| 2017-02-27 |
gmungoc | JAL-2416 seqspace.scm and PIDDistanceModel replaced...
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commit | commitdiff | tree |
| 2017-02-27 |
gmungoc | JAL-838 ScoreMatrix now respects SimilarityParams!
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commit | commitdiff | tree |
| 2017-02-27 |
gmungoc | JAL-838 tests for PID calculation with parameter options
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commit | commitdiff | tree |
| 2017-02-27 |
gmungoc | JAL-1632 dialog to calculate either Tree or PCA
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commit | commitdiff | tree |
| 2017-02-27 |
gmungoc | JAL-1632 similarity options on TreeChooser panel affect...
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commit | commitdiff | tree |
| 2017-02-27 |
gmungoc | JAL-1632 add score model params to PCAModel and PCA...
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commit | commitdiff | tree |
| 2017-02-27 |
gmungoc | JAL-1632 refactored NJTree constructor to include Similarity...
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commit | commitdiff | tree |
| 2017-02-27 |
gmungoc | JAL-2403 JAL-838 remove unused methods and unneeded...
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commit | commitdiff | tree |
| 2017-02-24 |
gmungoc | JAL-838 added 'SeqSpace' PID mode, added parameters...
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commit | commitdiff | tree |
| 2017-02-24 |
gmungoc | JAL-1403 preserve range of distance scores for similarity
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commit | commitdiff | tree |
| 2017-02-24 |
gmungoc | JAL-2403 PIDModel added (wip)
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commit | commitdiff | tree |
| 2017-02-24 |
gmungoc | JAL-2403 code tidy
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commit | commitdiff | tree |
| 2017-02-24 |
gmungoc | JAL-1483 PIDModel potential replacement for PIDDistanceModel...
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commit | commitdiff | tree |
| 2017-02-24 |
gmungoc | JAL-838 first version of PID parameters model
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commit | commitdiff | tree |
| 2017-02-24 |
gmungoc | JAL-2403 remove unused ScoreMatrix.symmetric
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commit | commitdiff | tree |
| 2017-02-24 |
gmungoc | JAL-2403 JAL-1483 push 'reverseRange' inside Matrix
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commit | commitdiff | tree |
| 2017-02-23 |
gmungoc | JAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
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commit | commitdiff | tree |
| 2017-02-23 |
gmungoc | JAL-2403 additional methods to support distance/similarity...
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commit | commitdiff | tree |
| 2017-02-21 |
gmungoc | JAL-2416 typo
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commit | commitdiff | tree |
| 2017-02-21 |
gmungoc | JAL-2416 ScoreMatrix.getMatrix() returns a defensive...
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commit | commitdiff | tree |
| 2017-02-21 |
gmungoc | JAL-2416 support roundtrip print/parse of ScoreMatrix
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commit | commitdiff | tree |
| 2017-02-21 |
gmungoc | Merge branch 'develop' into features/JAL-2393customMatrices
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commit | commitdiff | tree |
| 2017-02-21 |
gmungoc | JAL-2416 quality calculation now only depends on loaded...
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commit | commitdiff | tree |
| 2017-02-21 |
gmungoc | JAL-2416 more validation in ScoreMatrix constructor
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commit | commitdiff | tree |
| 2017-02-20 |
gmungoc | JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
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commit | commitdiff | tree |
| 2017-02-20 |
gmungoc | JAL-2416 replaced dependency on ResidueProperties with...
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commit | commitdiff | tree |
| 2017-02-20 |
gmungoc | JAL-2416 public constant for space gap character
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commit | commitdiff | tree |
| 2017-02-20 |
gmungoc | JAL-2416 remove unused pep, dna alphabets, unused methods...
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commit | commitdiff | tree |
| 2017-02-18 |
gmungoc | JAL-2416 better encapsulated 'constants' for BLOSUM62...
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2416 BLOSUM62 removed from ResidueProperties
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2416 removed DNA and PAM250 matrices from ResidueProperties
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2416 scoreMatrices removed from ResidueProperties
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2413 extracted new method SetUtils.countDisjunction()
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2423 refactored method to build panel title for...
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2416 SeqSpace PCA now provided as an alternative...
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2416 score models now held in order added
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2416 allow space in score matrix name
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2416 order score models by order of addition rather...
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2403 redundant 'implements' removed
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2403 extract method refactoring of FeatureScoreModel...
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commit | commitdiff | tree |
| 2017-02-17 |
gmungoc | JAL-2403 constants for "NJ", "AV"
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commit | commitdiff | tree |
| 2017-02-14 |
gmungoc | JAL-2393 example (unvalidated) blosum80 matrix to play...
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commit | commitdiff | tree |
| 2017-02-14 |
gmungoc | Parsing moved to (new) ScoreMatrixFile, drag and drop...
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commit | commitdiff | tree |
| 2017-02-13 |
gmungoc | JAL-2416 allow alphabet symbol (optional) in first...
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commit | commitdiff | tree |
| 2017-02-13 |
gmungoc | JAL-1632 JAL-2416 load score matrices from file, as...
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commit | commitdiff | tree |
| 2017-02-13 |
gmungoc | JAL-1632 first cut of Tree chooser dialog and ScoreModels...
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commit | commitdiff | tree |
| 2017-02-10 |
gmungoc | JAL-2371 small move of code, typo correction
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commit | commitdiff | tree |
| 2017-02-09 |
gmungoc | JAL-2401 tweaked button text, added Spanish
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commit | commitdiff | tree |
| 2017-02-09 |
gmungoc | JAL-2401 change 'Lower Case Colour' to checkbox with...
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commit | commitdiff | tree |
| 2017-02-09 |
gmungoc | JAL-2371 no test for lower case consensus as not expected...
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commit | commitdiff | tree |
| 2017-02-09 |
gmungoc | JAL-2371 ensure some colour scheme (may be None) is...
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commit | commitdiff | tree |
| 2017-02-09 |
gmungoc | Merge branch 'develop' into features/JAL-2379pcaMemory
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commit | commitdiff | tree |
| 2017-02-09 |
gmungoc | JAL-2371 skip upper-casing consensus as it already is
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commit | commitdiff | tree |
| 2017-02-09 |
gmungoc | JAL-2405 check for circular reference in SequenceGroup...
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commit | commitdiff | tree |
| 2017-02-09 |
gmungoc | JAL-2405 set initial selection group alignment context
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commit | commitdiff | tree |
| 2017-02-09 |
gmungoc | JAL-2405 enable nucleotide/peptide colour schemes in...
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commit | commitdiff | tree |
| 2017-02-08 |
gmungoc | JAL-2405 set context on selection group for tailored...
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commit | commitdiff | tree |
| 2017-02-08 |
gmungoc | JAL-2401 fix for NPE on selectedButtons, tweak for...
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commit | commitdiff | tree |
| 2017-02-07 |
gmungoc | JAL-2401 Lower Case Colour toggleable, help text added
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commit | commitdiff | tree |
| 2017-02-07 |
gmungoc | JAL-2379 removed unused commented code
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commit | commitdiff | tree |
| 2017-02-07 |
gmungoc | JAL-2397 flag provided for 2.10.1 PCA gap calculation...
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commit | commitdiff | tree |
| 2017-02-07 |
gmungoc | JAL-2398 include 'compatibility mode' for C->R score...
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commit | commitdiff | tree |
| 2017-02-07 |
gmungoc | JAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculation...
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commit | commitdiff | tree |
| 2017-02-07 |
gmungoc | JAL-2397 PCA gap cost uses last column of score matrix
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commit | commitdiff | tree |
| 2017-02-07 |
gmungoc | JAL-2398 corrected entry for C->R in Blosum62 matrix
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commit | commitdiff | tree |
| 2017-02-06 |
gmungoc | JAL-2379 computePairwiseScores() moved to ScoreMatrix
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commit | commitdiff | tree |
| 2017-02-03 |
gmungoc | JAL-2379 'direct' pairwise score calculation for PCA...
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commit | commitdiff | tree |
| 2017-02-01 |
gmungoc | JAL-2371 (slight!) simplification of isApplicableTo()
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commit | commitdiff | tree |
| 2017-02-01 |
gmungoc | JAL-2383 and Spanish!
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commit | commitdiff | tree |
| 2017-01-31 |
gmungoc | JAL-2371 commented code removed only
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commit | commitdiff | tree |
| 2017-01-31 |
gmungoc | JAL-2371 rename global/viewportColourScheme to residueShading
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commit | commitdiff | tree |
| 2017-01-31 |
gmungoc | JAL-2385 more tests/bug fixes mostly for gui.SliderPanel...
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commit | commitdiff | tree |
| 2017-01-27 |
gmungoc | JAL-2379 commented out code removed
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commit | commitdiff | tree |
| 2017-01-27 |
gmungoc | JAL-2371 CollectionColourScheme renamed ResidueShader...
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commit | commitdiff | tree |
| 2017-01-27 |
gmungoc | JAL-2099 belated unit test
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commit | commitdiff | tree |
| 2017-01-27 |
gmungoc | JAL-2360 JAL-2371 updates from review CR-JAL-1
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commit | commitdiff | tree |
| 2017-01-26 |
gmungoc | JAL-2360 corrected comment
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commit | commitdiff | tree |
| 2017-01-26 |
gmungoc | JAL-2360 C is Pink with consensus > 85% (not 100%)
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commit | commitdiff | tree |
| 2017-01-26 |
gmungoc | Merge branch 'features/JAL-2360colourSchemeApplicability...
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commit | commitdiff | tree |
| 2017-01-26 |
gmungoc | Merge branch 'develop' into features/JAL-2360colourSchemeApp...
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commit | commitdiff | tree |
| 2017-01-26 |
gmungoc | Merge branch 'develop' into features/JAL-2379pcaMemory
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commit | commitdiff | tree |
| 2017-01-26 |
gmungoc | JAL-2344 test fix and code tidy for review comments
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commit | commitdiff | tree |
| 2017-01-26 |
gmungoc | JAL-2380 code tidy after review
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commit | commitdiff | tree |
| 2017-01-25 |
gmungoc | JAL-2344 push Cache.getProperty("LAST_DIRECTORY") inside...
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commit | commitdiff | tree |
| 2017-01-23 |
gmungoc | JAL-2379 made SparseMatrix.divide() so as to exactly...
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commit | commitdiff | tree |
| 2017-01-23 |
gmungoc | JAL-2386 unit tests for change colour (and minor refactoring for
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commit | commitdiff | tree |
| 2017-01-23 |
gmungoc | JAL-2386 simplify changeColour (doesn't change colour...
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | Merge branch 'features/JAL-2360colourSchemeApplicability...
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | Merge branch 'develop' into features/JAL-2360colourSchemeApp...
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | JAL-2385 tweak to applet 'switch colour slider context'
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | Merge branch 'features/JAL-2360colourSchemeApplicability...
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | Merge branch 'develop' into features/JAL-2360colourSchemeApp...
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | JAL-2385 update slider settings when switching slider...
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | Merge branch 'features/JAL-2360colourSchemeApplicability...
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | JAL-2383 fixup from last merge
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | Merge branch 'develop' into features/JAL-2360colourSchemeApp...
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | JAL-2383 check for null, spelling
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | JAL-2383 make popup colour menu order and wording consistent
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | JAL-2383 restore group conservation slider setting...
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | Merge branch 'develop' into features/JAL-2360colourSchemeApp...
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commit | commitdiff | tree |
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