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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java
2023-11-02 James ProcterJAL-1551 formatting commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2023-05-25 James ProcterJAL-4134 popup menu and annotation row property to... commit | commitdiff
2023-05-22 James ProcterJAL-1551 spotless commit | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff
2023-02-22 James ProcterJAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MAT... commit | commitdiff
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... commit | commitdiff
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options commit | commitdiff
2022-10-17 Jim ProcterJAL-1551 formatting commit | commitdiff
2022-06-10 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... commit | commitdiff
2022-04-16 Jim ProcterJAL-3365 expand range of allowed DSSP secondary structu... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2022-02-16 Jim ProcterMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... commit | commitdiff
2019-06-18 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into merge... commit | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... commit | commitdiff
2018-08-02 Ben SoaresJAL-3053 commit | commitdiff
2018-07-30 bsoaresFixed bug ignoring "alpha" extended braces in RNA SS... commit | commitdiff
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759 commit | commitdiff
2018-01-16 kiramtJAL-2759 Moved alignment annotation code out of HiddenC... commit | commitdiff
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) commit | commitdiff
2017-11-10 Jim ProcterJAL-2828 allow CalcId to match on String equivalence... doc/JAL-2494_JAL-2828_mergefindAnnotation commit | commitdiff
2017-11-10 Jim ProcterJAL-2828 refactored duplicate code for searching lists... commit | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-09-01 gmungocJAL-2488 remove finalize methods commit | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList commit | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-06-09 Jim ProcterMerge branch 'develop' into features/JAL-2349_matrixvis commit | commitdiff
2017-05-16 gmungocJAL-2505 set helix number as feature group in SequenceF... commit | commitdiff
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges commit | commitdiff
2017-05-03 Jim ProcterJAL-2503 AlignmentAnnotation.isQuantitative() test commit | commitdiff
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... commit | commitdiff
2017-03-30 gmungocMerge branch 'develop' into bug/JAL-2346annotationChoice commit | commitdiff
2016-12-04 Jim ProcterJAL-2348 custom renderer type commit | commitdiff
2016-12-02 gmungocJAL-2346 unit test for annotation drop-down list builder commit | commitdiff
2016-12-01 Jim ProcterJAL-1933 update the bounds for the Gap annotation row... commit | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch commit | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting commit | commitdiff
2016-08-16 gmungocJAL-2171 matching bracket default character for rna... commit | commitdiff
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering... commit | commitdiff
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi... commit | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 commit | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright commit | commitdiff
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch commit | commitdiff
2015-10-07 Jim ProcterJAL-1912 formatting commit | commitdiff
2015-10-07 Jim ProcterJAL-1912 javadoc for adjustForAlignment stating current... commit | commitdiff
2015-10-07 Jim ProcterJAL-1912 efficiency: look up sequenceMapping once per... commit | commitdiff
2015-10-05 tcofoegbuJAL-1912 added null check for SequenceMapping variable... commit | commitdiff
2015-10-01 tcofoegbuJAL-1912 Double.NaN breaks JSON serialization - added... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports commit | commitdiff
2015-06-18 gmungocJAL-1781 annotation.sequenceRef now sequence id not... features/JAL-1781annotationXmlIds commit | commitdiff
2015-06-15 Jim ProcterJAL-1775 patch for regression from Anne Menard’s pseudo... commit | commitdiff
2015-06-15 Jim ProcterJAL-1775 patch for regression from Anne Menard’s pseudo... commit | commitdiff
2015-06-15 Jim ProcterJAL-1775 patch regression bug when displayChar is null... commit | commitdiff
2015-06-15 Jim Procterfix for JAL-1775 (and reorganise imports) commit | commitdiff
2015-06-15 Jim ProcterJAL-1775 patch regression bug when displayChar is null... commit | commitdiff
2015-06-15 Jim Procterfix for JAL-1775 (and reorganise imports) commit | commitdiff
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank... commit | commitdiff
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch commit | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... commit | commitdiff
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 commit | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes commit | commitdiff
2014-11-24 Jim ProcterJAL-1595 annotation score is total number of rna helices commit | commitdiff
2014-11-21 Jim ProcterJAL-1489 change initial value to distinguish non-rna... commit | commitdiff
2014-11-20 Jim ProcterJAL-1569 rna pair code in secondary structure character... commit | commitdiff
2014-11-20 Jim ProcterJAL-674 JAL-1569 mark RNA helix number in the value... commit | commitdiff
2014-11-03 Jim ProcterJAL-1578 formatting and imports commit | commitdiff
2014-11-03 Jim ProcterJAL-1551 formatting commit | commitdiff
2014-11-03 Jim ProcterJAL-674 JAL-961 JAL-1578 accessors and copy constructor... commit | commitdiff
2014-11-03 Jim Procterjavadoc commit | commitdiff
2014-10-31 Jim ProcterJAL-674 JAL-961 properties to stash additional informat... commit | commitdiff
2014-10-30 Jim ProcterJAL-674 helpful javadoc for remap method commit | commitdiff
2014-10-29 Jim ProcterJAL-674 JAL-1264 remap method to allow annotation posit... commit | commitdiff
2014-10-21 Jim ProcterJAL-1551 source formatting commit | commitdiff
2014-10-15 Jim ProcterJAL-348 JAL-674 JAL-1564 TODO and implementation error... commit | commitdiff
2014-10-15 Jim ProcterJAL-674 patch logic to test whether old and new sequenc... commit | commitdiff
2014-10-15 Jim ProcterJAL-674 JAL-1305 JAL-348 new liftOver method and test... commit | commitdiff
2014-07-18 j.procter@dundee... JAL-1520 switch between Protein and non-canonical RNA... commit | commitdiff
2014-06-06 Jim ProcterJAL-1520 fix unicode translation errors. commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 source formatting commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch commit | commitdiff
2014-05-22 Jim ProcterJAL-1503 update version in GPL header commit | commitdiff
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop commit | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices commit | commitdiff
2012-12-07 jprocterrevised renderer and annotation model to support differ... commit | commitdiff
2012-12-07 jprocterconvenience function to get the RNA model for an annota... commit | commitdiff
2012-12-07 jprocteruse new secstructure process algorithm commit | commitdiff
2012-11-15 jprocterMerge branch 'develop' into menard commit | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header commit | commitdiff
2012-10-03 jprocterformatting commit | commitdiff
2012-09-03 jprocterJAL-1153 ensure _linecolour is copied in copy constructor commit | commitdiff
2012-08-31 jprocterMerge branch 'develop' into menard commit | commitdiff
2012-08-29 jprocterJAL-1153 new runtime property set to first non-null... commit | commitdiff
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