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JAL-3285 code changes to Jalview2XML not included in merge
[jalview.git] / src / jalview / io /
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
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild... tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 fix issue where Stockholm file would print... tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 fix for NPE caused by incorrect initiation... tree | commitdiff
2017-08-23 tzvanaaltenJAL-2629 selected HMM is now a sequence, not a HMM tree | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList tree | commitdiff
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer tree | commitdiff
2017-08-18 TZVanaaltenJAL-2668 HMMFile export method moved to print method tree | commitdiff
2017-08-17 TZVanaaltenJAL-2599 move fillSymbol method to HMFile tree | commitdiff
2017-08-17 TZVanaaltenJAL-2599 some slight renaming of variables and methods tree | commitdiff
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 add GPL to main sources tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting tree | commitdiff
2017-08-16 TZVanaaltenJAL-2629 add hmmbuild validation check which also gets... tree | commitdiff
2017-08-15 tzvanaaltenJAL-2629 fix file loading issues on Mac tree | commitdiff
2017-08-15 TZVanaaltenJAL-2629 selected HMM name now shown in HMMER menu tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 remove gap padding, and now has option to... tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 add insert sequence at method on alignment tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 add padding for .sto annotations to fix issues... tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 fix incorrect gap insertions on HMM sequence tree | commitdiff
2017-08-13 TZVanaaltenJAL-2629 fix issue where HMM sequences would be too... tree | commitdiff
2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop tree | commitdiff
2017-08-10 tzvanaaltenJAL-2629 fix files permission issue on Mac tree | commitdiff
2017-08-08 TZVanaaltenJAL-2599 fix for index issue on node lookup tree | commitdiff
2017-08-07 TZVanaaltenJAL-2629 current hmmer commands are now executed in... tree | commitdiff
2017-08-02 TZVanaaltenJAL-2599 fix issue where parser exported map annotation... tree | commitdiff
2017-07-31 TZVanaaltenJAL-2629 add hmmalign command tree | commitdiff
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