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 |
2017-02-03 |
gmungoc | JAL-2379 'direct' pairwise score calculation for PCA... |
tree | commitdiff |
2017-01-26 |
gmungoc | Merge branch 'features/JAL-2360colourSchemeApplicabilit... |
tree | commitdiff |
2017-01-26 |
gmungoc | Merge branch 'develop' into features/JAL-2360colourSche... |
tree | commitdiff |
2017-01-26 |
gmungoc | Merge branch 'develop' into features/JAL-2379pcaMemory |
tree | commitdiff |
2017-01-26 |
gmungoc | JAL-2380 code tidy after review |
tree | commitdiff |
2017-01-17 |
gmungoc | JAL-2379 use SparseMatrix for encoded sequences, tidy... |
tree | commitdiff |
2017-01-04 |
gmungoc | JAL-2371 CollectionColourScheme wraps ColourSchemeI |
tree | commitdiff |
2016-12-16 |
gmungoc | JAL-1705 JAL-98 use SortedMap as more accurate type... |
tree | commitdiff |
2016-12-05 |
gmungoc | Merge branch 'features/JAL-1933_occupancy' into feature... |
tree | commitdiff |
2016-12-04 |
Jim Procter | JAL-1933 show occupancy count as a tooltip |
tree | commitdiff |
2016-12-04 |
Jim Procter | JAL-1933 switch from gap count to occupancy |
tree | commitdiff |
2016-12-02 |
gmungoc | Merge branch 'features/JAL-1933_occupancy' into feature... |
tree | commitdiff |
2016-12-02 |
gmungoc | JAL-1933 gap value as description; minor formatting |
tree | commitdiff |
2016-12-01 |
Jim Procter | JAL-1933 update the bounds for the Gap annotation row... |
tree | commitdiff |
2016-12-01 |
Jim Procter | JAL-1933 basic hack to get gap counts shown as an annot... |
tree | commitdiff |
2016-11-23 |
gmungoc | Merge branch 'develop' into features/JAL-2295setChimera... |
tree | commitdiff |
2016-11-22 |
Jim Procter | Merge branch 'features/JAL-1738_JAL-345_selectionfromhi... |
tree | commitdiff |
2016-11-17 |
gmungoc | JAL-98 ProfilesI container for profiles for columns |
tree | commitdiff |
2016-11-11 |
gmungoc | Merge branch 'develop' into features/JAL-2295setChimera... |
tree | commitdiff |
2016-11-08 |
gmungoc | JAL-2295 make RangeComparator a top level class for... |
tree | commitdiff |
2016-11-08 |
tcofoegbu | JAL-2292 updated method calls |
tree | commitdiff |
2016-11-04 |
tcofoegbu | JAL-2292 fix for wrong mapping output in sequence mappi... |
tree | commitdiff |
2016-11-03 |
gmungoc | JAL-2310 don't double-count sequence matches; code... |
tree | commitdiff |
2016-11-02 |
Jim Procter | JAL-1738 JAL-345 fix for JAL-2302 only report Matches... |
tree | commitdiff |
2016-11-02 |
gmungoc | JAL-98 JAL-1854 encapsulate 'magic number' threshold... |
tree | commitdiff |
2016-11-02 |
gmungoc | JAL-98 ProfileI interface for Profile |
tree | commitdiff |
2016-11-02 |
gmungoc | JAL-98 Profile and ResidueCount moved from analysis... |
tree | commitdiff |
2016-11-02 |
gmungoc | JAL-98 wording "negatively conserved" now "absence... |
tree | commitdiff |
2016-11-01 |
gmungoc | Conservation now using ResidueCount; tests added |
tree | commitdiff |
2016-11-01 |
gmungoc | JAL-98 typo in javadoc |
tree | commitdiff |
2016-10-28 |
Jim Procter | JAL-966 JAL-1738 JAL-345 interfaces for SearchResults... |
tree | commitdiff |
2016-10-25 |
gmungoc | JAL-98 javadoc corrected |
tree | commitdiff |
2016-10-25 |
gmungoc | JAL-98 javadoc added |
tree | commitdiff |
2016-10-25 |
gmungoc | JAL-98 minor fixes to / tests for annotation derivation |
tree | commitdiff |
2016-10-25 |
Jim Procter | JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch |
tree | commitdiff |
2016-10-25 |
gmungoc | JAL-98 small efficiency fix + commenting |
tree | commitdiff |
2016-10-25 |
gmungoc | JAL-98 javadoc / comments updated |
tree | commitdiff |
2016-10-24 |
gmungoc | JAL-98 fixme comment removed - nothing to do |
tree | commitdiff |
2016-10-24 |
gmungoc | JAL-98 ResidueCount 100% test coverage (and bug fixes!) |
tree | commitdiff |
2016-10-06 |
gmungoc | Merge branch 'develop' into bug/JAL-98consensusMemory |
tree | commitdiff |
2016-10-06 |
Jim Procter | JAL-2089 Merge branch releases/Release_2_10_Branch... |
tree | commitdiff |
2016-10-05 |
Jim Procter | JAL-2189 source formatting |
tree | commitdiff |
2016-10-03 |
gmungoc | JAL-98 use Profile to store consensus, ResidueCount... |
tree | commitdiff |
2016-10-03 |
Jim Procter | JAL-2210 hack to remove EMBL from Protein crossrefs... |
tree | commitdiff |
2016-10-03 |
Jim Procter | JAL-2210 explicit ‘doNotAdd’ list to prevent sequences... |
tree | commitdiff |
2016-10-02 |
Jim Procter | JAL-2210 two pass attempt to import retrieved sequences... |
tree | commitdiff |
2016-10-02 |
Jim Procter | JAL-2210 try to merge all sequences referenced by a... |
tree | commitdiff |
2016-10-02 |
Jim Procter | JAL-2210 comments |
tree | commitdiff |
2016-10-02 |
Jim Procter | JAL-2210 discover candidate dataset sequences for an... |
tree | commitdiff |
2016-10-01 |
Jim Procter | JAL-2210 factored out code for processing cross-referen... |
tree | commitdiff |
2016-10-01 |
Jim Procter | JAL-2210 refactor code to remove from a list of dbrefs... |
tree | commitdiff |
2016-09-30 |
Jim Procter | JAL-2210 some DBRef xref/ref correspondences may add... |
tree | commitdiff |
2016-09-30 |
Jim Procter | JAL-2210 CrossRef.findInDataset should search for prese... |
tree | commitdiff |
2016-09-30 |
gmungoc | Merge branch 'develop' into bug/JAL-98consensusMemory |
tree | commitdiff |
2016-09-27 |
gmungoc | JAL-2230 use correct mapping to transfer features to... |
tree | commitdiff |
2016-09-26 |
gmungoc | JAL-98 bug fix, string optimisation, sorted AA properties |
tree | commitdiff |
2016-09-26 |
gmungoc | JAL-98 don't include gaps in maxResidue! |
tree | commitdiff |
2016-09-23 |
gmungoc | JAL-98 performance tweaks to use of SparseIntArray |
tree | commitdiff |
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