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JAL-3675 release notes for JAL-3750 JAL-3751
[jalview.git] / src / jalview / analysis /
2020-08-10 gmungocJAL-3490 match count independent of contiguous matches... patch/Release_2_11_1_Branch_patch_JAL-3490 tree | commitdiff
2020-06-29 Jim ProcterMerge branch 'bug/JAL-3490findSpanHiddenGaps' into... tree | commitdiff
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files tree | commitdiff
2020-02-18 Mungo CarstairsJAL-3536 JAL-3187 don't create duplicate CDS-to-protein... bug/JAL-3536getCrossrefTwice tree | commitdiff
2020-01-28 gmungocJAL-3187 one more obsolete method removed tree | commitdiff
2019-12-12 gmungocJAL-3490 unit test for ignore hidden regions with selec... tree | commitdiff
2019-12-11 gmungocJAL-3490 tests for skip hidden regions (and a bug fix) tree | commitdiff
2019-12-11 gmungocJAL-3490 revised layout and search algorithm (more... tree | commitdiff
2019-11-29 gmungocJAL-3490 Finder match across entirely gapped hidden... tree | commitdiff
2019-11-01 Ben SoaresJAL-3474 removed all .cvsignore files stored in the... improvement/JAL-3474_lots_of_.cvsignore_files tree | commitdiff
2019-08-22 gmungocJAL-3187 one more obsolete method removed tree | commitdiff
2019-08-09 gmungocJAL-3187 removal of variant feature (non-virtual) trans... tree | commitdiff
2019-07-10 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-18 gmungocJAL-3313 don't double count mapped codons tree | commitdiff
2019-06-17 gmungocJAL-3187 update alignAs code and unit tests for 'shared... tree | commitdiff
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript tree | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... tree | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-04-11 Jim ProcterMerge branch 'develop' into task/JAL-3130_Java_11_inves... tree | commitdiff
2019-03-27 gmungocJAL-2620 improved error reporting on failure to load... tree | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... tree | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... tree | commitdiff
2019-03-11 gmungocJAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test... tree | commitdiff
2019-03-07 gmungocMerge branch 'feature/JAL-3205symmetricCalc' into develop tree | commitdiff
2019-03-05 gmungocMerge remote-tracking branch 'origin/features/JAL-2620a... tree | commitdiff
2019-03-05 gmungocMerge remote-tracking branch 'origin/bug/JAL-2839findWi... tree | commitdiff
2019-03-03 gmungocJAL-3205 faster calculation with symmetric score matrix tree | commitdiff
2019-02-28 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into merge... tree | commitdiff
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature... tree | commitdiff
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover... tree | commitdiff
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct... tree | commitdiff
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation... tree | commitdiff
2018-12-19 Jim ProcterMerge branch 'features/JAL-1767pcaInProject' into bug... tree | commitdiff
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch tree | commitdiff
2018-09-06 Jim ProcterJAL-3105 reallocate quality and consensus annotation... tree | commitdiff
2018-08-30 Jim ProcterJAL-3092 make sure base pair counter is always moved... tree | commitdiff
2018-05-07 gmungocJAL-1767 unit test for save and restore PCA features/JAL-1767pcaInProject tree | commitdiff
2018-05-07 gmungocJAL-1767 save PCA D and E vectors instead of 'details... tree | commitdiff
2018-05-04 gmungocJAL-1767 refactorings to enable faithful restore of... tree | commitdiff
2018-04-27 gmungocJAL-1767 refactoring and tidying of RotatableCanvas... tree | commitdiff
2018-04-26 gmungocJAL-2962 remove Change Parameters menu from PCA panel tree | commitdiff
2018-04-26 gmungocJAL-2962 code tidying/documentation (non-functional... tree | commitdiff
2018-04-25 gmungocJAL-1767 minor field tidying prior to functional changes tree | commitdiff
2018-03-19 gmungocJAL-2620 parse genetic code tables from standard file... tree | commitdiff
2018-03-16 gmungocJAL-2620 alternative genetic code translation tables tree | commitdiff
2018-03-14 gmungocJAL-2933 pass viewport in Finder constructor, find... bug/JAL-2839findWithHidden tree | commitdiff
2018-03-14 gmungocJAL-2933 gui and applet Finder hold a FinderI per viewport tree | commitdiff
2018-03-14 gmungocJAL-2839 refactored out getNextVisibleSequenceRegion tree | commitdiff
2018-03-13 gmungocJAL-2839 refactored analysis.Finder and tests tree | commitdiff
2018-03-09 gmungocJAL-2839 Finder refactoring prior to fixing the defect tree | commitdiff
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 tree | commitdiff
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666 tree | commitdiff
2018-02-09 gmungocJAL-2789 code format changes only (before functional... tree | commitdiff
2018-02-05 gmungocJAL-2897 more informative description on synonymous... tree | commitdiff
2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge tree | commitdiff
2018-02-05 gmungocJAL-2897 more informative description on synonymous... 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
2018-01-30 gmungocJAL-2897 formatting change only prior to functional... tree | commitdiff
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759 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
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-10-26 Jim ProcterMerge branch 'features/JAL-2685pairwiseSeqLimits' into... tree | commitdiff
2017-10-05 gmungocJAL-2738 update spikes/mungo tree | commitdiff
2017-10-05 gmungocJAL-2755 transfer chromosomal reference from transcript... tree | commitdiff
2017-10-04 gmungocJAL-2738 match consequence "Allele" to VCF allele;... tree | commitdiff
2017-10-03 kiramtJAL-2674 testing tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-09-29 kiramtJAL-2674 finish with iterators for now tree | commitdiff
2017-09-28 kiramtJAL-2647 more iterators tree | commitdiff
2017-09-26 gmungocJAL-2738 JAL-2154 add DBRef from transcript to synthesi... tree | commitdiff
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu... tree | commitdiff
2017-09-21 gmungocJAL-2738 compute VCF on peptide, extract AF (allele... tree | commitdiff
2017-09-04 gmungocJAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon tree | commitdiff
2017-09-01 gmungocJAL-2617 omit stop codon from synthesized CDS sequence tree | commitdiff
2017-08-30 gmungocJAL-2685 tweaks to output spacing, updated TestAlignSeq... tree | commitdiff
2017-08-30 gmungocJAL-2685 use actual selection for report of pairwise... tree | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList 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
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... tree | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch tree | commitdiff
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn tree | commitdiff
2017-05-31 gmungocJAL-2574 preparation for Sequence.findFeatures(col1... tree | commitdiff
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures tree | commitdiff
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const... tree | commitdiff
2017-05-23 gmungocJAL-2490 find features for export as GFF, JAL-2548... tree | commitdiff
2017-05-22 gmungocJAL-2544 check feature overlaps selection region tree | commitdiff
2017-05-19 gmungocJAL-2544 only include features in selected columns... tree | commitdiff
2017-05-19 gmungocJAL-2490 performant lookup of features for sorting tree | commitdiff
2017-05-19 gmungocJAL-2505 unit test for sort by feature density, Javadoc tree | commitdiff
2017-05-18 gmungocJAL-2490 initial unit tests prior to refactoring tree | commitdiff
2017-05-16 gmungocJAL-2505 refactored method removed tree | commitdiff
2017-05-16 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-16 gmungocJAL-2505 set helix number as feature group in SequenceF... tree | commitdiff
2017-05-16 gmungocJAL-2403 simplify instantiation / configuration of... tree | commitdiff
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