiff \| diff to current
2012-05-22	jprocter	update the copy constructor	blob \| commitdiff \| diff to current
2011-11-03	jprocter	(JAL-811) new 'annotation type' field for marking annot...	blob \| commitdiff \| diff to current
2011-10-28	jprocter	JAL-580 ensure WUSS annotation string is up to date...	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-10-04	jprocter	Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-08-18	jprocter	fix for JAL-701 - ensure '<' appears in tooltip in...	blob \| commitdiff \| diff to current
2011-07-25	janengelhardt	Further structure accessing feature	blob \| commitdiff \| diff to current
2011-07-25	janengelhardt	'Update to Covariaton color scheme' merge; JAL-580	blob \| commitdiff \| diff to current
2011-07-25	janengelhardt	Start merging of Laurens Code	blob \| commitdiff \| diff to current
2011-01-05	jprocter	graphThreshold not being copied by constructor	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2010-04-28	jprocter	group/annotation association housekeeping	blob \| commitdiff \| diff to current
2010-04-23	jprocter	javadoc	blob \| commitdiff \| diff to current
2010-04-16	jprocter	patch for bug #36198 - more to follow on Monday.	blob \| commitdiff \| diff to current
2010-03-22	jprocter	todo and sensible default setting of min/max for histog...	blob \| commitdiff \| diff to current
2010-03-11	jprocter	individual label format settings for each annotation...	blob \| commitdiff \| diff to current
2009-08-21	jprocter	todo	blob \| commitdiff \| diff to current
2009-07-24	jprocter	optional sequencegroup ref for annotation row	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-08-20	jprocter	tooltip displays formatted annotation row description...	blob \| commitdiff \| diff to current
2008-05-01	jprocter	fix for unicode char labels causing arrayOutOfBoundsExc...	blob \| commitdiff \| diff to current
2008-02-22	jprocter	possible fix for stockhom ss-annotation re-creation...	blob \| commitdiff \| diff to current
2007-11-30	jprocter	null pointer bugfix	blob \| commitdiff \| diff to current
2007-10-02	jprocter	convenience constructor for duplicating an annotation...	blob \| commitdiff \| diff to current
2007-05-28	jprocter	fix compact annotation array routine	blob \| commitdiff \| diff to current
2007-05-02	jprocter	checks for negative start column in restrict	blob \| commitdiff \| diff to current
2007-05-02	amwaterhouse	Padgaps is false by default	blob \| commitdiff \| diff to current
2007-05-01	amwaterhouse	Pad gaps method	blob \| commitdiff \| diff to current
2007-04-30	jprocter	pad should leave null annotations array null	blob \| commitdiff \| diff to current
2007-04-30	jprocter	convenient creation of 'score only' annotation.	blob \| commitdiff \| diff to current
2007-04-27	amwaterhouse	padGaps moved	blob \| commitdiff \| diff to current
2007-04-26	jprocter	score is a double, fix bugs for score only annotation...	blob \| commitdiff \| diff to current
2007-04-26	jprocter	score and visible copy construction	blob \| commitdiff \| diff to current
2007-04-26	jprocter	fix for null annotations	blob \| commitdiff \| diff to current
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