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Merge branch 'develop' into features/JAL-1793VCF
[jalview.git] / src / jalview /
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2682parseId' into develop tree | commitdiff
2017-10-23 gmungocJAL-2776 repaint everything on toggle group colour bug/JAL-2776toggleGroupColour tree | commitdiff
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2253' into develop tree | commitdiff
2017-10-23 gmungocJAL-1854 keep fallthrough but with comment to suppress... tree | commitdiff
2017-10-23 gmungocJAL-1854 remove fallthrough of switch case (Checkstyle... tree | commitdiff
2017-10-20 Jim ProcterJAL-2779 keep a reference to original Aqua manager... tree | commitdiff
2017-10-20 Jim ProcterJAL-2779 remove OSX platform specific import (not neede... tree | commitdiff
2017-10-20 gmungocPush 1793 latest to spike branch tree | commitdiff
2017-10-20 gmungocJAL-2253 pull up constant, additional unit test bug/JAL-2253 tree | commitdiff
2017-10-20 gmungocJAL-2755 update caller for method rename! tree | commitdiff
2017-10-20 gmungocJAL-2609 fully erase scale above, tidy code change tree | commitdiff
2017-10-19 gmungocJAL-2609 adjustments for test findings tree | commitdiff
2017-10-19 gmungocJAL-2755 find gene loci for fetched xrefs where possible tree | commitdiff
2017-10-19 gmungocJAL-2755 put chromosomal dbref first in report tree | commitdiff
2017-10-19 gmungocJAL-2755 add lookup of cds/cdna gene loci tree | commitdiff
2017-10-19 gmungocJAL-2755 add species lookup tree | commitdiff
2017-10-19 gmungocJAL-2755 add missing Javadoc tree | commitdiff
2017-10-19 gmungocJAL-2755 rename EnsemblInfo as EnsemblData, add 'true... tree | commitdiff
2017-10-19 kiramtMerge branch 'develop' into bug/JAL-2609attemptedmerge tree | commitdiff
2017-10-18 Jim ProcterJAL-2779 switch order for updating the current alignmen... tree | commitdiff
2017-10-18 Jim ProcterJAL-2779 remove dead code tree | commitdiff
2017-10-18 Jim ProcterJAL-2779 hook in our own AquaInternalFrameManager when... tree | commitdiff
2017-10-18 Jim ProcterJAL-2779 JAL-1551 source formatting tree | commitdiff
2017-10-18 Jim ProcterJAL-2779 patch so closing most recent frame doesn’t... tree | commitdiff
2017-10-18 Jim ProcterJAL-2779 original version of AquaInternalFrame Manager tree | commitdiff
2017-10-18 Jim ProcterMerge branch 'bugs/JAL-2777_whitespaceChain' into develop tree | commitdiff
2017-10-18 Jim ProcterJAL-2777 remove duplicate code outside conditional... tree | commitdiff
2017-10-17 Jim ProcterJAL-2773 renamed flags for clarity tree | commitdiff
2017-10-17 Jim ProcterJAL-2777 patch for whitespace chain bugs/JAL-2777_whitespaceChain tree | commitdiff
2017-10-17 Jim ProcterJAL-2481 patch to fix findFeatureColour for end-of... tree | commitdiff
2017-10-17 Jim ProcterJAL-2777 noticed exception raised on construction of... tree | commitdiff
2017-10-16 kiramtJAL-2775 added repaint clipping tree | commitdiff
2017-10-13 kiramtJAL-2774 Created single event for update to both start... tree | commitdiff
2017-10-12 Jim ProcterJAL-2773 add new flag to paintAlignment(updateOverview... features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview tree | commitdiff
2017-10-11 gmungocJAL-2772 check array bounds for sequence access bug/JAL-2772pdbArrayBounds tree | commitdiff
2017-10-11 gmungocJAL-2225 updates for review comments, Checkstyle tree | commitdiff
2017-10-11 gmungocJAL-2609 tidy label width code, some checkstyle warnings tree | commitdiff
2017-10-11 gmungocMerge branch 'bug/JAL-2742' into develop tree | commitdiff
2017-10-11 gmungocMerge branch 'bug/JAL-2757_uniprotftsbadquery' into... tree | commitdiff
2017-10-11 gmungocJAL-2757 fix PDB also; suppress stack trace and compile... bug/JAL-2757_uniprotftsbadquery tree | commitdiff
2017-10-11 gmungocJAL-2738 javadoc correction tree | commitdiff
2017-10-11 kiramtJAL-2742 removed unused getViewAsCigars tree | commitdiff
2017-10-11 kiramtJAL-2609attemptedmerge tidy tree | commitdiff
2017-10-10 kiramtMerge remote-tracking branch 'origin/features/JAL-2609f... tree | commitdiff
2017-10-10 kiramtJAL-2690attemptedmerge seems to work tree | commitdiff
2017-10-10 Jim ProcterJAL-2392 wrap public progress bar methods as InvokeLate... tree | commitdiff
2017-10-10 Jim ProcterJAL-2392 formatting tree | commitdiff
2017-10-10 Jim ProcterMerge branch 'codereviews/JAL-1990_IProgressIndicator_j... tree | commitdiff
2017-10-10 Jim ProcterMerge branch 'features/JAL-2523httpRetries' into develop tree | commitdiff
2017-10-10 kiramtJAL-2690attemptedmerge partial merge tree | commitdiff
2017-10-10 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-10-09 gmungocJAL-2480 use interface type for sequenceFeatureStore tree | commitdiff
2017-10-09 gmungocJAL-2523 basic sleep and retry (3 times) on 429 respons... features/JAL-2523httpRetries tree | commitdiff
2017-10-09 gmungocJAL-2523 convenience method to get model organisms tree | commitdiff
2017-10-09 Jim ProcterJAL-2446 remove duplicate code from pulled up method. tree | commitdiff
2017-10-09 gmungocJAL-2738 ensure variant feature is in forward sense tree | commitdiff
2017-10-09 gmungocJAL-2738 remove commented code, unit test coverage tree | commitdiff
2017-10-06 Jim ProcterJAL-2758 flag and tests for omitting uniprot accession... features/JAL-2758_shorteruniprot tree | commitdiff
2017-10-05 Jim ProcterJAL-2757 reset textbox after a non HTTP 200 response tree | commitdiff
2017-10-05 gmungocJAL-2738 update spikes/mungo tree | commitdiff
2017-10-05 gmungocJAL-2738 warn (in console) when non chromosomal coordin... tree | commitdiff
2017-10-05 gmungocJAL-2738 helper method for convolving mappings tree | commitdiff
2017-10-05 gmungocJAL-2755 transfer chromosomal reference from transcript... tree | commitdiff
2017-10-05 gmungocJAL-2738 method to compound / traverse / convolve two... tree | commitdiff
2017-10-05 gmungocJAL-2744 add score to feature details report, descripti... tree | commitdiff
2017-10-04 gmungocJAL-2738 fix bug of premature exit from adding attributes tree | commitdiff
2017-10-04 gmungocJAL-2523 start of refactoring... tree | commitdiff
2017-10-04 gmungocJAL-2738 match consequence "Allele" to VCF allele;... tree | commitdiff
2017-10-04 gmungocJAL-2744 handle null features list tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-10-03 gmungocJAL-2738 code formatting tree | commitdiff
2017-10-02 gmungocJAL-2738 code tidy up, null checks &c tree | commitdiff
2017-10-02 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-10-02 gmungocJAL-2525 lookup transcript features by Ontology tree | commitdiff
2017-10-02 gmungocJAL-2738 filter VEP consequence data to that for curren... tree | commitdiff
2017-09-29 Jim ProcterJAL-2748 formatting tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 JAL-2748 direct download of XML from uniprot.org tree | commitdiff
2017-09-29 Jim ProcterJAL-2748 formatting tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 JAL-2748 direct download of XML from uniprot.org tree | commitdiff
2017-09-29 gmungocJAL-2738 one sequence feature per (SNP) VCF allele tree | commitdiff
2017-09-29 gmungocJAL-2744 indent CSQ lines to catch the eye tree | commitdiff
2017-09-29 Jim ProcterRevert "JAL-2745 update SIFTS FTP URL to HTTPS" tree | commitdiff
2017-09-29 Jim ProcterRevert "JAL-2745 update SIFTS FTP URL to HTTPS" tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 update default EBI-eye search URL to HTTPS tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 update SIFTS FTP URL to HTTPS tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 update default EBI-eye search URL to HTTPS feature/JAL-2745ebiHttps tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 update SIFTS FTP URL to HTTPS tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 stderr rather than stdout for unexpected HTTP... tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 stderr rather than stdout for unexpected HTTP... tree | commitdiff
2017-09-29 gmungocJAL-2745 update www.ebi.ac.uk to https tree | commitdiff
2017-09-28 gmungocJAL-2745 update www.ebi.ac.uk to https tree | commitdiff
2017-09-28 gmungocJAL-2738 separate thread to load VCF; update FeatureSet... tree | commitdiff
2017-09-28 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-09-28 gmungocJAL-2036 set menus after fully loading AlignFrame tree | commitdiff
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry tree | commitdiff
2017-09-28 gmungocJAL-2744 simple Feature Details report from Popup menu tree | commitdiff
2017-09-28 gmungocJAL-2744 refactor PopupMenu constructor to enable addin... tree | commitdiff
2017-09-26 kiramtJAL-2742 fixed tree | commitdiff
2017-09-26 gmungocJAL-2738 transfer VCF variant features to CDS sequences tree | commitdiff
2017-09-26 gmungocJAL-2738 JAL-2154 add DBRef from transcript to synthesi... tree | commitdiff
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