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jalview.git
2017-03-06 gmungocJAL-2428 correct order of processing in joinClusters() commit | commitdiff | tree | snapshot
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree... commit | commitdiff | tree | snapshot
2017-03-03 gmungocJAL-2428 use BitSet for clusters and done flags commit | commitdiff | tree | snapshot
2017-02-28 gmungocJAL-1632 'includeGaps' applied to FeatureDistanceModel... commit | commitdiff | tree | snapshot
2017-02-28 gmungocJAL-1632 disable parameters not applicable for score... commit | commitdiff | tree | snapshot
2017-02-28 gmungocJAL-838 Javadoc tidy commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-2416 seqspace.scm and PIDDistanceModel replaced... commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-838 ScoreMatrix now respects SimilarityParams! commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-838 tests for PID calculation with parameter options commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-1632 dialog to calculate either Tree or PCA commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect... commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-1632 add score model params to PCAModel and PCA... commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-1632 refactored NJTree constructor to include Simil... commit | commitdiff | tree | snapshot
2017-02-27 gmungocJAL-2403 JAL-838 remove unused methods and unneeded... commit | commitdiff | tree | snapshot
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters... commit | commitdiff | tree | snapshot
2017-02-24 gmungocJAL-1403 preserve range of distance scores for similarity commit | commitdiff | tree | snapshot
2017-02-24 gmungocJAL-2403 PIDModel added (wip) commit | commitdiff | tree | snapshot
2017-02-24 gmungocJAL-2403 code tidy commit | commitdiff | tree | snapshot
2017-02-24 gmungocJAL-1483 PIDModel potential replacement for PIDDistance... commit | commitdiff | tree | snapshot
2017-02-24 gmungocJAL-838 first version of PID parameters model commit | commitdiff | tree | snapshot
2017-02-24 gmungocJAL-2403 remove unused ScoreMatrix.symmetric commit | commitdiff | tree | snapshot
2017-02-24 gmungocJAL-2403 JAL-1483 push 'reverseRange' inside Matrix commit | commitdiff | tree | snapshot
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy... commit | commitdiff | tree | snapshot
2017-02-23 gmungocJAL-2403 additional methods to support distance/similar... commit | commitdiff | tree | snapshot
2017-02-21 gmungocJAL-2416 typo commit | commitdiff | tree | snapshot
2017-02-21 gmungocJAL-2416 ScoreMatrix.getMatrix() returns a defensive... commit | commitdiff | tree | snapshot
2017-02-21 gmungocJAL-2416 support roundtrip print/parse of ScoreMatrix commit | commitdiff | tree | snapshot
2017-02-21 gmungocMerge branch 'develop' into features/JAL-2393customMatrices commit | commitdiff | tree | snapshot
2017-02-21 gmungocJAL-2416 quality calculation now only depends on loaded... commit | commitdiff | tree | snapshot
2017-02-21 gmungocJAL-2416 more validation in ScoreMatrix constructor commit | commitdiff | tree | snapshot
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix... commit | commitdiff | tree | snapshot
2017-02-20 gmungocJAL-2416 replaced dependency on ResidueProperties with... commit | commitdiff | tree | snapshot
2017-02-20 Jim ProcterMerge branch 'features/JAL-2379pcaMemory' into develop commit | commitdiff | tree | snapshot
2017-02-20 gmungocJAL-2416 public constant for space gap character commit | commitdiff | tree | snapshot
2017-02-20 gmungocJAL-2416 remove unused pep, dna alphabets, unused metho... commit | commitdiff | tree | snapshot
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62... commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2416 BLOSUM62 removed from ResidueProperties commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2416 removed DNA and PAM250 matrices from ResiduePr... commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2416 scoreMatrices removed from ResidueProperties commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2413 extracted new method SetUtils.countDisjunction() commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2423 refactored method to build panel title for... commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2416 SeqSpace PCA now provided as an alternative... commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2416 score models now held in order added commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2416 allow space in score matrix name commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2416 order score models by order of addition rather... commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2403 redundant 'implements' removed commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2403 extract method refactoring of FeatureScoreMode... commit | commitdiff | tree | snapshot
2017-02-17 gmungocJAL-2403 constants for "NJ", "AV" commit | commitdiff | tree | snapshot
2017-02-16 Jim ProcterMerge branch 'bug/JAL-2374_JAL-2419_overlappinggroups_c... commit | commitdiff | tree | snapshot
2017-02-15 Jim ProcterJAL-2374 JAL-2419 - TODO suspiciously redundant nested... bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu commit | commitdiff | tree | snapshot
2017-02-15 Jim Procterfix for JAL-2419 - don’t trash the current selection commit | commitdiff | tree | snapshot
2017-02-15 Jim ProcterJAL-2374 don’t search twice for containing group to... commit | commitdiff | tree | snapshot
2017-02-15 Jim ProcterJAL-2374 tests for SequenceGroup.contains commit | commitdiff | tree | snapshot
2017-02-15 Jim ProcterJAL-2374 JAL-1270 assign SequenceGroup tests to ‘Functi... commit | commitdiff | tree | snapshot
2017-02-15 Jim ProcterJAL-2374 new contains methods for seq and seq,apos commit | commitdiff | tree | snapshot
2017-02-15 Jim ProcterJAL-2374 javadoc - qualify that sequence argument to... commit | commitdiff | tree | snapshot
2017-02-14 gmungocJAL-2393 example (unvalidated) blosum80 matrix to play... commit | commitdiff | tree | snapshot
2017-02-14 gmungocParsing moved to (new) ScoreMatrixFile, drag and drop... commit | commitdiff | tree | snapshot
2017-02-13 gmungocJAL-2416 allow alphabet symbol (optional) in first... commit | commitdiff | tree | snapshot
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... commit | commitdiff | tree | snapshot
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode... commit | commitdiff | tree | snapshot
2017-02-10 gmungocJAL-2371 small move of code, typo correction commit | commitdiff | tree | snapshot
2017-02-09 Jim ProcterMerge branch 'features/JAL-2316' into develop commit | commitdiff | tree | snapshot
2017-02-09 Jim ProcterMerge branch 'develop' into features/JAL-2316 features/JAL-2316 commit | commitdiff | tree | snapshot
2017-02-09 gmungocJAL-2401 tweaked button text, added Spanish commit | commitdiff | tree | snapshot
2017-02-09 gmungocJAL-2401 change 'Lower Case Colour' to checkbox with... commit | commitdiff | tree | snapshot
2017-02-09 gmungocJAL-2371 no test for lower case consensus as not expect... commit | commitdiff | tree | snapshot
2017-02-09 gmungocJAL-2371 ensure some colour scheme (may be None) is... commit | commitdiff | tree | snapshot
2017-02-09 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory commit | commitdiff | tree | snapshot
2017-02-09 gmungocJAL-2371 skip upper-casing consensus as it already is commit | commitdiff | tree | snapshot
2017-02-09 gmungocJAL-2405 check for circular reference in SequenceGroup... commit | commitdiff | tree | snapshot
2017-02-09 gmungocJAL-2405 set initial selection group alignment context commit | commitdiff | tree | snapshot
2017-02-09 gmungocJAL-2405 enable nucleotide/peptide colour schemes in... commit | commitdiff | tree | snapshot
2017-02-08 Jim ProcterJAL-2316 tidying preferences help page commit | commitdiff | tree | snapshot
2017-02-08 Jim ProcterJAL-2316 tidied up documentation for Links tab commit | commitdiff | tree | snapshot
2017-02-08 gmungocJAL-2405 set context on selection group for tailored... commit | commitdiff | tree | snapshot
2017-02-08 gmungocJAL-2401 fix for NPE on selectedButtons, tweak for... commit | commitdiff | tree | snapshot
2017-02-08 kiramtMerge remote-tracking branch 'origin/develop' into... commit | commitdiff | tree | snapshot
2017-02-08 Jim ProcterJAL-2366 updated default URL to jalview.org/services... commit | commitdiff | tree | snapshot
2017-02-07 Jim ProcterMerge branch 'features/JAL-2371collectionColourScheme... commit | commitdiff | tree | snapshot
2017-02-07 gmungocJAL-2401 Lower Case Colour toggleable, help text added commit | commitdiff | tree | snapshot
2017-02-07 gmungocJAL-2379 removed unused commented code commit | commitdiff | tree | snapshot
2017-02-07 gmungocJAL-2397 flag provided for 2.10.1 PCA gap calculation... commit | commitdiff | tree | snapshot
2017-02-07 gmungocJAL-2398 include 'compatibility mode' for C->R score... commit | commitdiff | tree | snapshot
2017-02-07 gmungocJAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculat... commit | commitdiff | tree | snapshot
2017-02-07 gmungocJAL-2397 PCA gap cost uses last column of score matrix commit | commitdiff | tree | snapshot
2017-02-07 gmungocJAL-2398 corrected entry for C->R in Blosum62 matrix commit | commitdiff | tree | snapshot
2017-02-06 gmungocJAL-2379 computePairwiseScores() moved to ScoreMatrix commit | commitdiff | tree | snapshot
2017-02-03 gmungocJAL-2379 'direct' pairwise score calculation for PCA... commit | commitdiff | tree | snapshot
2017-02-01 gmungocJAL-2371 (slight!) simplification of isApplicableTo() commit | commitdiff | tree | snapshot
2017-02-01 gmungocJAL-2383 and Spanish! commit | commitdiff | tree | snapshot
2017-01-31 gmungocJAL-2371 commented code removed only commit | commitdiff | tree | snapshot
2017-01-31 gmungocJAL-2371 rename global/viewportColourScheme to residueS... commit | commitdiff | tree | snapshot
2017-01-31 gmungocJAL-2385 more tests/bug fixes mostly for gui.SliderPane... commit | commitdiff | tree | snapshot
2017-01-27 gmungocJAL-2379 commented out code removed commit | commitdiff | tree | snapshot
2017-01-27 gmungocJAL-2371 CollectionColourScheme renamed ResidueShader... commit | commitdiff | tree | snapshot
2017-01-27 gmungocJAL-2099 belated unit test commit | commitdiff | tree | snapshot
2017-01-27 gmungocJAL-2360 JAL-2371 updates from review CR-JAL-1 commit | commitdiff | tree | snapshot
2017-01-27 kiramtJAL-2366 Removed unneeded setEnabled calls commit | commitdiff | tree | snapshot
2017-01-26 gmungocJAL-2360 corrected comment commit | commitdiff | tree | snapshot
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