Merge branch 'develop' into releases/Release_2_11_Branch
[jalview.git] / src / jalview / analysis /
2019-04-11 Jim ProcterMerge branch 'develop' into task/JAL-3130_Java_11_inves...
2019-03-27 gmungocJAL-2620 improved error reporting on failure to load...
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with...
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat...
2019-03-11 gmungocJAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test...
2019-03-07 gmungocMerge branch 'feature/JAL-3205symmetricCalc' into develop
2019-03-05 gmungocMerge remote-tracking branch 'origin/features/JAL-2620a...
2019-03-05 gmungocMerge remote-tracking branch 'origin/bug/JAL-2839findWi...
2019-03-03 gmungocJAL-3205 faster calculation with symmetric score matrix
2019-02-28 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into merge...
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation...
2018-12-19 Jim ProcterMerge branch 'features/JAL-1767pcaInProject' into bug...
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch
2018-09-06 Jim ProcterJAL-3105 reallocate quality and consensus annotation...
2018-08-30 Jim ProcterJAL-3092 make sure base pair counter is always moved...
2018-05-07 gmungocJAL-1767 unit test for save and restore PCA features/JAL-1767pcaInProject
2018-05-07 gmungocJAL-1767 save PCA D and E vectors instead of 'details...
2018-05-04 gmungocJAL-1767 refactorings to enable faithful restore of...
2018-04-27 gmungocJAL-1767 refactoring and tidying of RotatableCanvas...
2018-04-26 gmungocJAL-2962 remove Change Parameters menu from PCA panel
2018-04-26 gmungocJAL-2962 code tidying/documentation (non-functional...
2018-04-25 gmungocJAL-1767 minor field tidying prior to functional changes
2018-03-19 gmungocJAL-2620 parse genetic code tables from standard file...
2018-03-16 gmungocJAL-2620 alternative genetic code translation tables
2018-03-14 gmungocJAL-2933 pass viewport in Finder constructor, find... bug/JAL-2839findWithHidden
2018-03-14 gmungocJAL-2933 gui and applet Finder hold a FinderI per viewport
2018-03-14 gmungocJAL-2839 refactored out getNextVisibleSequenceRegion
2018-03-13 gmungocJAL-2839 refactored analysis.Finder and tests
2018-03-09 gmungocJAL-2839 Finder refactoring prior to fixing the defect
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666
2018-02-09 gmungocJAL-2789 code format changes only (before functional...
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon...
2018-01-30 gmungocJAL-2897 formatting change only prior to functional...
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-27 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-26 Jim ProcterMerge branch 'features/JAL-2685pairwiseSeqLimits' into...
2017-10-05 gmungocJAL-2738 update spikes/mungo
2017-10-05 gmungocJAL-2755 transfer chromosomal reference from transcript...
2017-10-04 gmungocJAL-2738 match consequence "Allele" to VCF allele;...
2017-10-03 kiramtJAL-2674 testing
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-29 kiramtJAL-2674 finish with iterators for now
2017-09-28 kiramtJAL-2647 more iterators
2017-09-26 gmungocJAL-2738 JAL-2154 add DBRef from transcript to synthesi...
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu...
2017-09-21 gmungocJAL-2738 compute VCF on peptide, extract AF (allele...
2017-09-04 gmungocJAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon
2017-09-01 gmungocJAL-2617 omit stop codon from synthesized CDS sequence
2017-08-30 gmungocJAL-2685 tweaks to output spacing, updated TestAlignSeq...
2017-08-30 gmungocJAL-2685 use actual selection for report of pairwise...
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 add GPL to main sources
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn
2017-05-31 gmungocJAL-2574 preparation for Sequence.findFeatures(col1...
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-23 gmungocJAL-2490 find features for export as GFF, JAL-2548...
2017-05-22 gmungocJAL-2544 check feature overlaps selection region
2017-05-19 gmungocJAL-2544 only include features in selected columns...
2017-05-19 gmungocJAL-2490 performant lookup of features for sorting
2017-05-19 gmungocJAL-2505 unit test for sort by feature density, Javadoc
2017-05-18 gmungocJAL-2490 initial unit tests prior to refactoring
2017-05-16 gmungocJAL-2505 refactored method removed
2017-05-16 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-16 gmungocJAL-2505 set helix number as feature group in SequenceF...
2017-05-16 gmungocJAL-2403 simplify instantiation / configuration of...
2017-05-15 gmungocJAL-2480 redundant code removed
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s...
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final...
2017-05-04 Jim ProcterMerge branch 'features/JAL-2393customMatrices' into...
2017-05-04 Jim ProcterMerge branch 'features/JAL-2393customMatrices' into...
2017-05-03 Jim ProcterJAL-1933 show occupancy in tooltip for row
2017-05-02 gmungocJAL-2499 JAL-2403 push 'configure for view' inside...
2017-04-28 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-04-27 Jim ProcterJAL-1933 shade occupancy from light grey to black for...
2017-04-27 Jim ProcterJAL-1933 don’t show symbol counts under histogram ...
2017-04-12 gmungocJAL-2403 public static methods to convert distance...
2017-04-11 gmungocJAL-2403 improved ScoreModelI hierarchy as per Kira...
2017-04-11 gmungocJAL-2428 Javadoc
2017-04-10 gmungocJAL-2403 unit tests for PCA.computeSimilarity, signatur...
2017-04-10 gmungocJAL-2403 removed remaining jvCalcMode references from PCA
2017-04-09 gmungocJAL-2393 remove unused commented code
2017-04-07 gmungocJAL-2393 code tidying for review comments
2017-03-29 gmungocJAL-2416 JAL-728 reduced dependency on Blosum62 impleme...
2017-03-29 gmungocJAL-2416 revert to '*' not '-' in score matrix, handle...
2017-03-29 gmungocJAL-2416 explicit constant for unknown/unknown identity...
2017-03-28 gmungocJAL-2403 JAL-2416 pairwise score unexpected symbols...
2017-03-28 gmungocJAL-2416 JAL-2403 remove unused '*' row/column from...
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