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2017-10-09	gmungoc	JAL-2738 assertion for derived protein variant added	commit \| commitdiff \| tree
2017-10-09	gmungoc	JAL-2738 remove commented code, unit test coverage	commit \| commitdiff \| tree
2017-10-06	gmungoc	JAL-2753 add new jar to lib folder!	commit \| commitdiff \| tree
2017-10-06	gmungoc	JAL-2753 update to htsjdk 2.12.0 (requires Java 8)	commit \| commitdiff \| tree
2017-10-06	gmungoc	JAL-2754 update to Java 1.8	commit \| commitdiff \| tree
2017-10-06	gmungoc	JAL-2738 unit test for mapping failure case	commit \| commitdiff \| tree
2017-10-05	gmungoc	JAL-2738 warn (in console) when non chromosomal coordinates...	commit \| commitdiff \| tree
2017-10-05	gmungoc	JAL-2738 helper method for convolving mappings	commit \| commitdiff \| tree
2017-10-05	gmungoc	JAL-2755 transfer chromosomal reference from transcript...	commit \| commitdiff \| tree
2017-10-05	gmungoc	JAL-2738 method to compound / traverse / convolve two...	commit \| commitdiff \| tree
2017-10-05	gmungoc	JAL-2744 add score to feature details report, description...	commit \| commitdiff \| tree
2017-10-04	gmungoc	JAL-2738 fix bug of premature exit from adding attributes	commit \| commitdiff \| tree
2017-10-04	gmungoc	JAL-2738 match consequence "Allele" to VCF allele;...	commit \| commitdiff \| tree
2017-10-04	gmungoc	JAL-2744 handle null features list	commit \| commitdiff \| tree
2017-10-03	gmungoc	JAL-2738 update test for threaded VCFLoader	commit \| commitdiff \| tree
2017-10-03	gmungoc	JAL-2738 code formatting	commit \| commitdiff \| tree
2017-10-02	gmungoc	JAL-2738 code tidy up, null checks &c	commit \| commitdiff \| tree
2017-10-02	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	commit \| commitdiff \| tree
2017-10-02	gmungoc	JAL-2525 lookup transcript features by Ontology	commit \| commitdiff \| tree
2017-10-02	gmungoc	JAL-2738 filter VEP consequence data to that for current...	commit \| commitdiff \| tree
2017-09-29	gmungoc	JAL-2738 one sequence feature per (SNP) VCF allele	commit \| commitdiff \| tree
2017-09-29	gmungoc	JAL-2744 indent CSQ lines to catch the eye	commit \| commitdiff \| tree
2017-09-28	gmungoc	JAL-2745 update www.ebi.ac.uk to https	commit \| commitdiff \| tree
2017-09-28	gmungoc	JAL-2738 separate thread to load VCF; update FeatureSettings...	commit \| commitdiff \| tree
2017-09-28	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	commit \| commitdiff \| tree
2017-09-28	gmungoc	JAL-2036 set menus after fully loading AlignFrame	commit \| commitdiff \| tree
2017-09-28	gmungoc	JAL-1796 GeneLociI as distinguished DBRefEntry	commit \| commitdiff \| tree
2017-09-28	gmungoc	JAL-2744 simple Feature Details report from Popup menu	commit \| commitdiff \| tree
2017-09-28	gmungoc	JAL-2744 refactor PopupMenu constructor to enable adding...	commit \| commitdiff \| tree
2017-09-26	gmungoc	JAL-2738 transfer VCF variant features to CDS sequences	commit \| commitdiff \| tree
2017-09-26	gmungoc	JAL-2738 JAL-2154 add DBRef from transcript to synthesized...	commit \| commitdiff \| tree
2017-09-26	gmungoc	JAL-2738 unit test for reverse strand gene	commit \| commitdiff \| tree
2017-09-26	gmungoc	JAL-2738 promote setGeneLoci to SequenceI!	commit \| commitdiff \| tree
2017-09-25	gmungoc	JAL-2738 use complement base for a VCF variant on reverse...	commit \| commitdiff \| tree
2017-09-25	gmungoc	JAL-2738 getGeneLoci promoted to SequenceI	commit \| commitdiff \| tree
2017-09-25	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	commit \| commitdiff \| tree
2017-09-25	gmungoc	JAL-2525 return no features if none matches ontology...	commit \| commitdiff \| tree
2017-09-25	gmungoc	JAL-2738 query unindexed file, unit test for VCFLoader	commit \| commitdiff \| tree
2017-09-25	gmungoc	JAL-2738 one constant in codebase for "alleles" attribute of	commit \| commitdiff \| tree
2017-09-25	gmungoc	JAL-2738 extract SNP variants from SNP or MIXED variant...	commit \| commitdiff \| tree
2017-09-22	gmungoc	JAL-2738 extract utility method to MappingUtils	commit \| commitdiff \| tree
2017-09-22	gmungoc	JAL-2738 correct handling of reverse strand genes	commit \| commitdiff \| tree
2017-09-22	gmungoc	JAL-2738 lookup GRCh38/37 gene mapping	commit \| commitdiff \| tree
2017-09-21	gmungoc	JAL-2738 compute VCF on peptide, extract AF (allele...	commit \| commitdiff \| tree
2017-09-21	gmungoc	JAL-2738 add chromosome coordinate mappings to transcripts	commit \| commitdiff \| tree
2017-09-21	gmungoc	JAL-2738 PoC of Load VCF file on to gene sequence	commit \| commitdiff \| tree
2017-09-21	gmungoc	JAL-2738 GeneLoci holds mapping of sequence to chromosome	commit \| commitdiff \| tree
2017-09-19	gmungoc	JAL-1793 wrapper for plain or indexed VCF + simple...	commit \| commitdiff \| tree
2017-09-19	gmungoc	JAL-1793 simple tests of reading raw and indexed VCF...	commit \| commitdiff \| tree
2017-09-18	gmungoc	Merge remote-tracking branch 'origin/patch/JAL-2732...	commit \| commitdiff \| tree
2017-09-18	gmungoc	JAL-2728 fine tuned initial split of split frame view	commit \| commitdiff \| tree
2017-09-15	gmungoc	JAL-2728 use right denominator for min/max ratio calculations	commit \| commitdiff \| tree
2017-09-15	gmungoc	JAL-2728 limit divider to ensure seqs visible (wip!)	commit \| commitdiff \| tree
2017-09-15	gmungoc	JAL-741 add tooltip to feature group checkbox	commit \| commitdiff \| tree
2017-09-12	gmungoc	Merge branch 'bug/JAL-2721fastPaintNPE' into develop	commit \| commitdiff \| tree
2017-09-07	gmungoc	JAL-2511 invalidate scale panel holder on font change...	commit \| commitdiff \| tree
2017-09-06	gmungoc	JAL-2721 no fastPaint if img has been nulled by fontChanged!	commit \| commitdiff \| tree
2017-09-06	gmungoc	Merge remote-tracking branch 'origin/bug/JAL-2722'...	commit \| commitdiff \| tree
2017-09-05	gmungoc	JAL-2665 check for null selection group image	commit \| commitdiff \| tree
2017-09-05	gmungoc	JAL-2665 check for null selection group image	commit \| commitdiff \| tree
2017-08-31	gmungoc	JAL-2704 unit test for Above PID gap colour, simplified...	commit \| commitdiff \| tree
2017-08-30	gmungoc	JAL-2704 don't shade gap colour for PID/conservation	commit \| commitdiff \| tree
2017-08-25	gmungoc	JAL-2480 suppress debug timing output that got left in	commit \| commitdiff \| tree
2017-08-23	gmungoc	JAL-2435 last lost commit e926a5d redone	commit \| commitdiff \| tree
2017-08-23	gmungoc	JAL-2435 last lost commit e926a5d redone	commit \| commitdiff \| tree
2017-08-23	gmungoc	JAL-2481 a smidgin more test coverage of findFeatures	commit \| commitdiff \| tree
2017-08-22	gmungoc	JAL-2680 remove all mappings in test teardown	commit \| commitdiff \| tree
2017-08-22	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2017-08-21	gmungoc	JAL-2680 clear down all mappings before test	commit \| commitdiff \| tree
2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-10	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-10	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2017-08-10	gmungoc	JAL-2660 used saved value of ignoreGapsInConsensus...	commit \| commitdiff \| tree
2017-08-10	gmungoc	JAL-2505 apply changed description to new, not deleted...	commit \| commitdiff \| tree
2017-08-10	gmungoc	JAL-2658 ensure features dropdown entries are unique	commit \| commitdiff \| tree
2017-08-10	gmungoc	JAL-2593 don't filter out 'colour by label' features	commit \| commitdiff \| tree
2017-08-10	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-09	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-09	gmungoc	JAL-2480 inline one method, improve comments	commit \| commitdiff \| tree
2017-08-09	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-08	gmungoc	JAL-2560 alternative fix (reinstate lost line of code)	commit \| commitdiff \| tree
2017-08-08	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-08	gmungoc	JAL-2649 JAL-2650 wait for Conservation calc to complete...	commit \| commitdiff \| tree
2017-08-08	gmungoc	JAL-2650 configure new viewport settings before selecting...	commit \| commitdiff \| tree
2017-08-07	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-04	gmungoc	JAL-2500 JAL-2365 lightGray changed to lightgray for...	commit \| commitdiff \| tree
2017-08-04	gmungoc	JAL-2500 JAL-2365 lightGray changed to gray in example...	commit \| commitdiff \| tree
2017-08-03	gmungoc	JAL-2643 updated threshold on threshold value focus...	commit \| commitdiff \| tree
2017-08-03	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-03	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-03	gmungoc	JAL-2500 JAL-2365 feature colour "gray" _not_ "lightgray...	commit \| commitdiff \| tree
2017-08-03	gmungoc	JAL-2500 JAL-2365 lightGray changed to lightgray for...	commit \| commitdiff \| tree
2017-08-03	gmungoc	JAL-2500 JAL-2365 lightGray changed to gray in example...	commit \| commitdiff \| tree
2017-08-03	gmungoc	JAL-2435 test for 'mirror font' option visible (not...	commit \| commitdiff \| tree
2017-08-02	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-02	gmungoc	JAL-2418 corrected link url for "overview" target	commit \| commitdiff \| tree
2017-08-01	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-01	gmungoc	JAL-2611 reinstate missed merge - again!	commit \| commitdiff \| tree
2017-08-01	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	commit \| commitdiff \| tree
2017-08-01	gmungoc	Merge branch 'feature/JAL-2611' into develop	commit \| commitdiff \| tree
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