Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git] / src / jalview / datamodel / AlignedCodonFrame.java
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence...
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positio...
2021-03-04 Jim ProcterRevert "Merge branch 'bug/JAL-3806_mappingCoversSequenc...
2021-01-28 gmungocJAL-3806 more lax allowance (3 positions) for stop...
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped...
2020-10-22 gmungocJAL-3763 failsafe check for null
2020-10-22 gmungocJAL-3763 refactored getCoveringMapping for virtual...
2020-10-22 gmungocJAL-3700 additions and corrections to unit tests
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests task/JAL-3763_newDatasetForCds
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped...
2020-10-15 gmungocJAL-3763 unused method removed
2020-10-08 gmungocJAL-3763 failsafe check for null
2020-10-08 gmungocJAL-3763 refactored getCoveringMapping for virtual...
2020-09-23 Jim ProcterJAL-3748 not testing for sequence’s containment in... bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2
2020-09-23 Jim ProcterJAL-3748 fix compilation error
2020-09-23 Jim ProcterJAL-3748 allow AlignedCodonFrame.covers to optionally...
2020-09-17 gmungocJAL-3700 additions and corrections to unit tests bug/JAL-3700_mapSequenceSelection
2020-09-16 Jim ProcterJAL-3748 make findAlignedSequence require mapped from...
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return...
2020-09-16 Jim ProcterJAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq...
2020-09-16 Jim ProcterJAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true...
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching...
2020-08-05 gmungocJAL-3700 fix for propagation of sort commands
2020-08-03 gmungocJAL-3700 check for 'covering' mapping when matching...
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
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
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-04 gmungocJAL-2110 defensive check in code
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs
2016-06-16 Jim ProcterJAL-2110 equals and hashcode should check fromSeq
2016-06-16 Jim ProcterJAL-2110 typo caused infinite loop
2016-06-14 gmungocJAL-1686 JAL-2110 equals and/or hashCode method added
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align...
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
2016-03-28 gmungocJAL-1705 Javadoc / debug output tweaks
2016-02-19 gmungocJAL-1705 handle case of sequence with no dataset sequence
2016-01-21 gmungocJAL-1705 isEmpty() and (debug) toString() methods added
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge...
2015-11-30 gmungocJAL-653 (experimental) methods to resolve dummy to...
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
2015-09-22 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-09-14 gmungocJAL-1880 handle sequence offsets properly when mapping...
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
2015-06-05 Jim ProcterJAL-1551 formatting
2015-04-14 gmungocJAL-1693 generate multiple exon sequences for 1-many...
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
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
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2013-06-17 Jim ProcterJAL-1312 patch for regression noticed after patch to...
2012-10-22 jprocterJalview 2.8 Source Header
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-09-27 jprocterapply version 2.7 copyright
2010-09-23 jprocterJalview 2.6 source licence
2010-04-30 jprocterjalview 2.5 release banner
2009-06-08 jprocterapply gpl development license
2008-09-04 jproctermerge from 2_4_Release branch
2007-12-21 jproctertemporary bugfix ?
2007-07-13 jproctermapping bug fixes
2007-06-17 jprocterAlignedCodonFrame holds mapping information between...