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JAL-2989 refactoring to reduce code duplication
[jalview.git] / src /
2018-03-20 gmungocJAL-2629 InformationThread.findOrCreateAnnotation and... tree | commitdiff
2018-03-20 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe... tree | commitdiff
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-03-16 gmungocJAL-2922 update FeatureRenderer and repaint feature... tree | commitdiff
2018-03-16 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-03-16 gmungocMerge branch 'bug/JAL-2865removeGC' into develop tree | commitdiff
2018-03-16 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES tree | commitdiff
2018-03-14 gmungocJAL-2893 include ENSEMBLGENOMES as a 'roundtrip db... tree | commitdiff
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge tree | commitdiff
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge tree | commitdiff
2018-03-13 gmungocJAL-2913 use FIGURE_FIXEDIDWIDTH (not FIGURE_USERIDWIDTH) tree | commitdiff
2018-03-08 gmungocMerge remote-tracking branch 'origin/releases/Release_2... merges/JAL-2906_update2_11_from_2_10_4 tree | commitdiff
2018-03-08 gmungocJAL-2885 tests updated for code changes tree | commitdiff
2018-03-08 gmungocJAL-2930 use MouseWheelEvent.getPreciseWheelRotation... tree | commitdiff
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10... tree | commitdiff
2018-03-07 gmungocJAL-2922 [2] not [1] for Boolean column of table bugs/JAL-2922 tree | commitdiff
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10... tree | commitdiff
2018-03-07 gmungocJAL-2922 i18n and bespoke handler for Invert Selection tree | commitdiff
2018-03-07 gmungocMerge branch 'bug/JAL-2924nullTooltip' into releases... tree | commitdiff
2018-03-07 gmungocJAL-2926 fix copy group consensus (and paste sequence... tree | commitdiff
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group... tree | commitdiff
2018-03-07 gmungocJAL-2913 use FIGURE_USERIDWIDTH for fixed id width... tree | commitdiff
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM... tree | commitdiff
2018-03-01 gmungocJAL-2629 revising hmmer annotation updating (wip) tree | commitdiff
2018-02-28 gmungocJAL-2924 no tooltip over null annotation positions bug/JAL-2924nullTooltip tree | commitdiff
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip) tree | commitdiff
2018-02-27 gmungocJAL-2668 method name change for clarity tree | commitdiff
2018-02-27 gmungocJAL-2668 fix broken factory method for colour scheme tree | commitdiff
2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display... tree | commitdiff
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 tree | commitdiff
2018-02-27 Jim Procterfix for JAL-2922 - update states all at once and then... tree | commitdiff
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file... tree | commitdiff
2018-02-23 gmungocJAL-2599 corrected case-insensitive symbol indexing tree | commitdiff
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea... tree | commitdiff
2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double... tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 xfam https features/JAL-2885UniprotHttps tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 XFAM_DOMAIN->XFAM_BASEURL tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 renamed base URL getter from getDomain.. tree | commitdiff
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly tree | commitdiff
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... tree | commitdiff
2018-02-22 Jim ProcterJAL-984 ID width adjuster needs to be white ! tree | commitdiff
2018-02-22 Jim ProcterMerge branch 'bug/JAL-2666' into releases/Release_2_10_... tree | commitdiff
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... tree | commitdiff
2018-02-22 Jim ProcterJAL-984 remove all references to idwidth.gif and use... tree | commitdiff
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... tree | commitdiff
2018-02-22 Jim ProcterJAL-294 remove unneeded paint() method tree | commitdiff
2018-02-22 Jim ProcterJAL-984 remove commented/unnecessary if clause tree | commitdiff
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc tree | commitdiff
2018-02-21 Jim ProcterMerge branch 'bug/JAL-2778again' into releases/Release_... tree | commitdiff
2018-02-21 Jim ProcterJAL-2778 reinstate transparent windows to avoid ugly... bug/JAL-2778again tree | commitdiff
2018-02-21 gmungocJAL-2629 simplifying method signatures in Hmmer command... tree | commitdiff
2018-02-21 kiramtJAL-2778 Adjust cursor changes in overview panel tree | commitdiff
2018-02-21 kiramtJAL-2778 Revert back to old synchronisation tree | commitdiff
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and... tree | commitdiff
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-02-19 gmungocJAL-2629 refactoring of Hmmer preferences tree | commitdiff
2018-02-19 gmungocJAL-2629 partial refactoring of Hmmer command classes tree | commitdiff
2018-02-19 gmungocJAL-2629 formatting only tree | commitdiff
2018-02-13 Jim ProcterJAL-2780 JAL-2781 don’t create a mapping if sequence... tree | commitdiff
2018-02-13 Jim ProcterJAL-2780 JAL-2781 only create a mapping entry or write... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 JAL-2780 include sequence start number when... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 refactor ‘trim retrieved sequence’ preference... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 null local siftsClient variable if exception... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 refactor StructureSelectionManager.siftsClient... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 FIXME: value of sourceType parameter always... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 refactor possibly non-functional ‘extract... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 tidy up comments on getMapping/computeMapping tree | commitdiff
2018-02-12 Jim ProcterJAL-2780 JAL-2781 ahem - add a semicolon if there isn... tree | commitdiff
2018-02-11 Jim ProcterJAL-2781 use SIFTs mapping rather than maxChain AlignSe... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 use PDBe numbering to map between... tree | commitdiff
2018-02-11 Jim ProcterJAL-2781 mark aligned positions via StructureMapping... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 include a Mapping object in Structure... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 UNASSIGNED positions marked as Intege... tree | commitdiff
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666 tree | commitdiff
2018-02-09 gmungocJAL-2789 code format changes only (before functional... tree | commitdiff
2018-02-09 gmungocJAL-2666 fix failure to scroll split alignment of height 1 tree | commitdiff
2018-02-09 Jim ProcterUse the “PDBe” or “PDB” numbering (starts from 1, corre... tree | commitdiff
2018-02-09 Jim ProcterJAL-2780 JAL-2781 should always ensure SIFTS mappings... tree | commitdiff
2018-02-08 gmungocJAL-2666 basic initial fix for split screen scroll bug tree | commitdiff
2018-02-07 Jim ProcterJAL-2902 catch case where viewer is closed (therefore... tree | commitdiff
2018-02-07 Jim ProcterJAL-2902 thread off dialog close op to avoid deadlock... tree | commitdiff
2018-02-07 gmungocJAL-2808 ensure pattern field re-enabled when needed... tree | commitdiff
2018-02-07 Jim ProcterJAL-2902 - isBusy and hasMapping methods so client... tree | commitdiff
2018-02-07 Jim ProcterJAL-2780 JAL-2781 fix javadoc in line with behaviour... tree | commitdiff
2018-02-07 Jim ProcterJAL-2780 JAL-2781 JAL-2902 refactor ‘OK’ action to... tree | commitdiff
2018-02-07 Jim ProcterJAL-2780 JAL-2781 don’t assume contiguous mapping to... tree | commitdiff
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759 tree | commitdiff
2018-02-05 Jim ProcterJAL-2780 JAL-2781 programmatically select structures... tree | commitdiff
2018-02-05 Jim ProcterJAL-2780 JAL-2871 only look up current table view once tree | commitdiff
2018-02-05 Jim ProcterJAL-2780 JAL-2781 - patch and first test for AlignmentI... tree | commitdiff
2018-02-05 kiramtJAL-2759 Fix errant RangeElementsIterator (unit tests... tree | commitdiff
2018-02-05 kiramtJAL-2759 Rename getBoundedStartIterator tree | commitdiff
2018-02-05 kiramtJAL-2759 Changes to StartRegionIterator after review tree | commitdiff
2018-02-05 kiramtJAL-2788 possible adjustments to sequence accesses tree | commitdiff
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