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JAL-2738 unit test for mapping failure case
[jalview.git] / src /
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-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 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 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 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
2017-09-28 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 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
2017-09-26 gmungocJAL-2738 unit test for reverse strand gene tree | commitdiff
2017-09-26 gmungocJAL-2738 promote setGeneLoci to SequenceI! tree | commitdiff
2017-09-25 gmungocJAL-2738 use complement base for a VCF variant on rever... tree | commitdiff
2017-09-25 gmungocJAL-2738 getGeneLoci promoted to SequenceI tree | commitdiff
2017-09-25 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-09-25 gmungocJAL-2525 return no features if none matches ontology... tree | commitdiff
2017-09-25 gmungocJAL-2738 query unindexed file, unit test for VCFLoader tree | commitdiff
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu... tree | commitdiff
2017-09-25 gmungocJAL-2738 extract SNP variants from SNP or MIXED variant... tree | commitdiff
2017-09-22 gmungocJAL-2738 extract utility method to MappingUtils tree | commitdiff
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes tree | commitdiff
2017-09-22 gmungocJAL-2738 lookup GRCh38/37 gene mapping tree | commitdiff
2017-09-21 gmungocJAL-2738 compute VCF on peptide, extract AF (allele... tree | commitdiff
2017-09-21 gmungocJAL-2738 add chromosome coordinate mappings to transcripts tree | commitdiff
2017-09-21 gmungocJAL-2738 PoC of Load VCF file on to gene sequence tree | commitdiff
2017-09-21 gmungocJAL-2738 GeneLoci holds mapping of sequence to chromosome tree | commitdiff
2017-09-19 gmungocJAL-1793 wrapper for plain or indexed VCF + simple... tree | commitdiff
2017-09-18 gmungocMerge remote-tracking branch 'origin/patch/JAL-2732... tree | commitdiff
2017-09-18 gmungocJAL-2728 fine tuned initial split of split frame view tree | commitdiff
2017-09-15 Jim ProcterJAL-1625 ensure we don’t regress on JAL-20 - we always... patch/JAL-2732 tree | commitdiff
2017-09-15 Jim ProcterJAL-1625 javadoc tree | commitdiff
2017-09-15 Jim ProcterJAL-2733 redraw after changing the memory status displa... tree | commitdiff
2017-09-15 Jim ProcterJAL-1625 JAL-1900 preserve the original DesktopManager... tree | commitdiff
2017-09-15 Jim ProcterJAL-1900 JAL-1625 back out OSX specific double buffer... tree | commitdiff
2017-09-15 Jim ProcterJAL-1551 standard code formatting tree | commitdiff
2017-09-15 Jim ProcterJAL-2732 force a redraw after resize/drag to clear... tree | commitdiff
2017-09-15 gmungocJAL-2728 use right denominator for min/max ratio calcul... bug/JAL-2728splitFrameDivision tree | commitdiff
2017-09-15 gmungocJAL-2728 limit divider to ensure seqs visible (wip!) tree | commitdiff
2017-09-15 gmungocJAL-741 add tooltip to feature group checkbox tree | commitdiff
2017-09-12 gmungocMerge branch 'bug/JAL-2721fastPaintNPE' into develop tree | commitdiff
2017-09-07 gmungocJAL-2511 invalidate scale panel holder on font change... bug/JAL-2511idAlignment tree | commitdiff
2017-09-06 Jim ProcterJAL-2587 makes sure idWidthAdjuster is resized when... tree | commitdiff
2017-09-06 gmungocJAL-2721 no fastPaint if img has been nulled by fontCha... bug/JAL-2721fastPaintNPE tree | commitdiff
2017-09-06 Jim ProcterMerge branch 'releases/Release_2_10_2b1_Branch' into... tree | commitdiff
2017-09-06 Jim ProcterJAL-2724 patch to fix ClassCastException - method shoul... tree | commitdiff
2017-09-06 gmungocMerge remote-tracking branch 'origin/bug/JAL-2722'... portforward/JAL-2675_2102b1to2103 tree | commitdiff
2017-09-06 kiramtJAL-2587 Removed dissolve tree | commitdiff
2017-09-05 gmungocJAL-2665 check for null selection group image tree | commitdiff
2017-09-05 Jim ProcterMerge branch 'bug/JAL-2722' into releases/Release_2_10_... tree | commitdiff
2017-09-05 gmungocJAL-2665 check for null selection group image tree | commitdiff
2017-09-05 kiramtJAL-2722 Reinstate allGroups value setting in getResidu... tree | commitdiff
2017-09-05 Jim ProcterMerge branch 'bug/JAL-2665-2.10.3' into portforward... tree | commitdiff
2017-09-05 Jim ProcterMerge branch 'master' into portforward/JAL-2675_2102b1t... tree | commitdiff
2017-09-04 Jim ProcterJAL-2675 source license tree | commitdiff
2017-09-04 Jim ProcterMerge branch 'feature/JAL-2587' into documentation... tree | commitdiff
2017-09-04 Jim ProcterMerge branch 'bug/JAL-2673' into documentation/JAL... tree | commitdiff
2017-09-04 kiramtJAL-2673 turn off update to running flag from scrollUp... bug/JAL-2673 tree | commitdiff
2017-09-04 kiramtJAL-2673 Attempt to stop infinite scrolling etc tree | commitdiff
2017-09-04 Jim ProcterJAL-2527 move default colours for applet / application... tree | commitdiff
2017-09-04 Jim ProcterMerge branch 'bug/JAL-2704gapColourFading' into documen... tree | commitdiff
2017-09-04 Jim ProcterMerge branch 'releases/Release_2_10_2b1_Branch' of... tree | commitdiff
2017-09-04 kiramtJAL-2611 reinstated missed commit tree | commitdiff
2017-09-03 Jim ProcterMerge branch 'feature/JAL-2587' into documentation... tree | commitdiff
2017-09-03 Jim ProcterMerge branch 'bug/JAL-2691_nomultimermapping' into... tree | commitdiff
2017-09-03 Jim ProcterMerge branch 'bug/JAL-2665-2.10.2b' into documentation... bug/JAL-2673_mergewithproblem tree | commitdiff
2017-09-03 Jim ProcterMerge branch 'documentation/JAL-2675_release2102b1... tree | commitdiff
2017-09-03 Jim ProcterMerge branch 'feature/JAL-2527' into documentation... tree | commitdiff
2017-09-03 Jim ProcterMerge branch 'features/JAL-2681_duplicatecrossrefs... tree | commitdiff
2017-08-31 kiramtJAL-2527 Updated Spanish, adjusted UI so Spanish fits tree | commitdiff
2017-08-31 kiramtJAL-2527 Updates following code review tree | commitdiff
2017-08-31 gmungocJAL-2704 unit test for Above PID gap colour, simplified... bug/JAL-2704gapColourFading tree | commitdiff
2017-08-30 gmungocJAL-2704 don't shade gap colour for PID/conservation tree | commitdiff
2017-08-30 kiramtJAL-2527 Code comments, tidy tree | commitdiff
2017-08-30 kiramtJAL-2527 Added default setting/resetting and first... tree | commitdiff
2017-08-30 kiramtJAL-2527 Wired up cached values to overview tree | commitdiff
2017-08-30 kiramtMerge remote-tracking branch 'origin/feature/2588'... tree | commitdiff
2017-08-30 kiramtMerge branch 'feature/JAL-2664' into feature/JAL-2527 tree | commitdiff
2017-08-29 kiramtJAL-2664 Updates following review feature/JAL-2664 tree | commitdiff
2017-08-29 kiramtJAL-2527 Added overview prefs - don't get picked up... tree | commitdiff
2017-08-29 Jim ProcterJAL-2698 spawn a thread to test for and raise auto... tree | commitdiff
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