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

2022-12-14	Jim Procter	Merge branch 'develop' into update_212_Dec_merge_with_2...	blob \| commitdiff
2022-11-21	Jim Procter	Merge commit 'alpha/update_2_12_for_2_11_2_series_merge...	blob \| commitdiff \| diff to current
2022-04-16	Jim Procter	JAL-3365 expand range of allowed DSSP secondary structu...	blob \| commitdiff \| diff to current
2022-03-08	Jim Procter	JAL-3438 spotless for 2.11.2.0	blob \| commitdiff \| diff to current
2021-09-21	Ben Soares	JAL-3691 automatic insertion of Locale.ROOT to toUpperC...	blob \| commitdiff \| diff to current
2019-09-26	Jim Procter	JAL-3070 JAL-3066 AlignmentI.findOrAddAnnotation(Alignm...	blob \| commitdiff \| diff to current
2019-07-03	tva	JAL-2629 evalues and bit scores now conserved after...	blob \| commitdiff \| diff to current
2019-07-03	tva	JAL-2629 can now filter by sequence e-value or bit...	blob \| commitdiff \| diff to current
2019-06-05	tva	JAL-3285 add unmerged code to AlignmentAnnotation	blob \| commitdiff \| diff to current
2019-06-04	Jim Procter	Merge branch 'develop' into developtomchmmer	blob \| commitdiff \| diff to current
2019-03-20	Ben Soares	JAL-3130 Lots of deprecation fixes. See utils/deprecat...	blob \| commitdiff \| diff to current
2018-08-02	Ben Soares	JAL-3053	blob \| commitdiff \| diff to current
2018-07-30	bsoares	Fixed bug ignoring "alpha" extended braces in RNA SS...	blob \| commitdiff \| diff to current
2018-05-31	Jim Procter	Merge branch 'spike/JAL-1950_hmmer3client' into feature...	blob \| commitdiff \| diff to current
2018-05-31	Jim Procter	Merge branch 'develop' into spike/JAL-1950_hmmer3client	blob \| commitdiff \| diff to current
2018-03-16	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2018-03-07	gmungoc	JAL-2629 storage and lifecycle of alignment/group HMM...	blob \| commitdiff \| diff to current
2018-02-22	gmungoc	JAL-2629 tidy unit tests, constants etc	blob \| commitdiff \| diff to current
2018-02-20	gmungoc	Merge branch 'develop' into features/mchmmer	blob \| commitdiff \| diff to current
2018-02-06	kiramt	Merge branch 'develop' into feature/JAL-2759 feature/JAL-2759	blob \| commitdiff \| diff to current
2018-01-16	kiramt	JAL-2759 Moved alignment annotation code out of HiddenC...	blob \| commitdiff \| diff to current
2017-11-22	gmungoc	JAL-2069 spike updated with latest (FeatureTypeSettings)	blob \| commitdiff \| diff to current
2017-11-10	Jim Procter	JAL-2828 allow CalcId to match on String equivalence... doc/JAL-2494_JAL-2828_mergefindAnnotation	blob \| commitdiff \| diff to current
2017-11-10	Jim Procter	JAL-2828 refactored duplicate code for searching lists...	blob \| commitdiff \| diff to current
2017-10-27	gmungoc	JAL-1793 spike branch updated to latest	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-09-01	gmungoc	JAL-2488 remove finalize methods	blob \| commitdiff \| diff to current
2017-08-21	Jim Procter	Merge branch 'develop' into trial_merge/JAL-1950 spike/JAL-1950_hmmer3client	blob \| commitdiff \| diff to current
2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-18	TZVanaalten	Merge branch 'develop' into features/hmmer	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-08-02	TZVanaalten	JAL-2599 fix for information annotation buttons	blob \| commitdiff \| diff to current
2017-07-27	TZVanaalten	JAL-2629 moved HMM storage location to placeholder...	blob \| commitdiff \| diff to current
2017-07-18	TZVanaalten	JAL-2599 complete documentation for HMM and HMMFile...	blob \| commitdiff \| diff to current
2017-06-29	TZVanaalten	transferred the storage position of the HMM to annotations	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-05-16	gmungoc	JAL-2505 set helix number as feature group in SequenceF...	blob \| commitdiff \| diff to current
2017-05-05	kiramt	Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges	blob \| commitdiff \| diff to current
2017-05-03	Jim Procter	JAL-2503 AlignmentAnnotation.isQuantitative() test	blob \| commitdiff \| diff to current
2017-04-24	kiramt	JAL-2388 Hidden cols separated from column selection...	blob \| commitdiff \| diff to current
2017-03-30	gmungoc	Merge branch 'develop' into bug/JAL-2346annotationChoice	blob \| commitdiff \| diff to current
2016-12-05	Jim Procter	Merge branch 'develop' into spike/JAL-1950_hmmer3client	blob \| commitdiff \| diff to current
2016-12-02	gmungoc	JAL-2346 unit test for annotation drop-down list builder	blob \| commitdiff \| diff to current
2016-12-01	Jim Procter	JAL-1933 update the bounds for the Gap annotation row...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
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 \| diff to current
2016-09-25	Jim Procter	Merge branch 'develop' into spike/JAL-1950_hmmer3client	blob \| commitdiff \| diff to current
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
2016-04-12	Jim Procter	Merge branch 'develop' into trialmerge/JAL-1950_hmmer3c...	blob \| commitdiff \| diff to current
2015-11-16	tcofoegbu	JAL-1967 JAL-1479 refactored sequence<->structure mappi...	blob \| commitdiff \| diff to current
2015-11-09	Jim Procter	JAL-1950 javadoc: clarify AlignmentAnnotation.createSeq...	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
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