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JAL-3541 removed clover report generation debug flag (utf-8 encoding enforcement...
[jalview.git] / src / jalview / datamodel / Alignment.java
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... blob | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3072scrollThread' into merge... blob | commitdiff | diff to current
2019-03-04 gmungocMerge branch 'bug/JAL-3099alignmentVisibleWidth' into... blob | commitdiff | diff to current
2018-11-28 gmungocJAL-3164 redraw complement overview on hide columns bug/JAL-3164complementOverview blob | commitdiff | diff to current
2018-09-10 gmungocJAL-3099 new method AlignmentI.getVisibleWidth() blob | commitdiff | diff to current
2018-07-25 gmungocJAL-3074 don't scroll up/down on drag out of scale... blob | commitdiff | diff to current
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 blob | commitdiff | diff to current
2018-02-21 Jim ProcterMerge branch 'bug/JAL-2778again' into releases/Release_... blob | commitdiff | diff to current
2018-02-21 kiramtJAL-2778 Revert back to old synchronisation blob | commitdiff | diff to current
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759 blob | commitdiff | diff to current
2018-02-05 Jim ProcterJAL-2780 JAL-2781 - patch and first test for AlignmentI... blob | commitdiff | diff to current
2018-02-05 kiramtJAL-2788 possible adjustments to sequence accesses blob | commitdiff | diff to current
2018-01-26 kiramtJAL-2778 try another way to draw sequences with reduced... blob | commitdiff | diff to current
2018-01-19 kiramtJAL-2759 Moved propagateInsertions out of HiddenColumns blob | commitdiff | diff to current
2018-01-15 kiramtJAL-2759 Rename hideInsertionsFor to hideList, after... blob | commitdiff | diff to current
2018-01-15 kiramtJAL-2759 Refactor of hideInsertionsFor after review blob | commitdiff | diff to current
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) blob | commitdiff | diff to current
2017-11-10 Jim ProcterJAL-2828 allow CalcId to match on String equivalence... doc/JAL-2494_JAL-2828_mergefindAnnotation blob | commitdiff | diff to current
2017-11-10 Jim ProcterJAL-2828 refactored duplicate code for searching lists... blob | commitdiff | diff to current
2017-11-01 kiramtJAL-2778 remove unnecessary code running in repaint blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList blob | commitdiff | diff to current
2017-08-16 Jim ProcterJAL-2418 source formatting blob | commitdiff | diff to current
2017-07-24 gmungocspike branch updated from latest features/JAL-2446 blob | commitdiff | diff to current
2017-06-27 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2446 merged to spike branch blob | commitdiff | diff to current
2017-06-07 kiramtJAL-2591 More refactoring (incomplete) blob | commitdiff | diff to current
2017-06-02 kiramtJAL-2576 Proposed fix bug/JAL-2576 blob | commitdiff | diff to current
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup blob | commitdiff | diff to current
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into blob | commitdiff | diff to current
2017-04-27 Jim ProcterJAL-2494 fixed behaviour for null parameters in line... blob | commitdiff | diff to current
2017-04-27 Jim ProcterJAL-2494 javadoc for AnnotatedCollectionI.findAnnotations blob | commitdiff | diff to current
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... blob | commitdiff | diff to current
2017-03-31 gmungocJAL-2405 additional checks for circular reference in... blob | commitdiff | diff to current
2017-03-17 kiramtJAL-2437 Synchronization corrections and unit tests blob | commitdiff | diff to current
2017-03-10 kiramtJAL-2437 Fixed reordering of sequences when hiding... blob | commitdiff | diff to current
2017-03-07 kiramtJAL-2388 Missed commit blob | commitdiff | diff to current
2017-03-03 kiramtJAL-2388 Initial removal of hidden cols/seqs out of... blob | commitdiff | diff to current
2017-01-06 gmungocMerge branch 'develop' into features/JAL-2360colourSche... blob | commitdiff | diff to current
2017-01-05 gmungocJAL-2374 fix popup out by one and multiple groups bugs blob | commitdiff | diff to current
2016-12-14 gmungocJAL-2360 added check for null annotations array blob | commitdiff | diff to current
2016-12-12 gmungocJAL-2360 simplify nucleotide flag, remove setter blob | commitdiff | diff to current
2016-11-25 gmungocMerge branch 'develop' into trialMerge blob | commitdiff | diff to current
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults... blob | commitdiff | diff to current
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch blob | commitdiff | diff to current
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... blob | commitdiff | diff to current
2016-10-04 gmungocJAL-2232 JAL-2154 update dbrefs to newly created datase... blob | commitdiff | diff to current
2016-09-22 gmungocJAL-2216 finalize() refactored so not called programmat... blob | commitdiff | diff to current
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum blob | commitdiff | diff to current
2016-08-22 Jim ProcterJAL-2154 always check dataset sequence for sequence... blob | commitdiff | diff to current
2016-08-19 Jim ProcterJAL-2154 refactor setSequenceAt to replaceSequenceAt... blob | commitdiff | diff to current
2016-08-07 Jim ProcterJAL-2154 add in missing class for createDatasetAlignmen... blob | commitdiff | diff to current
2016-08-04 Jim ProcterJAL-2154 make sure all sequences referenced via DBRefEn... blob | commitdiff | diff to current
2016-07-18 Jim ProcterJAL-2121 cleanup TODO blob | commitdiff | diff to current
2016-07-14 Jim ProcterJAL-1115 change implementation to avoid possibility... blob | commitdiff | diff to current
2016-07-14 Jim ProcterJAL-1270 test coverage TODO Alignment.append(AlignmentI) blob | commitdiff | diff to current
2016-07-12 Jim ProcterJAL-2110 javadoc and TODO re shortcomings of implementation blob | commitdiff | diff to current
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds blob | commitdiff | diff to current
2016-07-04 gmungocJAL-2110 unused method removed blob | commitdiff | diff to current
2016-06-20 Jim ProcterJAL-2110 copy alcodonframes only if copy constructor... blob | commitdiff | diff to current
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview... blob | commitdiff | diff to current
2016-06-16 Jim ProcterJAL-2110 todo - select mappings involving sequences... blob | commitdiff | diff to current
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame... blob | commitdiff | diff to current
2016-04-11 tcofoegbuJAL-2054 Renamed getStartEnd in AlignFrame to getVisibl... blob | commitdiff | diff to current
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... blob | commitdiff | diff to current
2015-12-22 gmungocJAL-653 realise virtual mappings and align when adding... blob | commitdiff | diff to current
2015-12-03 gmungocJAL-653 mappings always reside on the dataset alignment... blob | commitdiff | diff to current
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 blob | commitdiff | diff to current
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports blob | commitdiff | diff to current
2015-07-30 tcofoegbuJAL-1443 modified exception notifications blob | commitdiff | diff to current
2015-07-21 tcofoegbuJAL-1443 bugfix to prevent loading of unidentifiable... blob | commitdiff | diff to current
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe... blob | commitdiff | diff to current
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch blob | commitdiff | diff to current
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... blob | commitdiff | diff to current
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... blob | commitdiff | diff to current
2015-01-09 Jim ProcterMerge branch 'JAL-1372_referenceseq' into feature_29... blob | commitdiff | diff to current
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 blob | commitdiff | diff to current
2014-12-15 Jim ProcterJAL-1620 version bump and release notes blob | commitdiff | diff to current
2014-11-28 gmungocJAL-1610 check reference annotations against alignment... blob | commitdiff | diff to current
2014-11-17 Jim Procterformatting blob | commitdiff | diff to current
2014-11-17 Jim ProcterJAL-1587 JAL-407 instrument setDataset to add dataset... blob | commitdiff | diff to current
2014-10-10 gmungocJAL-1264 reverted (removed added method) blob | commitdiff | diff to current
2014-10-08 gmungocMerge branch 'Release_2_8_2_Branch' into blob | commitdiff | diff to current
2014-10-07 gmungocJAL-1264 wip blob | commitdiff | diff to current
2014-09-27 darolmarJAL-1355 blob | commitdiff | diff to current
2014-09-23 darolmarJAL-1355 blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 source formatting blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 blob | commitdiff | diff to current
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 blob | commitdiff | diff to current
2014-05-22 Jim ProcterJAL-1503 update version in GPL header blob | commitdiff | diff to current
2014-05-02 Jim ProcterMerge branch 'Release_2_8_1_Branch' into JAL-1372_refer... blob | commitdiff | diff to current
2014-05-01 Jim ProcterJAL-1492 JAL-1397 make AnnotatedCollectionI context... blob | commitdiff | diff to current
2014-01-29 Jim ProcterJAL-1432 updated copyright notices blob | commitdiff | diff to current
2013-10-11 Jim ProcterJAL-1114 promote start/end attributes to gettable field... blob | commitdiff | diff to current
2013-08-30 Jim ProcterJAL-1367 promote the existing representative sequence... blob | commitdiff | diff to current
2013-06-23 Jim ProcterJAL-1230 proxy method for synchronising internal Alignm... blob | commitdiff | diff to current
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE blob | commitdiff | diff to current
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