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