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jalview.git
2018-02-15 Jim ProcterJAL-2906 bump release version and cut new release note... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2780 scan all test IDs before testing and reporting... bugs/JAL-2780_JAL-2781_pdbnegativenums commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2780 SequenceI.findFeatures takes column numbers... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2780 JAL-2781 don’t create a mapping if sequence... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2780 JAL-2781 only create a mapping entry or write... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2781 JAL-2780 include sequence start number when... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2781 ensure Trim is disabled before test starts commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2781 refactor ‘trim retrieved sequence’ preference... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2781 null local siftsClient variable if exception... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2781 refactor StructureSelectionManager.siftsClient... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2781 FIXME: value of sourceType parameter always... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2781 refactor possibly non-functional ‘extract... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2781 tidy up comments on getMapping/computeMapping commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2781 report exactly which residues do not receive... commit | commitdiff | tree | snapshot
2018-02-13 Jim ProcterJAL-2905 added additional jvmarg for testng task condit... commit | commitdiff | tree | snapshot
2018-02-12 Jim ProcterJAL-2780 JAL-2781 extra column in mapping array commit | commitdiff | tree | snapshot
2018-02-12 Jim ProcterJAL-2904 JAL-2780 JAL-2781 update JmolCommandsTest... commit | commitdiff | tree | snapshot
2018-02-12 Jim ProcterJAL-2780 JAL-2781 ahem - add a semicolon if there isn... commit | commitdiff | tree | snapshot
2018-02-12 Jim ProcterJAL-2780 use value of ’UNASSIGNED’ constant in assert... commit | commitdiff | tree | snapshot
2018-02-12 Jim ProcterJAL-2904 replaced assert for (getEnd()-getStart()+1... commit | commitdiff | tree | snapshot
2018-02-11 Jim ProcterJAL-2781 use SIFTs mapping rather than maxChain AlignSe... commit | commitdiff | tree | snapshot
2018-02-11 Jim ProcterJAL-2780 JAL-2781 use PDBe numbering to map between... commit | commitdiff | tree | snapshot
2018-02-11 Jim ProcterJAL-2781 mark aligned positions via StructureMapping... commit | commitdiff | tree | snapshot
2018-02-11 Jim ProcterJAL-2780 JAL-2781 include a Mapping object in Structure... commit | commitdiff | tree | snapshot
2018-02-11 Jim ProcterJAL-2780 JAL-2781 UNASSIGNED positions marked as Intege... commit | commitdiff | tree | snapshot
2018-02-11 Jim ProcterJAL-2781 fix test data for full length annotation commit | commitdiff | tree | snapshot
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666 commit | commitdiff | tree | snapshot
2018-02-09 gmungocJAL-2789 code format changes only (before functional... commit | commitdiff | tree | snapshot
2018-02-09 gmungocJAL-2666 fix failure to scroll split alignment of height 1 commit | commitdiff | tree | snapshot
2018-02-09 Jim ProcterUse the “PDBe” or “PDB” numbering (starts from 1, corre... commit | commitdiff | tree | snapshot
2018-02-09 Jim ProcterJAL-2780 JAL-2781 should always ensure SIFTS mappings... commit | commitdiff | tree | snapshot
2018-02-08 gmungocJAL-2666 basic initial fix for split screen scroll bug commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2780 JAL-2781 run sequentially and ensure windows... commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2780 JAL-2891 clear all windows always beforeTest... commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2902 catch case where viewer is closed (therefore... commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2902 thread off dialog close op to avoid deadlock... commit | commitdiff | tree | snapshot
2018-02-07 gmungocJAL-2808 ensure pattern field re-enabled when needed... commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2780 JAL-2781 first pass at failing test for incorr... commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2780 JAL-2781 JAL-2902 refactored helper method... commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2902 - isBusy and hasMapping methods so client... commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2780 JAL-2781 fix javadoc in line with behaviour... commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2780 JAL-2781 JAL-2902 refactor ‘OK’ action to... commit | commitdiff | tree | snapshot
2018-02-07 Jim ProcterJAL-2780 JAL-2781 don’t assume contiguous mapping to... commit | commitdiff | tree | snapshot
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759 commit | commitdiff | tree | snapshot
2018-02-05 Jim ProcterJAL-2780 JAL-2781 (failing) test comparing location... commit | commitdiff | tree | snapshot
2018-02-05 Jim ProcterJAL-2780 JAL-2781 programmatically select structures... commit | commitdiff | tree | snapshot
2018-02-05 Jim ProcterJAL-2780 JAL-2871 only look up current table view once commit | commitdiff | tree | snapshot
2018-02-05 Jim ProcterJAL-2780 JAL-2781 test AlignmentI.findAnnotations locat... commit | commitdiff | tree | snapshot
2018-02-05 Jim ProcterJAL-2780 JAL-2781 - patch and first test for AlignmentI... commit | commitdiff | tree | snapshot
2018-02-05 kiramtJAL-2759 Fix errant RangeElementsIterator (unit tests... commit | commitdiff | tree | snapshot
2018-02-05 kiramtJAL-2759 Rename getBoundedStartIterator commit | commitdiff | tree | snapshot
2018-02-05 kiramtJAL-2759 Changes to StartRegionIterator after review commit | commitdiff | tree | snapshot
2018-02-05 kiramtJAL-2788 possible adjustments to sequence accesses commit | commitdiff | tree | snapshot
2018-02-05 gmungocJAL-2897 more informative description on synonymous... commit | commitdiff | tree | snapshot
2018-02-05 gmungocJAL-2897 more informative description on synonymous... commit | commitdiff | tree | snapshot
2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge commit | commitdiff | tree | snapshot
2018-02-05 kiramtJAL-2778 Sequence width benchmark commit | commitdiff | tree | snapshot
2018-02-05 gmungocJAL-2897 more informative description on synonymous... commit | commitdiff | tree | snapshot
2018-02-02 gmungocJAL-984 merged to spikes-mungo commit | commitdiff | tree | snapshot
2018-02-02 gmungocMerge branch 'feature/JAL-984splitAdjuster' into featur... commit | commitdiff | tree | snapshot
2018-02-02 gmungocJAL-984 use cursor for drag regions to adjust annotatio... commit | commitdiff | tree | snapshot
2018-02-02 gmungocJAL-984 better behaved panel height adjuster commit | commitdiff | tree | snapshot
2018-02-01 kiramtJAL-2759 Added in JAL-2851 fix commit | commitdiff | tree | snapshot
2018-02-01 kiramtJAL-2759 use right iterator for getVisibleColsIterator commit | commitdiff | tree | snapshot
2018-01-31 kiramtJAL-2759 Rationalise VisibleColsIterator and HiddenCols... commit | commitdiff | tree | snapshot
2018-01-31 kiramtJAL-2759 Generalised HiddenColsIterator naming commit | commitdiff | tree | snapshot
2018-01-31 gmungocJAL-2792 added tooltip to menu items in case of truncation commit | commitdiff | tree | snapshot
2018-01-31 kiramtJAL-2759 test renaming commit | commitdiff | tree | snapshot
2018-01-31 kiramtJAL-2759 minor refactor to hiding bitsets commit | commitdiff | tree | snapshot
2018-01-30 gmungocJAL-2069 menu item now "Variable colour..." to hint... commit | commitdiff | tree | snapshot
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and... commit | commitdiff | tree | snapshot
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences commit | commitdiff | tree | snapshot
2018-01-30 kiramtJAL-2759 Add missing hiddenColumns empty check commit | commitdiff | tree | snapshot
2018-01-30 kiramtJAL-2759 updateForDeletedRegion no longer needed commit | commitdiff | tree | snapshot
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon... commit | commitdiff | tree | snapshot
2018-01-30 gmungocJAL-2897 formatting change only prior to functional... commit | commitdiff | tree | snapshot
2018-01-30 kiramtJAL-2759 Rationalising hidden cols cursor, and sorting... commit | commitdiff | tree | snapshot
2018-01-30 kiramtJAL-2759 comment commit | commitdiff | tree | snapshot
2018-01-30 kiramtJAL-2759 Additional tests and tweaks to numColumns... commit | commitdiff | tree | snapshot
2018-01-30 kiramtJAL-2759 Keep numColumns up to date commit | commitdiff | tree | snapshot
2018-01-29 kiramtJAL-2759 remove unneeded cast commit | commitdiff | tree | snapshot
2018-01-29 kiramtMerge branch 'feature/JAL-2759' of https://source.jalvi... commit | commitdiff | tree | snapshot
2018-01-29 kiramtJAL-2759 Combine findRegionForColumn code in HiddenColu... commit | commitdiff | tree | snapshot
2018-01-29 gmungocMerge branch 'feature/JAL-2759' of https://source.jalvi... commit | commitdiff | tree | snapshot
2018-01-29 gmungocJAL-1270 testPadGaps() added commit | commitdiff | tree | snapshot
2018-01-29 kiramtJAL-2759 numColumns reset commit | commitdiff | tree | snapshot
2018-01-29 kiramtJAL-2759 remove redundant hiddenColumns.clear() commit | commitdiff | tree | snapshot
2018-01-29 kiramtJAL-2759 Tidy commit | commitdiff | tree | snapshot
2018-01-29 kiramtJAL-2759 make a new cursor instead of resetting, update... commit | commitdiff | tree | snapshot
2018-01-29 kiramtJAL-2759 Fix unintended type change commit | commitdiff | tree | snapshot
2018-01-29 gmungocJAL-2743 recoded EnsemblLookup without lambda expressio... commit | commitdiff | tree | snapshot
2018-01-26 Jim ProcterMerge branch 'releases/Release_2_10_3_Branch' into... commit | commitdiff | tree | snapshot
2018-01-26 kiramtJAL-2778 try another way to draw sequences with reduced... commit | commitdiff | tree | snapshot
2018-01-26 gmungocMerge branch 'develop' into features/JAL-1793VCF commit | commitdiff | tree | snapshot
2018-01-26 kiramtJAL-2778 tightened up use of resetAlignmentDims commit | commitdiff | tree | snapshot
2018-01-25 kiramtJAL-2778 Tidy commit | commitdiff | tree | snapshot
2018-01-25 kiramtJAL-2778 added JAL-2851 fix to avoid confusion commit | commitdiff | tree | snapshot
2018-01-25 kiramtJAL-2778 Reinstate id width adjuster commit | commitdiff | tree | snapshot
2018-01-24 Jim ProcterMerge branch 'develop' into releases/Release_2_10_3_Branch releases/Release_2_10_3_Branch Release_2_10_3b1 commit | commitdiff | tree | snapshot
2018-01-24 Jim ProcterJAL-2858 update release date and rejig what's new message commit | commitdiff | tree | snapshot
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