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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git] / src /
2017-06-12 gmungocJAL-2577 mirror hide/select columns by annotation acros... tree | commitdiff
2017-06-09 gmungocJAL-2589 render colour scheme gap colour in overview bug/JAL-2589gapColour tree | commitdiff
2017-06-09 gmungocJAL-2594 avoid stack trace creating feature on gapped... tree | commitdiff
2017-06-09 gmungocJAL-2480 tidy javadoc tree | commitdiff
2017-06-09 gmungocJAL-2593 avoid redundant rendering of co-located features tree | commitdiff
2017-06-08 gmungocJAL-2526 correct boundary conditions for sequence left... tree | commitdiff
2017-06-08 gmungocJAL-2386 JAL-2570 use ResidueShader copy constructor... bug/JAL-2386groupConservationColouring tree | commitdiff
2017-06-08 kiramtMerge branch 'bug/JAL-2586' into develop tree | commitdiff
2017-06-08 kiramtJAL-2586 Clarification to URL link code bug/JAL-2586 tree | commitdiff
2017-06-08 kiramtJAL-2591 made redraw volatile tree | commitdiff
2017-06-08 kiramtJAL-2591 Refactor HiddenColumns to use ArrayList instea... tree | commitdiff
2017-06-08 kiramtJAL-2591 More HiddenColumns refactoring. Tests passing. tree | commitdiff
2017-06-08 gmungocJAL-2526 cache first/last residue column positions... tree | commitdiff
2017-06-08 gmungocJAL-2526 setStatusMessage avoid redundant findPosition... tree | commitdiff
2017-06-08 gmungocJAL-2526 reuse findIndex result if start==end tree | commitdiff
2017-06-07 kiramtJAL-2591 Further refactoring (still incomplete) tree | commitdiff
2017-06-07 kiramtJAL-2591 More refactoring (incomplete) tree | commitdiff
2017-06-07 kiramtJAL-2591 Hidden columns regions can be output to string... tree | commitdiff
2017-06-07 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-07 kiramtJAL-2591 updated HiddenColumns::findHiddenRegionPositio... tree | commitdiff
2017-06-07 kiramtJAL-2591 Overview changes ported to applet tree | commitdiff
2017-06-07 kiramtJAL-2591 More rationalising of hiddencols tree | commitdiff
2017-06-07 gmungocJAL-2386 ensure group conservation shading is applied... tree | commitdiff
2017-06-07 kiramtJAL-2591 Increased granularity of overview panel update... tree | commitdiff
2017-06-07 kiramtJAL-2591 simplifying hidden columns usage tree | commitdiff
2017-06-06 kiramtJAL-2591 Removed getHiddenRegions()==null checks which... tree | commitdiff
2017-06-06 kiramtJAL-2591 Added readwrite locking on HiddenColumns tree | commitdiff
2017-06-06 gmungocJAL-2589 correct colour for Gap in Score and User Defin... tree | commitdiff
2017-06-06 gmungocJAL-2526 less stringent test for invalid cursor tree | commitdiff
2017-06-06 kiramtMerge remote-tracking branch 'origin/bug/JAL-2576'... tree | commitdiff
2017-06-05 Jim ProcterJAL-2590 patch for rendering eggnog trees with polytomi... tree | commitdiff
2017-06-05 Jim ProcterMerge branch 'bug/JAL-2576' into develop tree | commitdiff
2017-06-05 kiramtJAL-2586 Checkstyle flagged fix of unintended fall... tree | commitdiff
2017-06-05 gmungocJAL-2505 comments updated tree | commitdiff
2017-06-05 gmungocJAL-2480 remove redundant method, further test coverage tree | commitdiff
2017-06-05 gmungocJAL-2505 explicit (and final) contactFeature property tree | commitdiff
2017-06-05 gmungocMerge branch 'features/JAL-2526sequenceCursor' into tree | commitdiff
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into tree | commitdiff
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor tree | commitdiff
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-04 Jim ProcterJAL-2228 java 1.7 compliance tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 only hide/show columns intersecting with curre... tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 get bitset representing hidden columns tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 use HiddenColumns.hideMarkedBits and take... tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 method taking a BitSet for hiding columns tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 bug fix - BitSet.set is [start,end+1) tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 ‘Hide Insertions’ now operates on selection... tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 SequenceI.getInsertionsAsBits for convenient... tree | commitdiff
2017-06-04 Jim ProcterJAL-2582 comment about IDs being lost if they resembl... tree | commitdiff
2017-06-04 Jim ProcterJAL-2582 recognise ENS…P peptide IDs and make two getPa... tree | commitdiff
2017-06-02 Jim ProcterMerge branch 'bug/JAL-2578' into develop tree | commitdiff
2017-06-02 Jim ProcterMerge branch 'bug/JAL-2577' into develop tree | commitdiff
2017-06-02 Jim ProcterMerge branch 'features/JAL-2228_featureSetCounts_minRan... tree | commitdiff
2017-06-02 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-06-02 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-06-02 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-02 gmungocJAL-2526 additional tests for findPosition with/without... tree | commitdiff
2017-06-02 tcofoegbuJAL-2473 revised default minimum dimension for Alignmen... tree | commitdiff
2017-06-02 Jim ProcterJAL-2228 always create zero score annotations, since... tree | commitdiff
2017-06-02 Jim ProcterJAL-2228 always set minimum for count to zero for annot... tree | commitdiff
2017-06-02 kiramtJAL-2576 Proposed fix bug/JAL-2576 tree | commitdiff
2017-06-02 kiramtJAL-2577 Don't allow viewport ranges below 0. Unit... bug/JAL-2577 tree | commitdiff
2017-06-02 kiramtJAL-2578 Moved hidden columns reveal to before selectio... bug/JAL-2578 tree | commitdiff
2017-06-02 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-06-01 gmungocJAL-2526 additional calls to sequenceChanged() after... tree | commitdiff
2017-06-01 gmungocJAL-2526 zapCursor() renamed sequenceChanged() tree | commitdiff
2017-06-01 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-06-01 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn tree | commitdiff
2017-06-01 Jim ProcterMerge branch 'features/JAL-1648_cache_user_inputs'... tree | commitdiff
2017-05-31 Jim ProcterMerge branch 'JAL-2571' into develop tree | commitdiff
2017-05-31 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-05-31 gmungocJAL-2483 JAL-2575 don't sort newly discovered features tree | commitdiff
2017-05-31 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2017-05-31 tcofoegbuFixed failing tests tree | commitdiff
2017-05-31 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-05-31 gmungocJAL-2574 preparation for Sequence.findFeatures(col1... tree | commitdiff
2017-05-31 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-31 gmungocJAL-2547 handle contact features 'around' a gap correctly tree | commitdiff
2017-05-30 kiramtJAL-2573 Fixes for alignment < viewport width, and... JAL-2571 tree | commitdiff
2017-05-30 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-05-30 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-30 gmungocJAL-2547 tooltip/AmendFeatures on gap straddled by... tree | commitdiff
2017-05-30 kiramtJAL-2571 Corrected alignment width/height checks to... tree | commitdiff
2017-05-30 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-05-30 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-30 gmungocJAL-2570 don't zap group colour scheme when mapping... tree | commitdiff
2017-05-30 gmungocJAL-2526 first draft of findIndex/findPosition with... tree | commitdiff
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2034contextchange' into develop tree | commitdiff
2017-05-29 tcofoegbuJAL-1648 improvement on finder searchbox keyboard contr... tree | commitdiff
2017-05-29 Jim ProcterMerge branch 'features/JAL-2465_No-mapping_Jmol-structu... tree | commitdiff
2017-05-29 Jim ProcterJAL-2533 update javadoc features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url tree | commitdiff
2017-05-29 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-29 tcofoegbuJAL-1648 code fix - enter key should pick selected... tree | commitdiff
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2536' into develop tree | commitdiff
2017-05-29 Jim ProcterJAL-2536 tweak javadoc wording tree | commitdiff
2017-05-29 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-29 gmungocJAL-2526 Sequence.findPositions to get residue position... tree | commitdiff
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2517cancelAppletColour' into... tree | commitdiff
2017-05-27 Jim ProcterMerge branch 'bug/JAL-2491' into develop tree | commitdiff
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