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JAL-3490 match count independent of contiguous matches count
[jalview.git] / src / jalview / analysis / scoremodels /
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... tree | commitdiff
2019-03-11 gmungocJAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test... tree | commitdiff
2019-03-03 gmungocJAL-3205 faster calculation with symmetric score matrix tree | commitdiff
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct... tree | commitdiff
2018-05-07 gmungocJAL-1767 unit test for save and restore PCA features/JAL-1767pcaInProject tree | commitdiff
2018-04-26 gmungocJAL-2962 remove Change Parameters menu from PCA panel tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 add GPL to main sources tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting tree | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch tree | commitdiff
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn tree | commitdiff
2017-05-16 gmungocJAL-2403 simplify instantiation / configuration of... tree | commitdiff
2017-05-02 gmungocJAL-2499 JAL-2403 push 'configure for view' inside... 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
2017-03-29 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-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-2403 PIDDistanceModel deleted as superseded by... tree | commitdiff
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca... 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
2017-02-28 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
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters... tree | commitdiff
2017-02-24 gmungocJAL-2403 PIDModel added (wip) 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
2017-02-23 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 more validation in ScoreMatrix constructor tree | commitdiff
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix... tree | commitdiff
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62... 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-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
2017-02-14 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
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch tree | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... tree | commitdiff
2016-04-23 Jim ProcterJAL-2075 fix: use AlignmentView.getVisibleContigs and... tree | commitdiff
2016-02-12 gmungocJAL-2008 avoid unnecessary repaints; signatures changed... tree | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 tree | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 licencing for new files in src tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports tree | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... tree | commitdiff
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 patches to make test case pass: hamming distan... tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 organise imports tree | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes tree | commitdiff
2014-08-08 j.procter@dundee... JAL-1483 reformatting and use new feature renderer... tree | commitdiff
2014-06-13 Jim ProcterMerge branch 'Release_2_8_2_Branch' into JAL-1483_featu... tree | commitdiff
2014-06-06 Jim ProcterJAL-1517 source formatting tree | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 tree | commitdiff
2014-04-21 Jim ProcterJAL-1483 cut and paste from SW score model to allow... tree | commitdiff
2014-04-21 Jim ProcterJAL-1473 refactor score matrices and tree score calcula... tree | commitdiff