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