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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / datamodel / Alignment.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-10-23 James ProcterMerge branch 'develop' into improvement/JAL-4124_dont_d... commit | commitdiff
2023-09-26 James ProcterJAL-3858 JAL-4090 avoid NPE when given out of bound... commit | commitdiff
2023-09-01 James ProcterJAL-4124 matrix is saved in dataset, with forward refer... commit | commitdiff
2023-05-22 James ProcterJAL-1551 spotless commit | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff
2023-05-18 James ProcterJAL-4134 colour by annotation needs distinct annotation... commit | commitdiff
2023-05-12 James ProcterJAL-2349 allow PAE or other contact matrices to hold... commit | commitdiff
2023-03-20 James ProcterJAL-2349 fix off by one when resolving columns for... commit | commitdiff
2023-02-27 James ProcterJAL-4134 allow tree groups to be stored/recovered on... commit | commitdiff
2022-10-20 Jim ProcterJAL-2349 JAL-3855 off by one and daft return commit | commitdiff
2022-10-20 Jim ProcterJAL-3855 JAL-2349 AlignmentI.getContactList takes care... commit | commitdiff
2022-10-17 Jim ProcterJAL-2349 JAL-3855 Integrate pAE retrieval in StructureF... commit | commitdiff
2022-10-15 Jim ProcterJAL-2349 reusable contact map holder for SequenceI... commit | commitdiff
2022-06-10 Jim ProcterJAL-4027 getter for contact matrices on the Alignment. commit | commitdiff
2022-06-10 Jim ProcterJAL-1551 formatting commit | commitdiff
2022-06-10 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2021-08-18 Jim ProcterJAL-2349 allow contact map to be associated with a... commit | commitdiff
2021-08-11 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into feature... commit | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge commit | commitdiff
2019-06-18 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into merge... commit | commitdiff
2019-04-18 hansonrminor code clean up commit | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... commit | commitdiff
2019-03-13 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3072scrollThread' into merge... commit | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3099alignmentVisibleWidth' into... commit | commitdiff
2019-01-29 hansonriterators commit | commitdiff
2018-11-28 gmungocJAL-3164 redraw complement overview on hide columns bug/JAL-3164complementOverview commit | commitdiff
2018-09-10 gmungocJAL-3099 new method AlignmentI.getVisibleWidth() commit | commitdiff
2018-07-25 gmungocJAL-3074 don't scroll up/down on drag out of scale... commit | commitdiff
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 commit | commitdiff
2018-02-21 Jim ProcterMerge branch 'bug/JAL-2778again' into releases/Release_... commit | commitdiff
2018-02-21 kiramtJAL-2778 Revert back to old synchronisation commit | commitdiff
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759 commit | commitdiff
2018-02-05 Jim ProcterJAL-2780 JAL-2781 - patch and first test for AlignmentI... commit | commitdiff
2018-02-05 kiramtJAL-2788 possible adjustments to sequence accesses commit | commitdiff
2018-01-26 kiramtJAL-2778 try another way to draw sequences with reduced... commit | commitdiff
2018-01-19 kiramtJAL-2759 Moved propagateInsertions out of HiddenColumns commit | commitdiff
2018-01-15 kiramtJAL-2759 Rename hideInsertionsFor to hideList, after... commit | commitdiff
2018-01-15 kiramtJAL-2759 Refactor of hideInsertionsFor after review commit | commitdiff
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) commit | commitdiff
2017-11-10 Jim ProcterJAL-2828 allow CalcId to match on String equivalence... doc/JAL-2494_JAL-2828_mergefindAnnotation commit | commitdiff
2017-11-10 Jim ProcterJAL-2828 refactored duplicate code for searching lists... commit | commitdiff
2017-11-01 kiramtJAL-2778 remove unnecessary code running in repaint 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
2017-07-24 gmungocspike branch updated from latest features/JAL-2446 commit | commitdiff
2017-06-27 gmungocMerge branch 'develop' into features/JAL-2446NCList commit | commitdiff
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-06-09 Jim ProcterMerge branch 'develop' into features/JAL-2349_matrixvis commit | commitdiff
2017-06-07 kiramtJAL-2591 More refactoring (incomplete) commit | commitdiff
2017-06-02 kiramtJAL-2576 Proposed fix bug/JAL-2576 commit | commitdiff
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup commit | commitdiff
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into commit | commitdiff
2017-04-27 Jim ProcterJAL-2494 fixed behaviour for null parameters in line... commit | commitdiff
2017-04-27 Jim ProcterJAL-2494 javadoc for AnnotatedCollectionI.findAnnotations commit | commitdiff
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... commit | commitdiff
2017-03-31 gmungocJAL-2405 additional checks for circular reference in... commit | commitdiff
2017-03-17 kiramtJAL-2437 Synchronization corrections and unit tests commit | commitdiff
2017-03-10 kiramtJAL-2437 Fixed reordering of sequences when hiding... commit | commitdiff
2017-03-07 kiramtJAL-2388 Missed commit commit | commitdiff
2017-03-03 kiramtJAL-2388 Initial removal of hidden cols/seqs out of... commit | commitdiff
2017-02-10 Jim ProcterMerge branch 'develop' into spike/matrix_annot commit | commitdiff
2017-01-23 Jim ProcterJAL-2349 ContactMatrixI provided max/min getters commit | commitdiff
2017-01-06 gmungocMerge branch 'develop' into features/JAL-2360colourSche... commit | commitdiff
2017-01-05 gmungocJAL-2374 fix popup out by one and multiple groups bugs commit | commitdiff
2016-12-14 gmungocJAL-2360 added check for null annotations array commit | commitdiff
2016-12-12 gmungocJAL-2360 simplify nucleotide flag, remove setter commit | commitdiff
2016-12-04 Jim ProcterJAL-2348 JAL-2349 make contact maps non-editable so... commit | commitdiff
2016-12-04 Jim ProcterJAL-2349 interfaces and logic for adding contact matric... commit | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge 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
2016-10-04 gmungocJAL-2232 JAL-2154 update dbrefs to newly created datase... commit | commitdiff
2016-09-22 gmungocJAL-2216 finalize() refactored so not called programmat... commit | commitdiff
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum commit | commitdiff
2016-08-22 Jim ProcterJAL-2154 always check dataset sequence for sequence... commit | commitdiff
2016-08-19 Jim ProcterJAL-2154 refactor setSequenceAt to replaceSequenceAt... commit | commitdiff
2016-08-07 Jim ProcterJAL-2154 add in missing class for createDatasetAlignmen... commit | commitdiff
2016-08-04 Jim ProcterJAL-2154 make sure all sequences referenced via DBRefEn... commit | commitdiff
2016-07-18 Jim ProcterJAL-2121 cleanup TODO commit | commitdiff
2016-07-14 Jim ProcterJAL-1115 change implementation to avoid possibility... commit | commitdiff
2016-07-14 Jim ProcterJAL-1270 test coverage TODO Alignment.append(AlignmentI) commit | commitdiff
2016-07-12 Jim ProcterJAL-2110 javadoc and TODO re shortcomings of implementation commit | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds commit | commitdiff
2016-07-04 gmungocJAL-2110 unused method removed commit | commitdiff
2016-06-20 Jim ProcterJAL-2110 copy alcodonframes only if copy constructor... commit | commitdiff
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview... commit | commitdiff
2016-06-16 Jim ProcterJAL-2110 todo - select mappings involving sequences... commit | commitdiff
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame... commit | commitdiff
2016-04-11 tcofoegbuJAL-2054 Renamed getStartEnd in AlignFrame to getVisibl... commit | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... commit | commitdiff
2015-12-22 gmungocJAL-653 realise virtual mappings and align when adding... commit | commitdiff
2015-12-03 gmungocJAL-653 mappings always reside on the dataset alignment... commit | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 commit | commitdiff
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