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Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git] / src / jalview / datamodel / Sequence.java
2023-01-30 Jim ProcterMerge branch 'JAL-3878_ws-overhaul-3' into with_ws_over... blob | commitdiff
2022-12-14 Jim ProcterMerge branch 'develop' into update_212_Dec_merge_with_2... blob | commitdiff | diff to current
2022-11-21 Jim ProcterMerge commit 'alpha/update_2_12_for_2_11_2_series_merge... blob | commitdiff | diff to current
2022-04-05 Mateusz WarownyJAL-3878 Add char[] constructor to Sequence blob | commitdiff | diff to current
2022-03-25 Jim ProcterJAL-3980 JAL-3979 TODOs bug/JAL-3980_JAL-3981_tooltips_sequence_details blob | commitdiff | diff to current
2021-09-20 Jim ProcterJAL-3829 ensure nulls are not wildcards when retrieving... blob | commitdiff | diff to current
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching... blob | commitdiff | diff to current
2020-05-18 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... blob | commitdiff | diff to current
2020-04-23 Jim ProcterMerge branch 'develop' into alpha/JAL-3362_Jalview_212_... blob | commitdiff | diff to current
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop blob | commitdiff | diff to current
2020-02-27 Jim ProcterMerge branch 'bug/JAL-3296changeStartInvalidateCursor... blob | commitdiff | diff to current
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop blob | commitdiff | diff to current
2019-09-26 Jim ProcterJAL-3070 allow SequenceI.findPositions(0,column+1)... blob | commitdiff | diff to current
2019-09-26 gmungocJAL-2481 remove code duplication left by merge blob | commitdiff | diff to current
2019-08-13 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... blob | commitdiff | diff to current
2019-07-30 gmungocJAL-3198 more efficient Sequence.getDisplayId() blob | commitdiff | diff to current
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge blob | commitdiff | diff to current
2019-07-10 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... blob | commitdiff | diff to current
2019-06-10 gmungocJAL-3296 ensure sequence cursor reset when sequence... bug/JAL-3296changeStartInvalidateCursor blob | commitdiff | diff to current
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... blob | commitdiff | diff to current
2019-06-04 Jim ProcterMerge branch 'develop' into developtomchmmer blob | commitdiff | diff to current
2019-04-18 hansonrminor code clean up blob | commitdiff | diff to current
2019-03-13 gmungocMerge branch 'develop' into trialMerge blob | commitdiff | diff to current
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
2019-02-04 hansonrrefactoring for DBMODList blob | commitdiff | diff to current
2019-01-26 hansonrPlatform.timecheck calls removed or commented out. blob | commitdiff | diff to current
2019-01-26 hansonrremoving cyclic call blob | commitdiff | diff to current
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... 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 gmungocMerge branch 'develop' into features/mchmmer blob | commitdiff | diff to current
2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue... blob | commitdiff | diff to current
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe... blob | commitdiff | diff to current
2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications blob | commitdiff | diff to current
2018-03-16 gmungocMerge branch 'develop' into trialMerge blob | commitdiff | diff to current
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... blob | commitdiff | diff to current
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip) blob | commitdiff | diff to current
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file... blob | commitdiff | diff to current
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly blob | commitdiff | diff to current
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc blob | commitdiff | diff to current
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and... blob | commitdiff | diff to current
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer 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
2017-08-29 osboxesJAL-2629 HMMs dropped on the alignment now map to the... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild... 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
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer blob | commitdiff | diff to current
2017-08-16 Jim ProcterJAL-2418 source formatting blob | commitdiff | diff to current
2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group blob | commitdiff | diff to current
2017-08-10 TZVanaaltenJAL-2629 hmmalign now correctly creates a new frame blob | commitdiff | diff to current
2017-08-08 TZVanaaltenJAL-2599 fix for index issue on node lookup blob | commitdiff | diff to current
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment blob | commitdiff | diff to current
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder... 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
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