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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / datamodel / AlignedCodonFrame.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2 commit | commitdiff
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence... commit | commitdiff
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positio... commit | commitdiff
2021-03-04 Jim ProcterRevert "Merge branch 'bug/JAL-3806_mappingCoversSequenc... commit | commitdiff
2021-01-28 gmungocJAL-3806 more lax allowance (3 positions) for stop... commit | commitdiff
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests commit | commitdiff
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped... commit | commitdiff
2020-10-22 gmungocJAL-3763 failsafe check for null commit | commitdiff
2020-10-22 gmungocJAL-3763 refactored getCoveringMapping for virtual... commit | commitdiff
2020-10-22 gmungocJAL-3700 additions and corrections to unit tests commit | commitdiff
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests task/JAL-3763_newDatasetForCds commit | commitdiff
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped... commit | commitdiff
2020-10-15 gmungocJAL-3763 unused method removed commit | commitdiff
2020-10-08 gmungocJAL-3763 failsafe check for null commit | commitdiff
2020-10-08 gmungocJAL-3763 refactored getCoveringMapping for virtual... commit | commitdiff
2020-09-23 Jim ProcterJAL-3748 not testing for sequence’s containment in... bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2 commit | commitdiff
2020-09-23 Jim ProcterJAL-3748 fix compilation error commit | commitdiff
2020-09-23 Jim ProcterJAL-3748 allow AlignedCodonFrame.covers to optionally... commit | commitdiff
2020-09-17 gmungocJAL-3700 additions and corrections to unit tests bug/JAL-3700_mapSequenceSelection commit | commitdiff
2020-09-16 Jim ProcterJAL-3748 make findAlignedSequence require mapped from... commit | commitdiff
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return... commit | commitdiff
2020-09-16 Jim ProcterJAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq... commit | commitdiff
2020-09-16 Jim ProcterJAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true... commit | commitdiff
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands commit | commitdiff
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching... commit | commitdiff
2020-08-05 gmungocJAL-3700 fix for propagation of sort commands commit | commitdiff
2020-08-03 gmungocJAL-3700 check for 'covering' mapping when matching... commit | commitdiff
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript commit | commitdiff
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct... commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo 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
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... commit | commitdiff
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults... 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
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds commit | commitdiff
2016-07-04 gmungocJAL-2110 defensive check in code commit | commitdiff
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs commit | commitdiff
2016-06-16 Jim ProcterJAL-2110 equals and hashcode should check fromSeq commit | commitdiff
2016-06-16 Jim ProcterJAL-2110 typo caused infinite loop commit | commitdiff
2016-06-14 gmungocJAL-1686 JAL-2110 equals and/or hashCode method added commit | commitdiff
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align... commit | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... commit | commitdiff
2016-03-28 gmungocJAL-1705 Javadoc / debug output tweaks commit | commitdiff
2016-02-19 gmungocJAL-1705 handle case of sequence with no dataset sequence commit | commitdiff
2016-01-21 gmungocJAL-1705 isEmpty() and (debug) toString() methods added commit | commitdiff
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge... commit | commitdiff
2015-11-30 gmungocJAL-653 (experimental) methods to resolve dummy to... 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
2015-09-22 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch commit | commitdiff
2015-09-14 gmungocJAL-1880 handle sequence offsets properly when mapping... 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
2015-06-05 Jim ProcterJAL-1551 formatting commit | commitdiff
2015-04-14 gmungocJAL-1693 generate multiple exon sequences for 1-many... 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
2014-12-15 Jim ProcterJAL-1620 version bump and release notes 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
2014-05-22 Jim ProcterJAL-1503 update version in GPL header commit | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices commit | commitdiff
2013-06-17 Jim ProcterJAL-1312 patch for regression noticed after patch to... commit | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header commit | commitdiff
2011-10-10 jprocterupdate author list in license for (JAL-826) commit | commitdiff
2011-09-27 jprocterapply version 2.7 copyright commit | commitdiff
2010-09-23 jprocterJalview 2.6 source licence commit | commitdiff
2010-04-30 jprocterjalview 2.5 release banner commit | commitdiff
2009-06-08 jprocterapply gpl development license commit | commitdiff
2008-09-04 jproctermerge from 2_4_Release branch commit | commitdiff
2007-12-21 jproctertemporary bugfix ? commit | commitdiff
2007-07-13 jproctermapping bug fixes commit | commitdiff
2007-06-17 jprocterAlignedCodonFrame holds mapping information between... commit | commitdiff