Merge branch 'bug/JAL-3567virtualFeatureCoordinates' into develop
[jalview.git] / src / jalview / datamodel /
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
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-25 gmungocJAL-2505 simplifying number of SequenceFeature construc...
2017-05-24 gmungocJAL-2505 make SequenceFeature type, begin, end, feature...
2017-05-24 gmungocJAL-2506 relocate Uniprot binding classes, bind to...
2017-05-24 gmungocJAL-2505 remove setters for SequenceFeature.begin,end...
2017-05-24 gmungocMerge branch 'bug/JAL-2541cutWithFeatures' into feature...
2017-05-24 gmungocJAL-2505 JAL-2542 SequenceFeatures.shift() to shift...
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup
2017-05-23 gmungocJAL-2490 tidy code and tests for feature export in...
2017-05-23 gmungocJAL-2480 methods to get features for group
2017-05-22 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-22 gmungocJAL-2480 always include all non-positional features...
2017-05-22 kiramtMerge remote-tracking branch 'origin/bug/JAL-2256'...
2017-05-22 Jim ProcterJAL-2418 patch build - broken htsjdk import
2017-05-18 Jim ProcterJAL-2388 return empty hidden columns for fully visible...
2017-05-18 gmungocJAL-2541 fix to initSeqFrom (and minor code tidy);...
2017-05-18 kiramtJAL-2256 Corrected AllCols/Rows iterator behaviour... bug/JAL-2256
2017-05-16 gmungocJAL-2505 unreachable code (for many years) removed
2017-05-16 gmungocJAL-2505 set helix number as feature group in SequenceF...
2017-05-16 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-16 kiramtJAL-2388 Rationalised hashCode method in HiddenColumns
2017-05-15 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s...
2017-05-12 gmungocJAL-2480 more efficient contains check on add; tidied...
2017-05-12 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into...
2017-05-11 Jim ProcterJAL-2507 test if an annotation is ‘whitespace’
2017-05-11 Jim ProcterJAL-2507 Annotation.EMPTY_ANNOTATION - non-null whitesp...
2017-05-09 gmungocJAL-2480 include sequenceFeatureStore in createDatasetS...
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final...
2017-05-08 gmungocJAL-2505 refactored SequenceFeature construction so...
2017-05-08 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-05 kiramtMerge remote-tracking branch
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into
2017-05-04 gmungocJAL-2505 delete and readd amended sequence feature
2017-05-04 gmungocJAL-2480 JAL-2505 guard against duplicating links
2017-05-03 Jim ProcterJAL-2503 AlignmentAnnotation.isQuantitative() test
2017-05-03 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-02 Jim ProcterMerge branch 'develop' into features/JAL-2393customMatrices
2017-05-02 Jim ProcterMerge branch 'bug/JAL-2424getVisibleContigs' into develop
2017-04-28 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-04-28 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-04-27 Jim ProcterJAL-2494 fix: updated behaviour for SequenceGroup.findA...
2017-04-27 Jim ProcterJAL-2494 fixed behaviour for null parameters in line...
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