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JAL-3070 use ArgumentI in all public constructors, convert to service specific argume...
[jalview.git] / src / jalview / io /
2018-07-23 Jim ProcterMerge branch 'features/mchmmer' into merge/wsinterfaces... tree | commitdiff
2018-06-26 Jim ProcterJAL-3042 don't allow user to change default history... tree | commitdiff
2018-06-05 gmungocJAL-3011 include annotation scores in sequence id toolt... tree | commitdiff
2018-05-29 gmungocJAL-3005 refactor updateRecentlyOpened to enable reuse tree | commitdiff
2018-05-28 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-05-24 gmungocJAL-2997 additional tests tree | commitdiff
2018-05-23 gmungocJAL-2997 handle tab-delimited trailing column number... tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 ensure default is ‘parseImmediately=true’ tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 isParseImmediately() allows the parse() method... tree | commitdiff
2018-04-23 gmungocJAL-2956 save/restore HMMER profile to/from Jalview... tree | commitdiff
2018-04-17 gmungocJAL-2629 choice of hmm profile now a parameter not... tree | commitdiff
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe... tree | commitdiff
2018-03-30 gmungocJAL-2599 MapList from HMM nodes to consensus dataset... tree | commitdiff
2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications tree | commitdiff
2018-03-29 gmungocJAL-2907 bug fix redone on HMMER branch tree | commitdiff
2018-03-28 gmungocJAL-1265 output all dbrefs in Stockholm (+tests) (... tree | commitdiff
2018-03-16 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file... tree | commitdiff
2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double... tree | commitdiff
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly tree | commitdiff
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc tree | commitdiff
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759 tree | commitdiff
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and... tree | commitdiff
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences tree | commitdiff
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon... tree | commitdiff
2018-01-16 kiramtJAL-2759 Moved alignment annotation code out of HiddenC... tree | commitdiff
2018-01-15 kiramtJAL-2759 Rename hideInsertionsFor to hideList, after... tree | commitdiff
2018-01-15 kiramtJAL-2759 Refactor of hideInsertionsFor after review tree | commitdiff
2018-01-10 gmungocJAL-1793 update spike branch to latest tree | commitdiff
2017-12-08 gmungocJAL-2843 read/write feature filters from/to Jalview... tree | commitdiff
2017-12-05 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-12-04 gmungocJAL-2808 JAL-2850 update spike build to latest tree | commitdiff
2017-12-04 gmungocMerge branch 'spikes/mungo' into features/JAL-1793VCF tree | commitdiff
2017-12-04 gmungocJAL-2850 JAL-1766 option to load contig sequence refere... tree | commitdiff
2017-12-04 gmungocJAL-2845 locate reverse strand insertion as complement... tree | commitdiff
2017-12-04 gmungocJAL-2835 small refactor to only extract transcript... tree | commitdiff
2017-12-01 gmungocJAL-2835 spike updated to latest (use specific SO term... tree | commitdiff
2017-12-01 gmungocJAL-2835 refactored to extract specific consequence... tree | commitdiff
2017-12-01 gmungocJAL-2835 additional sub-terms of sequence_variant added tree | commitdiff
2017-11-30 gmungocJAL-2850 improved use of htsjdk api to read contig... tree | commitdiff
2017-11-30 Jim ProcterJAL-2849 fix tree | commitdiff
2017-11-27 gmungocJAL-2850 VCFLoader refactored to load VCF to contig... tree | commitdiff
2017-11-23 gmungocJAL-2808 update spike to latest (filter range, Present... tree | commitdiff
2017-11-23 gmungocJAL-2808 removed field filters; sort CSQ data by key tree | commitdiff
2017-11-15 gmungocJAL-2835 spike updated with latest tree | commitdiff
2017-11-15 gmungocJAL-2835 take all CSQ fields; catch invalid field match... tree | commitdiff
2017-11-15 gmungocJAL-2835 support filter/colour by nested attribute... tree | commitdiff
2017-11-15 gmungocJAL-2835 add filters for VCF/VEP 'fields of interest' tree | commitdiff
2017-11-13 gmungocJAL-2738 stubs for filtering VEP and VCF fields of... tree | commitdiff
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-11-13 Jim ProcterMerge branch 'imp/JAL-2810_ftsIDtab' into develop tree | commitdiff
2017-11-13 gmungocJAL-2176 removed unused Sequence.index tree | commitdiff
2017-11-07 gmungocJAL-2069 update spike branch with latest tree | commitdiff
2017-11-06 gmungocJAL-2820 include attribute value used for feature colou... tree | commitdiff
2017-10-27 Jim ProcterJAL-2804 kludge method to test if last key event handle... tree | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest tree | commitdiff
2017-10-27 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-10-27 gmungocJAL-2792 capture feature metadata and render in Feature... tree | commitdiff
2017-10-26 Jim ProcterMerge branch 'feature/JAL-2488finalize' into develop tree | commitdiff
2017-10-26 gmungocJAL-2792 html table for Feature Details report tree | commitdiff
2017-10-25 gmungocJAL-2743 fall back to parsing description if chromosome... tree | commitdiff
2017-10-24 gmungocJAL-2743 slightly fancier species/assembly matching... tree | commitdiff
2017-10-24 gmungocJAL-2738 update spike branch with latest tree | commitdiff
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd... tree | commitdiff
2017-10-20 gmungocPush 1793 latest to spike branch tree | commitdiff
2017-10-20 gmungocJAL-2755 update caller for method rename! tree | commitdiff
2017-10-19 gmungocJAL-2755 put chromosomal dbref first in report tree | commitdiff
2017-10-12 Jim ProcterJAL-2773 add new flag to paintAlignment(updateOverview... features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview tree | commitdiff
2017-10-11 gmungocJAL-2738 javadoc correction 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
2017-10-05 gmungocJAL-2738 update spikes/mungo tree | commitdiff
2017-10-05 gmungocJAL-2738 warn (in console) when non chromosomal coordin... 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
2017-10-03 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 gmungocJAL-2738 filter VEP consequence data to that for curren... tree | commitdiff
2017-09-29 gmungocJAL-2738 one sequence feature per (SNP) VCF allele tree | commitdiff
2017-09-28 gmungocJAL-2738 separate thread to load VCF; update FeatureSet... tree | commitdiff
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry tree | commitdiff
2017-09-26 gmungocJAL-2738 transfer VCF variant features to CDS sequences tree | commitdiff
2017-09-26 gmungocJAL-2738 unit test for reverse strand gene tree | commitdiff
2017-09-25 gmungocJAL-2738 use complement base for a VCF variant on rever... 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 PoC of Load VCF file on to gene sequence tree | commitdiff
2017-09-01 TZVanaaltenJAL-2629 fix hmmbuild failing due to RF longer than... features/hmmer tree | commitdiff
2017-09-01 TZVanaaltenJAL-2629 manual curation of HMMs via reference annotati... tree | commitdiff
2017-09-01 gmungocJAL-2488 remove finalize methods tree | commitdiff
2017-08-29 osboxesJAL-2629 HMMs dropped on the alignment now map to the... tree | commitdiff
2017-08-28 TZVanaaltenJAL-2629 fix issue where HMM would not be added to... tree | commitdiff
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