2017-06-14 |
gmungoc | JAL-2598 Sequence.getSequence return a copy of the... |
tree | commitdiff |
2017-06-01 |
gmungoc | JAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn |
tree | commitdiff |
2017-05-31 |
gmungoc | JAL-2574 preparation for Sequence.findFeatures(col1... |
tree | commitdiff |
2017-05-25 |
gmungoc | JAL-2557 removal of Sequence.sequenceFeatures |
tree | commitdiff |
2017-05-25 |
gmungoc | JAL-2050 make SequenceFeature.score final, adjust const... |
tree | commitdiff |
2017-05-23 |
gmungoc | JAL-2490 find features for export as GFF, JAL-2548... |
tree | commitdiff |
2017-05-22 |
gmungoc | JAL-2544 check feature overlaps selection region |
tree | commitdiff |
2017-05-19 |
gmungoc | JAL-2544 only include features in selected columns... |
tree | commitdiff |
2017-05-19 |
gmungoc | JAL-2490 performant lookup of features for sorting |
tree | commitdiff |
2017-05-19 |
gmungoc | JAL-2505 unit test for sort by feature density, Javadoc |
tree | commitdiff |
2017-05-18 |
gmungoc | JAL-2490 initial unit tests prior to refactoring |
tree | commitdiff |
2017-05-16 |
gmungoc | JAL-2505 refactored method removed |
tree | commitdiff |
2017-05-16 |
gmungoc | Merge branch 'develop' into features/JAL-2446NCList |
tree | commitdiff |
2017-05-16 |
gmungoc | JAL-2505 set helix number as feature group in SequenceF... |
tree | commitdiff |
2017-05-16 |
gmungoc | JAL-2403 simplify instantiation / configuration of... |
tree | commitdiff |
2017-05-15 |
gmungoc | JAL-2480 redundant code removed |
tree | commitdiff |
2017-05-12 |
gmungoc | JAL-2525 get sequence features for Ontology term(s... |
tree | commitdiff |
2017-05-09 |
gmungoc | JAL-2505 use constructors to set (what will be) final... |
tree | commitdiff |
2017-05-04 |
Jim Procter | Merge branch 'features/JAL-2393customMatrices' into... |
tree | commitdiff |
2017-05-04 |
Jim Procter | Merge branch 'features/JAL-2393customMatrices' into... |
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2017-05-03 |
Jim Procter | JAL-1933 show occupancy in tooltip for row |
tree | commitdiff |
2017-05-02 |
gmungoc | JAL-2499 JAL-2403 push 'configure for view' inside... |
tree | commitdiff |
2017-04-28 |
gmungoc | Merge branch 'develop' into features/JAL-2393customMatrices |
tree | commitdiff |
2017-04-27 |
Jim Procter | JAL-1933 shade occupancy from light grey to black for... |
tree | commitdiff |
2017-04-27 |
Jim Procter | JAL-1933 don’t show symbol counts under histogram ... |
tree | commitdiff |
2017-04-12 |
gmungoc | JAL-2403 public static methods to convert distance... |
tree | commitdiff |
2017-04-11 |
gmungoc | JAL-2403 improved ScoreModelI hierarchy as per Kira... |
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2017-04-11 |
gmungoc | JAL-2428 Javadoc |
tree | commitdiff |
2017-04-10 |
gmungoc | JAL-2403 unit tests for PCA.computeSimilarity, signatur... |
tree | commitdiff |
2017-04-10 |
gmungoc | JAL-2403 removed remaining jvCalcMode references from PCA |
tree | commitdiff |
2017-04-09 |
gmungoc | JAL-2393 remove unused commented code |
tree | commitdiff |
2017-04-07 |
gmungoc | JAL-2393 code tidying for review comments |
tree | commitdiff |
2017-03-29 |
gmungoc | JAL-2416 JAL-728 reduced dependency on Blosum62 impleme... |
tree | commitdiff |
2017-03-29 |
gmungoc | JAL-2416 revert to '*' not '-' in score matrix, handle... |
tree | commitdiff |
2017-03-29 |
gmungoc | JAL-2416 explicit constant for unknown/unknown identity... |
tree | commitdiff |
2017-03-28 |
gmungoc | JAL-2403 JAL-2416 pairwise score unexpected symbols... |
tree | commitdiff |
2017-03-28 |
gmungoc | JAL-2416 JAL-2403 remove unused '*' row/column from... |
tree | commitdiff |
2017-03-28 |
gmungoc | JAL-2403 further test coverage for ScoreMatrix, min... |
tree | commitdiff |
2017-03-27 |
gmungoc | JAL-2416 parse score matrices in either NCBI or AAindex... |
tree | commitdiff |
2017-03-27 |
gmungoc | JAL-2416 tidy up after switch from ' ' to '-' in score... |
tree | commitdiff |
2017-03-27 |
gmungoc | JAL-2416 score matrix gap symbol (if any) dynamically... |
tree | commitdiff |
2017-03-27 |
gmungoc | JAL-2416 add score model description field for tooltip... |
tree | commitdiff |
2017-03-27 |
gmungoc | JAL-2403 SWDistanceModel now SmithWatermanModel - a... |
tree | commitdiff |
2017-03-27 |
gmungoc | JAL-2416 use '-' not space for gap in score matrices |
tree | commitdiff |
2017-03-27 |
gmungoc | JAL-2428 unused method deleted |
tree | commitdiff |
2017-03-27 |
gmungoc | JAL-2403 PIDDistanceModel deleted as superseded by... |
tree | commitdiff |
2017-03-27 |
gmungoc | JAL-2428 pass AlignmentView to TreeModel so Show Input... |
tree | commitdiff |
2017-03-24 |
gmungoc | JAL-2428 simplify TreeModel constructors, add getOrigin... |
tree | commitdiff |
2017-03-24 |
gmungoc | JAL-838 move two callers off Comparison.PID and depreca... |
tree | commitdiff |
2017-03-23 |
gmungoc | JAL-2397 scale PCA by PID to alignment width to match... |
tree | commitdiff |
2017-03-23 |
gmungoc | JAL-838 class javadoc added |
tree | commitdiff |
2017-03-23 |
gmungoc | JAL-2393 code tidy and comments, PIDDistanceModel depre... |
tree | commitdiff |
2017-03-23 |
gmungoc | Merge branch 'develop' into features/JAL-2393customMatrices |
tree | commitdiff |
2017-03-16 |
Jim Procter | JAL-1933 refactor parameter for code clarity |
tree | commitdiff |
2017-03-06 |
gmungoc | JAL-2428 correct order of processing in joinClusters() |
tree | commitdiff |
2017-03-06 |
gmungoc | JAL-2428 separate TreeModel from TreeBuilder/NJTree... |
tree | commitdiff |
2017-03-03 |
gmungoc | JAL-2428 use BitSet for clusters and done flags |
tree | commitdiff |
2017-03-01 |
gmungoc | Merge branch 'features/JAL-2295setChimeraAttributes... |
tree | commitdiff |
2017-02-28 |
gmungoc | JAL-1632 'includeGaps' applied to FeatureDistanceModel... |
tree | commitdiff |
2017-02-27 |
gmungoc | JAL-2416 seqspace.scm and PIDDistanceModel replaced... |
tree | commitdiff |
2017-02-27 |
gmungoc | JAL-838 ScoreMatrix now respects SimilarityParams! |
tree | commitdiff |
2017-02-27 |
gmungoc | JAL-838 tests for PID calculation with parameter options |
tree | commitdiff |
2017-02-27 |
gmungoc | JAL-1632 similarity options on TreeChooser panel affect... |
tree | commitdiff |
2017-02-27 |
gmungoc | JAL-1632 add score model params to PCAModel and PCA... |
tree | commitdiff |
2017-02-27 |
gmungoc | JAL-1632 refactored NJTree constructor to include Simil... |
tree | commitdiff |
2017-02-27 |
gmungoc | JAL-2403 JAL-838 remove unused methods and unneeded... |
tree | commitdiff |
2017-02-24 |
gmungoc | JAL-838 added 'SeqSpace' PID mode, added parameters... |
tree | commitdiff |
2017-02-24 |
gmungoc | JAL-1403 preserve range of distance scores for similarity |
tree | commitdiff |
2017-02-24 |
gmungoc | JAL-2403 PIDModel added (wip) |
tree | commitdiff |
2017-02-24 |
gmungoc | JAL-2403 code tidy |
tree | commitdiff |
2017-02-24 |
gmungoc | JAL-1483 PIDModel potential replacement for PIDDistance... |
tree | commitdiff |
2017-02-24 |
gmungoc | JAL-838 first version of PID parameters model |
tree | commitdiff |
2017-02-24 |
gmungoc | JAL-2403 remove unused ScoreMatrix.symmetric |
tree | commitdiff |
2017-02-24 |
gmungoc | JAL-2403 JAL-1483 push 'reverseRange' inside Matrix |
tree | commitdiff |
2017-02-23 |
gmungoc | JAL-2403 JAL-1483 changes to ScoreModelI hierarchy... |
tree | commitdiff |
2017-02-21 |
gmungoc | JAL-2416 ScoreMatrix.getMatrix() returns a defensive... |
tree | commitdiff |
2017-02-21 |
gmungoc | JAL-2416 support roundtrip print/parse of ScoreMatrix |
tree | commitdiff |
2017-02-21 |
gmungoc | Merge branch 'develop' into features/JAL-2393customMatrices |
tree | commitdiff |
2017-02-21 |
gmungoc | JAL-2416 quality calculation now only depends on loaded... |
tree | commitdiff |
2017-02-21 |
gmungoc | JAL-2416 more validation in ScoreMatrix constructor |
tree | commitdiff |
2017-02-20 |
gmungoc | JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix... |
tree | commitdiff |
2017-02-20 |
gmungoc | JAL-2416 replaced dependency on ResidueProperties with... |
tree | commitdiff |
2017-02-20 |
gmungoc | JAL-2416 remove unused pep, dna alphabets, unused metho... |
tree | commitdiff |
2017-02-18 |
gmungoc | JAL-2416 better encapsulated 'constants' for BLOSUM62... |
tree | commitdiff |
2017-02-17 |
gmungoc | JAL-2416 BLOSUM62 removed from ResidueProperties |
tree | commitdiff |
2017-02-17 |
gmungoc | JAL-2416 removed DNA and PAM250 matrices from ResiduePr... |
tree | commitdiff |
2017-02-17 |
gmungoc | JAL-2416 scoreMatrices removed from ResidueProperties |
tree | commitdiff |
2017-02-17 |
gmungoc | JAL-2413 extracted new method SetUtils.countDisjunction() |
tree | commitdiff |
2017-02-17 |
gmungoc | JAL-2423 refactored method to build panel title for... |
tree | commitdiff |
2017-02-17 |
gmungoc | JAL-2416 order score models by order of addition rather... |
tree | commitdiff |
2017-02-17 |
gmungoc | JAL-2403 redundant 'implements' removed |
tree | commitdiff |
2017-02-17 |
gmungoc | JAL-2403 extract method refactoring of FeatureScoreMode... |
tree | commitdiff |
2017-02-17 |
gmungoc | JAL-2403 constants for "NJ", "AV" |
tree | commitdiff |
2017-02-14 |
gmungoc | Parsing moved to (new) ScoreMatrixFile, drag and drop... |
tree | commitdiff |
2017-02-13 |
gmungoc | JAL-2416 allow alphabet symbol (optional) in first... |
tree | commitdiff |
2017-02-13 |
gmungoc | JAL-1632 JAL-2416 load score matrices from file, as... |
tree | commitdiff |
2017-02-13 |
gmungoc | JAL-1632 first cut of Tree chooser dialog and ScoreMode... |
tree | commitdiff |
2017-02-09 |
gmungoc | Merge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory |
tree | commitdiff |
2017-02-07 |
gmungoc | JAL-2379 removed unused commented code |
tree | commitdiff |
2017-02-06 |
gmungoc | JAL-2379 computePairwiseScores() moved to ScoreMatrix |
tree | commitdiff |
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