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JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings
[jalview.git] / src / jalview / datamodel / Sequence.java
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... blob | commitdiff
2019-03-01 gmungocMerge branch 'feature/intervalStoreJ' into merge/JAL... blob | commitdiff | diff to current
2019-02-28 gmungocJAL-3140 confine intervalstore imports to jalview.datam... blob | commitdiff | diff to current
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures blob | commitdiff | diff to current
2018-11-29 gmungocJAL-3140 NCList now via IntervalStore library blob | commitdiff | diff to current
2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue... blob | commitdiff | diff to current
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... blob | commitdiff | diff to current
2018-01-29 kiramtJAL-2759 Fix unintended type change blob | commitdiff | diff to current
2018-01-22 kiramtJAL-2579 Moved locateVisibleStartOfSequence to Sequence... blob | commitdiff | diff to current
2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after... blob | commitdiff | diff to current
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) blob | commitdiff | diff to current
2017-11-22 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-11-21 kiramtMerge branch 'develop' into feature/JAL-2759 blob | commitdiff | diff to current
2017-11-16 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures blob | commitdiff | diff to current
2017-11-16 Jim ProcterMerge branch 'bug/JAL-2829deleteCharsWithGaps' into... blob | commitdiff | diff to current
2017-11-15 gmungocJAL-2835 spike updated with latest blob | commitdiff | diff to current
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-11-13 gmungocJAL-2176 removed unused Sequence.index blob | commitdiff | diff to current
2017-11-13 gmungocMerge branch 'bug/JAL-2829deleteCharsWithGaps' into blob | commitdiff | diff to current
2017-11-10 gmungocJAL-2829 fixes and unit tests bug/JAL-2829deleteCharsWithGaps blob | commitdiff | diff to current
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759 blob | commitdiff | diff to current
2017-11-06 Jim ProcterMerge branch 'bug/JAL-2541cutRelocateFeatures' into... blob | commitdiff | diff to current
2017-10-27 gmungocJAL-1793 spike branch updated to latest blob | commitdiff | diff to current
2017-10-24 gmungocJAL-2738 tidy Javadoc, remove debug logging blob | commitdiff | diff to current
2017-10-24 gmungocJAL-2738 update spike branch with latest blob | commitdiff | diff to current
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd... blob | commitdiff | diff to current
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2682parseId' into develop blob | commitdiff | diff to current
2017-10-20 gmungocPush 1793 latest to spike branch blob | commitdiff | diff to current
2017-10-11 gmungocJAL-2772 check array bounds for sequence access bug/JAL-2772pdbArrayBounds blob | commitdiff | diff to current
2017-10-10 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-10-09 gmungocJAL-2480 use interface type for sequenceFeatureStore blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry blob | commitdiff | diff to current
2017-09-26 gmungocJAL-2738 promote setGeneLoci to SequenceI! blob | commitdiff | diff to current
2017-09-25 gmungocJAL-2738 getGeneLoci promoted to SequenceI blob | commitdiff | diff to current
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes blob | commitdiff | diff to current
2017-09-21 kiramtJAL-2674 Rewrote propagateInsertions blob | commitdiff | diff to current
2017-09-21 gmungocJAL-2738 GeneLoci holds mapping of sequence to chromosome blob | commitdiff | diff to current
2017-09-14 gmungocJAL-2541 length check in deleteChars (redoing lost... blob | commitdiff | diff to current
2017-09-14 gmungocJAL-2541 working Cut/Undo with feature relocation blob | commitdiff | diff to current
2017-09-14 gmungocJAL-2541 revised cut with features (work in progress) blob | commitdiff | diff to current
2017-08-23 gmungocJAL-2682 non-regex sequence id parsing, and tests added 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
2017-06-24 gmungocJAL-2547 fix case of gap followed by enclosing contact... blob | commitdiff | diff to current
2017-06-22 gmungocJAL-2481 JAL-2593 JAL-2526 further optimisation of... blob | commitdiff | diff to current
2017-06-20 gmungocJAL-2526 don't retain lastColumnPosition from an invali... 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
2017-06-08 gmungocJAL-2526 correct boundary conditions for sequence left... blob | commitdiff | diff to current
2017-06-08 gmungocJAL-2526 cache first/last residue column positions... blob | commitdiff | diff to current
2017-06-06 gmungocJAL-2526 less stringent test for invalid cursor blob | commitdiff | diff to current
2017-06-05 gmungocMerge branch 'features/JAL-2526sequenceCursor' into blob | commitdiff | diff to current
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into blob | commitdiff | diff to current
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor blob | commitdiff | diff to current
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-06-04 Jim ProcterJAL-2291 bug fix - BitSet.set is [start,end+1) blob | commitdiff | diff to current
2017-06-04 Jim ProcterJAL-2291 SequenceI.getInsertionsAsBits for convenient... blob | commitdiff | diff to current
2017-06-02 gmungocJAL-2526 additional tests for findPosition with/without... blob | commitdiff | diff to current
2017-06-01 gmungocJAL-2526 additional calls to sequenceChanged() after... blob | commitdiff | diff to current
2017-06-01 gmungocJAL-2526 zapCursor() renamed sequenceChanged() blob | commitdiff | diff to current
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn blob | commitdiff | diff to current
2017-05-30 gmungocJAL-2526 first draft of findIndex/findPosition with... blob | commitdiff | diff to current
2017-05-29 gmungocJAL-2526 Sequence.findPositions to get residue position... blob | commitdiff | diff to current
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures blob | commitdiff | diff to current
2017-05-24 gmungocMerge branch 'bug/JAL-2541cutWithFeatures' into feature... blob | commitdiff | diff to current
2017-05-18 gmungocJAL-2541 fix to initSeqFrom (and minor code tidy);... blob | commitdiff | diff to current
2017-05-09 gmungocJAL-2480 include sequenceFeatureStore in createDatasetS... blob | commitdiff | diff to current
2017-04-27 gmungocJAL-2480 don't allow null type in SequenceFeature blob | commitdiff | diff to current
2017-04-26 gmungocJAL-2490 findFeaturesAtRes with performant feature... blob | commitdiff | diff to current
2017-04-19 gmungocJAL-2483 use SequenceFeatures to look up groups, types... blob | commitdiff | diff to current
2017-04-18 gmungocJAL-2480 SequenceFeaturesI encapsulates features api blob | commitdiff | diff to current
2017-04-17 gmungocJAL-2446 add call to SequenceFeatures.delete(); use... blob | commitdiff | diff to current
2017-03-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-653_JAL-1766_htslib_refseqsupport blob | commitdiff | diff to current
2017-03-20 gmungocJAL-2446 FeatureStore with NCList - work in progress blob | commitdiff | diff to current
2016-11-14 gmungocJAL-2296 report whether SequenceFeature actually added... 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
2016-10-05 Jim ProcterJAL-2189 source formatting blob | commitdiff | diff to current
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad... blob | commitdiff | diff to current
2016-09-28 Jim ProcterJAL-2235 raise exceptions if self reference or referenc... blob | commitdiff | diff to current
2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries blob | commitdiff | diff to current
2016-09-27 Jim ProcterJAL-2210 promote direct dbrefs from verified sources... blob | commitdiff | diff to current
2016-09-27 Jim ProcterJAL-2210 resolve todo - addDBRef adds to dataset sequen... blob | commitdiff | diff to current
2016-09-16 gmungocJAL-2157 JAL-1803 refactored Sequence.updatePDBIds... blob | commitdiff | diff to current
2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry blob | commitdiff | diff to current
2016-09-06 gmungocJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid... blob | commitdiff | diff to current
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs blob | commitdiff | diff to current
2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:... blob | commitdiff | diff to current
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings blob | commitdiff | diff to current
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB blob | commitdiff | diff to current
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision... blob | commitdiff | diff to current
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... blob | commitdiff | diff to current
2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that... blob | commitdiff | diff to current
2016-08-04 Jim ProcterJAL-2046 stack trace for implementation warning blob | commitdiff | diff to current
2016-08-02 Jim ProcterJAL-2046 additional logic to suppress spurious implemen... blob | commitdiff | diff to current
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method blob | commitdiff | diff to current
2016-05-31 gmungocJAL-2110 refactor + tests to allow a dbref version... blob | commitdiff | diff to current
2016-04-05 Jim ProcterJAL-2046 add/delete SequenceFeature operate on dataset... blob | commitdiff | diff to current
2016-04-05 Jim ProcterJAL-2046 setSequenceFeature contract implementation... blob | commitdiff | diff to current
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