JAL-4019 Clarification of position on 'X' in help text
[jalview.git] / src / jalview / analysis /
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...
2017-03-28 gmungocJAL-2403 further test coverage for ScoreMatrix, min...
2017-03-27 gmungocJAL-2416 parse score matrices in either NCBI or AAindex...
2017-03-27 gmungocJAL-2416 tidy up after switch from ' ' to '-' in score...
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically...
2017-03-27 gmungocJAL-2416 add score model description field for tooltip...
2017-03-27 gmungocJAL-2403 SWDistanceModel now SmithWatermanModel - a...
2017-03-27 gmungocJAL-2416 use '-' not space for gap in score matrices
2017-03-27 gmungocJAL-2428 unused method deleted
2017-03-27 gmungocJAL-2403 PIDDistanceModel deleted as superseded by...
2017-03-27 gmungocJAL-2428 pass AlignmentView to TreeModel so Show Input...
2017-03-24 gmungocJAL-2428 simplify TreeModel constructors, add getOrigin...
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca...
2017-03-23 gmungocJAL-2397 scale PCA by PID to alignment width to match...
2017-03-23 gmungocJAL-838 class javadoc added
2017-03-23 gmungocJAL-2393 code tidy and comments, PIDDistanceModel depre...
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-03-16 Jim ProcterJAL-1933 refactor parameter for code clarity
2017-03-06 gmungocJAL-2428 correct order of processing in joinClusters()
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree...
2017-03-03 gmungocJAL-2428 use BitSet for clusters and done flags
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes...
2017-02-28 gmungocJAL-1632 'includeGaps' applied to FeatureDistanceModel...
2017-02-27 gmungocJAL-2416 seqspace.scm and PIDDistanceModel replaced...
2017-02-27 gmungocJAL-838 ScoreMatrix now respects SimilarityParams!
2017-02-27 gmungocJAL-838 tests for PID calculation with parameter options
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect...
2017-02-27 gmungocJAL-1632 add score model params to PCAModel and PCA...
2017-02-27 gmungocJAL-1632 refactored NJTree constructor to include Simil...
2017-02-27 gmungocJAL-2403 JAL-838 remove unused methods and unneeded...
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters...
2017-02-24 gmungocJAL-1403 preserve range of distance scores for similarity
2017-02-24 gmungocJAL-2403 PIDModel added (wip)
2017-02-24 gmungocJAL-2403 code tidy
2017-02-24 gmungocJAL-1483 PIDModel potential replacement for PIDDistance...
2017-02-24 gmungocJAL-838 first version of PID parameters model
2017-02-24 gmungocJAL-2403 remove unused ScoreMatrix.symmetric
2017-02-24 gmungocJAL-2403 JAL-1483 push 'reverseRange' inside Matrix
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
2017-02-21 gmungocJAL-2416 ScoreMatrix.getMatrix() returns a defensive...
2017-02-21 gmungocJAL-2416 support roundtrip print/parse of ScoreMatrix
2017-02-21 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-02-21 gmungocJAL-2416 quality calculation now only depends on loaded...
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