Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java
2022-12-14 Jim ProcterMerge branch 'develop' into update_212_Dec_merge_with_2...
2022-11-21 Jim ProcterMerge commit 'alpha/update_2_12_for_2_11_2_series_merge...
2022-04-16 Jim ProcterJAL-3365 expand range of allowed DSSP secondary structu...
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC...
2019-09-26 Jim ProcterJAL-3070 JAL-3066 AlignmentI.findOrAddAnnotation(Alignm...
2019-07-03 tvaJAL-2629 evalues and bit scores now conserved after...
2019-07-03 tvaJAL-2629 can now filter by sequence e-value or bit...
2019-06-05 tvaJAL-3285 add unmerged code to AlignmentAnnotation
2019-06-04 Jim ProcterMerge branch 'develop' into developtomchmmer
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat...
2018-08-02 Ben SoaresJAL-3053
2018-07-30 bsoaresFixed bug ignoring "alpha" extended braces in RNA SS...
2018-05-31 Jim ProcterMerge branch 'spike/JAL-1950_hmmer3client' into feature...
2018-05-31 Jim ProcterMerge branch 'develop' into spike/JAL-1950_hmmer3client
2018-03-16 gmungocMerge branch 'develop' into trialMerge
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM...
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759
2018-01-16 kiramtJAL-2759 Moved alignment annotation code out of HiddenC...
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings)
2017-11-10 Jim ProcterJAL-2828 allow CalcId to match on String equivalence... doc/JAL-2494_JAL-2828_mergefindAnnotation
2017-11-10 Jim ProcterJAL-2828 refactored duplicate code for searching lists...
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-01 gmungocJAL-2488 remove finalize methods
2017-08-21 Jim ProcterMerge branch 'develop' into trial_merge/JAL-1950 spike/JAL-1950_hmmer3client
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-08-02 TZVanaaltenJAL-2599 fix for information annotation buttons
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder...
2017-07-18 TZVanaaltenJAL-2599 complete documentation for HMM and HMMFile...
2017-06-29 TZVanaaltentransferred the storage position of the HMM to annotations
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-05-16 gmungocJAL-2505 set helix number as feature group in SequenceF...
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
2017-05-03 Jim ProcterJAL-2503 AlignmentAnnotation.isQuantitative() test
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection...
2017-03-30 gmungocMerge branch 'develop' into bug/JAL-2346annotationChoice
2016-12-05 Jim ProcterMerge branch 'develop' into spike/JAL-1950_hmmer3client
2016-12-02 gmungocJAL-2346 unit test for annotation drop-down list builder
2016-12-01 Jim ProcterJAL-1933 update the bounds for the Gap annotation row...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-09-25 Jim ProcterMerge branch 'develop' into spike/JAL-1950_hmmer3client
2016-08-16 gmungocJAL-2171 matching bracket default character for rna...
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering...
2016-04-12 Jim ProcterMerge branch 'develop' into trialmerge/JAL-1950_hmmer3c...
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi...
2015-11-09 Jim ProcterJAL-1950 javadoc: clarify AlignmentAnnotation.createSeq...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-10-07 Jim ProcterJAL-1912 formatting
2015-10-07 Jim ProcterJAL-1912 javadoc for adjustForAlignment stating current...
2015-10-07 Jim ProcterJAL-1912 efficiency: look up sequenceMapping once per...
2015-10-05 tcofoegbuJAL-1912 added null check for SequenceMapping variable...
2015-10-01 tcofoegbuJAL-1912 Double.NaN breaks JSON serialization - added...
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-06-18 gmungocJAL-1781 annotation.sequenceRef now sequence id not... features/JAL-1781annotationXmlIds
2015-06-15 Jim ProcterJAL-1775 patch for regression from Anne Menard’s pseudo...
2015-06-15 Jim ProcterJAL-1775 patch for regression from Anne Menard’s pseudo...
2015-06-15 Jim ProcterJAL-1775 patch regression bug when displayChar is null...
2015-06-15 Jim Procterfix for JAL-1775 (and reorganise imports)
2015-06-15 Jim ProcterJAL-1775 patch regression bug when displayChar is null...
2015-06-15 Jim Procterfix for JAL-1775 (and reorganise imports)
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank...
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-11-24 Jim ProcterJAL-1595 annotation score is total number of rna helices
2014-11-21 Jim ProcterJAL-1489 change initial value to distinguish non-rna...
2014-11-20 Jim ProcterJAL-1569 rna pair code in secondary structure character...
2014-11-20 Jim ProcterJAL-674 JAL-1569 mark RNA helix number in the value...
2014-11-03 Jim ProcterJAL-1578 formatting and imports
2014-11-03 Jim ProcterJAL-1551 formatting
2014-11-03 Jim ProcterJAL-674 JAL-961 JAL-1578 accessors and copy constructor...
2014-11-03 Jim Procterjavadoc
2014-10-31 Jim ProcterJAL-674 JAL-961 properties to stash additional informat...
2014-10-30 Jim ProcterJAL-674 helpful javadoc for remap method
2014-10-29 Jim ProcterJAL-674 JAL-1264 remap method to allow annotation posit...
2014-10-21 Jim ProcterJAL-1551 source formatting
2014-10-15 Jim ProcterJAL-348 JAL-674 JAL-1564 TODO and implementation error...
2014-10-15 Jim ProcterJAL-674 patch logic to test whether old and new sequenc...
2014-10-15 Jim ProcterJAL-674 JAL-1305 JAL-348 new liftOver method and test...
2014-07-18 j.procter@dundee... JAL-1520 switch between Protein and non-canonical RNA...
2014-06-06 Jim ProcterJAL-1520 fix unicode translation errors.
2014-06-06 Jim ProcterJAL-1517 source formatting
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2012-12-07 jprocterrevised renderer and annotation model to support differ...
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