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JAL-2473 revised default minimum dimension for Alignment Frame windows
[jalview.git] / src / jalview / analysis /
2017-05-22 gmungocJAL-2544 check feature overlaps selection region tree | commitdiff
2017-05-16 gmungocJAL-2403 simplify instantiation / configuration of... tree | commitdiff
2017-05-04 Jim ProcterMerge branch 'features/JAL-2393customMatrices' into... tree | commitdiff
2017-05-04 Jim ProcterMerge branch 'features/JAL-2393customMatrices' into... tree | commitdiff
2017-05-03 Jim ProcterJAL-1933 show occupancy in tooltip for row tree | commitdiff
2017-05-02 gmungocJAL-2499 JAL-2403 push 'configure for view' inside... tree | commitdiff
2017-04-28 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-04-27 Jim ProcterJAL-1933 shade occupancy from light grey to black for... tree | commitdiff
2017-04-27 Jim ProcterJAL-1933 don’t show symbol counts under histogram ... tree | commitdiff
2017-04-12 gmungocJAL-2403 public static methods to convert distance... tree | commitdiff
2017-04-11 gmungocJAL-2403 improved ScoreModelI hierarchy as per Kira... tree | commitdiff
2017-04-11 gmungocJAL-2428 Javadoc tree | commitdiff
2017-04-10 gmungocJAL-2403 unit tests for PCA.computeSimilarity, signatur... tree | commitdiff
2017-04-10 gmungocJAL-2403 removed remaining jvCalcMode references from PCA tree | commitdiff
2017-04-09 gmungocJAL-2393 remove unused commented code tree | commitdiff
2017-04-07 gmungocJAL-2393 code tidying for review comments tree | commitdiff
2017-03-29 gmungocJAL-2416 JAL-728 reduced dependency on Blosum62 impleme... tree | commitdiff
2017-03-29 gmungocJAL-2416 revert to '*' not '-' in score matrix, handle... tree | commitdiff
2017-03-29 gmungocJAL-2416 explicit constant for unknown/unknown identity... tree | commitdiff
2017-03-28 gmungocJAL-2403 JAL-2416 pairwise score unexpected symbols... tree | commitdiff
2017-03-28 gmungocJAL-2416 JAL-2403 remove unused '*' row/column from... tree | commitdiff
2017-03-28 gmungocJAL-2403 further test coverage for ScoreMatrix, min... tree | commitdiff
2017-03-27 gmungocJAL-2416 parse score matrices in either NCBI or AAindex... tree | commitdiff
2017-03-27 gmungocJAL-2416 tidy up after switch from ' ' to '-' in score... tree | commitdiff
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically... tree | commitdiff
2017-03-27 gmungocJAL-2416 add score model description field for tooltip... tree | commitdiff
2017-03-27 gmungocJAL-2403 SWDistanceModel now SmithWatermanModel - a... tree | commitdiff
2017-03-27 gmungocJAL-2416 use '-' not space for gap in score matrices tree | commitdiff
2017-03-27 gmungocJAL-2428 unused method deleted tree | commitdiff
2017-03-27 gmungocJAL-2403 PIDDistanceModel deleted as superseded by... tree | commitdiff
2017-03-27 gmungocJAL-2428 pass AlignmentView to TreeModel so Show Input... tree | commitdiff
2017-03-24 gmungocJAL-2428 simplify TreeModel constructors, add getOrigin... tree | commitdiff
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca... tree | commitdiff
2017-03-23 gmungocJAL-2397 scale PCA by PID to alignment width to match... tree | commitdiff
2017-03-23 gmungocJAL-838 class javadoc added tree | commitdiff
2017-03-23 gmungocJAL-2393 code tidy and comments, PIDDistanceModel depre... tree | commitdiff
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-03-16 Jim ProcterJAL-1933 refactor parameter for code clarity tree | commitdiff
2017-03-06 gmungocJAL-2428 correct order of processing in joinClusters() tree | commitdiff
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree... tree | commitdiff
2017-03-03 gmungocJAL-2428 use BitSet for clusters and done flags tree | commitdiff
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... tree | commitdiff
2017-02-28 gmungocJAL-1632 'includeGaps' applied to FeatureDistanceModel... tree | commitdiff
2017-02-27 gmungocJAL-2416 seqspace.scm and PIDDistanceModel replaced... tree | commitdiff
2017-02-27 gmungocJAL-838 ScoreMatrix now respects SimilarityParams! tree | commitdiff
2017-02-27 gmungocJAL-838 tests for PID calculation with parameter options tree | commitdiff
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect... tree | commitdiff
2017-02-27 gmungocJAL-1632 add score model params to PCAModel and PCA... tree | commitdiff
2017-02-27 gmungocJAL-1632 refactored NJTree constructor to include Simil... tree | commitdiff
2017-02-27 gmungocJAL-2403 JAL-838 remove unused methods and unneeded... tree | commitdiff
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters... tree | commitdiff
2017-02-24 gmungocJAL-1403 preserve range of distance scores for similarity tree | commitdiff
2017-02-24 gmungocJAL-2403 PIDModel added (wip) tree | commitdiff
2017-02-24 gmungocJAL-2403 code tidy tree | commitdiff
2017-02-24 gmungocJAL-1483 PIDModel potential replacement for PIDDistance... tree | commitdiff
2017-02-24 gmungocJAL-838 first version of PID parameters model tree | commitdiff
2017-02-24 gmungocJAL-2403 remove unused ScoreMatrix.symmetric tree | commitdiff
2017-02-24 gmungocJAL-2403 JAL-1483 push 'reverseRange' inside Matrix tree | commitdiff
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy... tree | commitdiff
2017-02-21 gmungocJAL-2416 ScoreMatrix.getMatrix() returns a defensive... tree | commitdiff
2017-02-21 gmungocJAL-2416 support roundtrip print/parse of ScoreMatrix tree | commitdiff
2017-02-21 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-02-21 gmungocJAL-2416 quality calculation now only depends on loaded... tree | commitdiff
2017-02-21 gmungocJAL-2416 more validation in ScoreMatrix constructor tree | commitdiff
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix... tree | commitdiff
2017-02-20 gmungocJAL-2416 replaced dependency on ResidueProperties with... tree | commitdiff
2017-02-20 gmungocJAL-2416 remove unused pep, dna alphabets, unused metho... tree | commitdiff
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62... tree | commitdiff
2017-02-17 gmungocJAL-2416 BLOSUM62 removed from ResidueProperties tree | commitdiff
2017-02-17 gmungocJAL-2416 removed DNA and PAM250 matrices from ResiduePr... tree | commitdiff
2017-02-17 gmungocJAL-2416 scoreMatrices removed from ResidueProperties tree | commitdiff
2017-02-17 gmungocJAL-2413 extracted new method SetUtils.countDisjunction() tree | commitdiff
2017-02-17 gmungocJAL-2423 refactored method to build panel title for... tree | commitdiff
2017-02-17 gmungocJAL-2416 order score models by order of addition rather... tree | commitdiff
2017-02-17 gmungocJAL-2403 redundant 'implements' removed tree | commitdiff
2017-02-17 gmungocJAL-2403 extract method refactoring of FeatureScoreMode... tree | commitdiff
2017-02-17 gmungocJAL-2403 constants for "NJ", "AV" tree | commitdiff
2017-02-14 gmungocParsing moved to (new) ScoreMatrixFile, drag and drop... tree | commitdiff
2017-02-13 gmungocJAL-2416 allow alphabet symbol (optional) in first... tree | commitdiff
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... tree | commitdiff
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode... tree | commitdiff
2017-02-09 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory tree | commitdiff
2017-02-07 gmungocJAL-2379 removed unused commented code tree | commitdiff
2017-02-06 gmungocJAL-2379 computePairwiseScores() moved to ScoreMatrix tree | commitdiff
2017-02-03 gmungocJAL-2379 'direct' pairwise score calculation for PCA... tree | commitdiff
2017-01-26 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory tree | commitdiff
2017-01-26 gmungocJAL-2380 code tidy after review tree | commitdiff
2017-01-17 gmungocJAL-2379 use SparseMatrix for encoded sequences, tidy... tree | commitdiff
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI tree | commitdiff
2016-12-16 gmungocJAL-1705 JAL-98 use SortedMap as more accurate type... tree | commitdiff
2016-12-05 gmungocMerge branch 'features/JAL-1933_occupancy' into feature... tree | commitdiff
2016-12-04 Jim ProcterJAL-1933 show occupancy count as a tooltip tree | commitdiff
2016-12-04 Jim ProcterJAL-1933 switch from gap count to occupancy tree | commitdiff
2016-12-02 gmungocMerge branch 'features/JAL-1933_occupancy' into feature... tree | commitdiff
2016-12-02 gmungocJAL-1933 gap value as description; minor formatting tree | commitdiff
2016-12-01 Jim ProcterJAL-1933 update the bounds for the Gap annotation row... tree | commitdiff
2016-12-01 Jim ProcterJAL-1933 basic hack to get gap counts shown as an annot... tree | commitdiff
2016-11-23 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
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