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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / datamodel / Sequence.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2023-07-07 James ProcterJAL-4221 update description when transferring annotatio... commit | commitdiff
2023-05-25 James ProcterJAL-2381 copy and paste sequence also copies contact... 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
2023-05-14 James ProcterJAL-2349 fix up tests for Java 11 compatibility and... 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
2022-03-25 Jim ProcterJAL-3980 JAL-3979 TODOs bug/JAL-3980_JAL-3981_tooltips_sequence_details commit | commitdiff
2021-09-20 Jim ProcterJAL-3829 ensure nulls are not wildcards when retrieving... commit | commitdiff
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching... commit | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2020-02-27 Jim ProcterMerge branch 'bug/JAL-3296changeStartInvalidateCursor... commit | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-09-26 gmungocJAL-2481 remove code duplication left by merge commit | commitdiff
2019-07-30 gmungocJAL-3198 more efficient Sequence.getDisplayId() commit | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge commit | commitdiff
2019-06-10 gmungocJAL-3296 ensure sequence cursor reset when sequence... bug/JAL-3296changeStartInvalidateCursor commit | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... commit | commitdiff
2019-04-18 hansonrminor code clean up commit | commitdiff
2019-03-13 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2019-03-01 gmungocMerge branch 'feature/intervalStoreJ' into merge/JAL... commit | commitdiff
2019-02-28 gmungocJAL-3140 confine intervalstore imports to jalview.datam... commit | commitdiff
2019-02-04 hansonrrefactoring for DBMODList commit | commitdiff
2019-01-26 hansonrPlatform.timecheck calls removed or commented out. commit | commitdiff
2019-01-26 hansonrremoving cyclic call commit | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... commit | commitdiff
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures commit | commitdiff
2018-11-29 gmungocJAL-3140 NCList now via IntervalStore library commit | commitdiff
2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue... commit | commitdiff
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... commit | commitdiff
2018-01-29 kiramtJAL-2759 Fix unintended type change commit | commitdiff
2018-01-22 kiramtJAL-2579 Moved locateVisibleStartOfSequence to Sequence... commit | commitdiff
2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after... commit | commitdiff
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) commit | commitdiff
2017-11-22 gmungocMerge branch 'develop' into features/JAL-1793VCF commit | commitdiff
2017-11-21 kiramtMerge branch 'develop' into feature/JAL-2759 commit | commitdiff
2017-11-16 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures commit | commitdiff
2017-11-16 Jim ProcterMerge branch 'bug/JAL-2829deleteCharsWithGaps' into... commit | commitdiff
2017-11-15 gmungocJAL-2835 spike updated with latest commit | commitdiff
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF commit | commitdiff
2017-11-13 gmungocJAL-2176 removed unused Sequence.index commit | commitdiff
2017-11-13 gmungocMerge branch 'bug/JAL-2829deleteCharsWithGaps' into commit | commitdiff
2017-11-10 gmungocJAL-2829 fixes and unit tests bug/JAL-2829deleteCharsWithGaps commit | commitdiff
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759 commit | commitdiff
2017-11-06 Jim ProcterMerge branch 'bug/JAL-2541cutRelocateFeatures' into... commit | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest commit | commitdiff
2017-10-24 gmungocJAL-2738 tidy Javadoc, remove debug logging commit | commitdiff
2017-10-24 gmungocJAL-2738 update spike branch with latest commit | commitdiff
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd... commit | commitdiff
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2682parseId' into develop commit | commitdiff
2017-10-20 gmungocPush 1793 latest to spike branch commit | commitdiff
2017-10-11 gmungocJAL-2772 check array bounds for sequence access bug/JAL-2772pdbArrayBounds commit | commitdiff
2017-10-10 gmungocMerge branch 'develop' into features/JAL-1793VCF commit | commitdiff
2017-10-09 gmungocJAL-2480 use interface type for sequenceFeatureStore commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry commit | commitdiff
2017-09-26 gmungocJAL-2738 promote setGeneLoci to SequenceI! commit | commitdiff
2017-09-25 gmungocJAL-2738 getGeneLoci promoted to SequenceI commit | commitdiff
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes commit | commitdiff
2017-09-21 kiramtJAL-2674 Rewrote propagateInsertions commit | commitdiff
2017-09-21 gmungocJAL-2738 GeneLoci holds mapping of sequence to chromosome commit | commitdiff
2017-09-14 gmungocJAL-2541 length check in deleteChars (redoing lost... commit | commitdiff
2017-09-14 gmungocJAL-2541 working Cut/Undo with feature relocation commit | commitdiff
2017-09-14 gmungocJAL-2541 revised cut with features (work in progress) commit | commitdiff
2017-08-23 gmungocJAL-2682 non-regex sequence id parsing, and tests added 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
2017-06-24 gmungocJAL-2547 fix case of gap followed by enclosing contact... commit | commitdiff
2017-06-22 gmungocJAL-2481 JAL-2593 JAL-2526 further optimisation of... commit | commitdiff
2017-06-20 gmungocJAL-2526 don't retain lastColumnPosition from an invali... 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
2017-06-08 gmungocJAL-2526 correct boundary conditions for sequence left... commit | commitdiff
2017-06-08 gmungocJAL-2526 cache first/last residue column positions... commit | commitdiff
2017-06-06 gmungocJAL-2526 less stringent test for invalid cursor commit | commitdiff
2017-06-05 gmungocMerge branch 'features/JAL-2526sequenceCursor' into commit | commitdiff
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into commit | commitdiff
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor commit | commitdiff
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList commit | commitdiff
2017-06-04 Jim ProcterJAL-2291 bug fix - BitSet.set is [start,end+1) commit | commitdiff
2017-06-04 Jim ProcterJAL-2291 SequenceI.getInsertionsAsBits for convenient... commit | commitdiff
2017-06-02 gmungocJAL-2526 additional tests for findPosition with/without... commit | commitdiff
2017-06-01 gmungocJAL-2526 additional calls to sequenceChanged() after... commit | commitdiff
2017-06-01 gmungocJAL-2526 zapCursor() renamed sequenceChanged() commit | commitdiff
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn commit | commitdiff
2017-05-30 gmungocJAL-2526 first draft of findIndex/findPosition with... commit | commitdiff
2017-05-29 gmungocJAL-2526 Sequence.findPositions to get residue position... commit | commitdiff
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures commit | commitdiff
2017-05-24 gmungocMerge branch 'bug/JAL-2541cutWithFeatures' into feature... commit | commitdiff
2017-05-18 gmungocJAL-2541 fix to initSeqFrom (and minor code tidy);... commit | commitdiff
2017-05-09 gmungocJAL-2480 include sequenceFeatureStore in createDatasetS... commit | commitdiff
2017-04-27 gmungocJAL-2480 don't allow null type in SequenceFeature commit | commitdiff
2017-04-26 gmungocJAL-2490 findFeaturesAtRes with performant feature... commit | commitdiff
2017-04-19 gmungocJAL-2483 use SequenceFeatures to look up groups, types... commit | commitdiff
2017-04-18 gmungocJAL-2480 SequenceFeaturesI encapsulates features api commit | commitdiff
2017-04-17 gmungocJAL-2446 add call to SequenceFeatures.delete(); use... commit | commitdiff
2017-03-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-653_JAL-1766_htslib_refseqsupport commit | commitdiff
2017-03-20 gmungocJAL-2446 FeatureStore with NCList - work in progress commit | commitdiff
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