JAL-3141 Moved 'Previously saved scheme' combo box preference out to 'Cancel changes...
[jalview.git] / src / jalview / datamodel /
2017-09-25 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-09-25 gmungocJAL-2525 return no features if none matches ontology...
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes
2017-09-22 kiramtJAL-2674 add bounds to findHiddenRegionPositions
2017-09-21 kiramtJAL-2674 Rewrote propagateInsertions
2017-09-21 gmungocJAL-2738 GeneLoci holds mapping of sequence to chromosome
2017-09-20 kiramtJAL-2674 fix up interface of locateVisibleBoundsOfSequence
2017-09-14 gmungocJAL-2541 save/Undo only 'diffs' for features with Cut...
2017-09-14 gmungocJAL-2541 length check in deleteChars (redoing lost...
2017-09-14 gmungocJAL-2541 working Cut/Undo with feature relocation
2017-09-14 gmungocJAL-2541 revised cut with features (work in progress)
2017-09-05 Jim ProcterMerge branch 'master' into portforward/JAL-2675_2102b1t...
2017-09-04 Jim ProcterJAL-2675 source license
2017-09-03 Jim ProcterMerge branch 'bug/JAL-2665-2.10.2b' into documentation... bug/JAL-2673_mergewithproblem
2017-09-03 Jim ProcterMerge branch 'documentation/JAL-2675_release2102b1...
2017-09-03 Jim ProcterMerge branch 'feature/JAL-2527' into documentation...
2017-09-01 gmungocJAL-2488 remove finalize methods
2017-08-30 kiramtMerge branch 'feature/JAL-2664' into feature/JAL-2527
2017-08-29 kiramtJAL-2664 Updates following review feature/JAL-2664
2017-08-28 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-08-28 kiramtMerge remote-tracking branch 'origin/releases/Release_2...
2017-08-28 kiramtJAL-2665 Changes for review comments; printing with... bug/JAL-2665
2017-08-23 gmungocJAL-2682 non-regex sequence id parsing, and tests added
2017-08-22 Jim ProcterJAL-1551 formatting
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-08-16 kiramtJAL-2665 Added hidden columns group selection - almost...
2017-08-16 kiramtJAL-2665 Added sequence group update event.
2017-08-09 gmungocJAL-2480 inline one method, improve comments
2017-08-01 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-07-24 gmungocspike branch updated from latest features/JAL-2446
2017-07-22 kiramtMerge branch 'develop' into feature/JAL-2611
2017-07-19 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-07-13 kiramtJAL-2613 Unit tests and a fix. Phew.
2017-07-05 gmungocJAL-147 additions to unit test, check for negative...
2017-07-05 gmungocJAL-147 prevent overview box move up over hidden first...
2017-06-30 gmungocJAL-2505 correct handling of change of feature type
2017-06-30 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-29 kiramtJAL-2597 Fix and unit test bug/JAL-2597
2017-06-27 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-24 gmungocMerge branch 'features/JAL-2446NCList' into spikes...
2017-06-24 gmungocJAL-2547 fix case of gap followed by enclosing contact...
2017-06-24 gmungocMerge branch 'features/JAL-2446NCList' into spikes...
2017-06-23 gmungocJAL-1858 handle hidden columns when computing region...
2017-06-22 gmungocJAL-2481 JAL-2593 JAL-2526 further optimisation of...
2017-06-22 gmungocJAL-2480 simpler and safer test to avoid adding duplicates
2017-06-21 gmungocJAL-2480 tidy generic initialisations, SequenceFeatures...
2017-06-20 gmungocJAL-2526 don't retain lastColumnPosition from an invali...
2017-06-15 gmungocMerge branch 'bug/JAL-2386groupConservationColouring...
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-12 kiramtJAL-2591 Updates following code review
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-09 gmungocJAL-2480 tidy javadoc
2017-06-08 gmungocJAL-2526 correct boundary conditions for sequence left...
2017-06-08 gmungocJAL-2386 JAL-2570 use ResidueShader copy constructor... bug/JAL-2386groupConservationColouring
2017-06-08 kiramtJAL-2591 Refactor HiddenColumns to use ArrayList instea...
2017-06-08 kiramtJAL-2591 More HiddenColumns refactoring. Tests passing.
2017-06-08 gmungocJAL-2526 cache first/last residue column positions...
2017-06-08 gmungocJAL-2526 reuse findIndex result if start==end
2017-06-07 kiramtJAL-2591 Further refactoring (still incomplete)
2017-06-07 kiramtJAL-2591 More refactoring (incomplete)
2017-06-07 kiramtJAL-2591 Hidden columns regions can be output to string...
2017-06-07 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-07 kiramtJAL-2591 updated HiddenColumns::findHiddenRegionPositio...
2017-06-07 gmungocJAL-2386 ensure group conservation shading is applied...
2017-06-07 kiramtJAL-2591 simplifying hidden columns usage
2017-06-06 kiramtJAL-2591 Added readwrite locking on HiddenColumns
2017-06-06 gmungocJAL-2526 less stringent test for invalid cursor
2017-06-06 kiramtMerge remote-tracking branch 'origin/bug/JAL-2576'...
2017-06-05 Jim ProcterMerge branch 'bug/JAL-2576' into develop
2017-06-05 gmungocJAL-2505 comments updated
2017-06-05 gmungocJAL-2480 remove redundant method, further test coverage
2017-06-05 gmungocJAL-2505 explicit (and final) contactFeature property
2017-06-05 gmungocMerge branch 'features/JAL-2526sequenceCursor' into
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-04 Jim ProcterJAL-2291 get bitset representing hidden columns
2017-06-04 Jim ProcterJAL-2291 method taking a BitSet for hiding columns
2017-06-04 Jim ProcterJAL-2291 bug fix - BitSet.set is [start,end+1)
2017-06-04 Jim ProcterJAL-2291 SequenceI.getInsertionsAsBits for convenient...
2017-06-02 gmungocJAL-2526 additional tests for findPosition with/without...
2017-06-02 kiramtJAL-2576 Proposed fix bug/JAL-2576
2017-06-02 gmungocMerge branch 'features/JAL-2446NCList' into features...
2017-06-01 gmungocJAL-2526 additional calls to sequenceChanged() after...
2017-06-01 gmungocJAL-2526 zapCursor() renamed sequenceChanged()
2017-06-01 gmungocMerge branch 'features/JAL-2446NCList' into features...
2017-06-01 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn
2017-05-31 Jim ProcterMerge branch 'JAL-2571' into develop
2017-05-30 kiramtJAL-2571 Corrected alignment width/height checks to...
2017-05-30 gmungocMerge branch 'features/JAL-2446NCList' into features...
2017-05-30 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-30 gmungocJAL-2570 don't zap group colour scheme when mapping...
2017-05-30 gmungocJAL-2526 first draft of findIndex/findPosition with...
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2034contextchange' into develop
2017-05-29 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-29 gmungocJAL-2526 Sequence.findPositions to get residue position...
2017-05-27 Jim ProcterJAL-2562 javadoc TODO
2017-05-26 gmungocJAL-2480 move ContiguousI and Range to jalview.datamodel
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