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

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

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