| 2017-03-29 |
gmungoc | JAL-2416 JAL-728 reduced dependency on Blosum62 implementati...
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commit | commitdiff | tree |
| 2017-03-29 |
gmungoc | JAL-2416 revert to '*' not '-' in score matrix, handle...
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commit | commitdiff | tree |
| 2017-03-29 |
gmungoc | JAL-2416 explicit constant for unknown/unknown identity...
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commit | commitdiff | tree |
| 2017-03-28 |
gmungoc | JAL-2416 format matrix more readably
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commit | commitdiff | tree |
| 2017-03-28 |
gmungoc | JAL-2403 JAL-2416 pairwise score unexpected symbols...
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commit | commitdiff | tree |
| 2017-03-28 |
gmungoc | JAL-2416 JAL-2403 remove unused '*' row/column from...
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commit | commitdiff | tree |
| 2017-03-28 |
gmungoc | JAL-2403 further test coverage for ScoreMatrix, min...
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commit | commitdiff | tree |
| 2017-03-28 |
gmungoc | JAL-2416 more test coverage of matrix parser
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2416 parse score matrices in either NCBI or AAindex...
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2416 amended to AAindex format
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2416 amended to (as near as possible) strict NCBI...
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2416 class Javadoc updates prior to parsing changes
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2468 change score model in PCAModel when switching
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2416 tidy up after switch from ' ' to '-' in score...
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2416 score matrix gap symbol (if any) dynamically...
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2416 tooltip with descriptions for score models...
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2416 add score model description field for tooltip...
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2403 SWDistanceModel now SmithWatermanModel - a...
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2416 use '-' not space for gap in score matrices
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2428 unused method deleted
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2403 PIDDistanceModel deleted as superseded by...
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commit | commitdiff | tree |
| 2017-03-27 |
gmungoc | JAL-2428 pass AlignmentView to TreeModel so Show Input...
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commit | commitdiff | tree |
| 2017-03-24 |
gmungoc | Merge branch 'develop' into features/JAL-2393customMatrices
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commit | commitdiff | tree |
| 2017-03-24 |
gmungoc | JAL-2428 simplify TreeModel constructors, add getOriginalData
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commit | commitdiff | tree |
| 2017-03-24 |
gmungoc | JAL-2428 use 'correct' name for selected score model
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commit | commitdiff | tree |
| 2017-03-24 |
gmungoc | JAL-1632 TreeChooser renamed CalculationChooser, text...
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commit | commitdiff | tree |
| 2017-03-24 |
gmungoc | JAL-1632 named parameters
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commit | commitdiff | tree |
| 2017-03-24 |
gmungoc | JAL-2398 corrected BLOSUM62 C -> R score in resource...
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commit | commitdiff | tree |
| 2017-03-24 |
gmungoc | JAL-2416 tests added for ScoreMatrix
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commit | commitdiff | tree |
| 2017-03-24 |
gmungoc | JAL-838 move two callers off Comparison.PID and deprecate it
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commit | commitdiff | tree |
| 2017-03-23 |
gmungoc | JAL-2397 scale PCA by PID to alignment width to match...
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commit | commitdiff | tree |
| 2017-03-23 |
gmungoc | JAL-2397 formatting only
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commit | commitdiff | tree |
| 2017-03-23 |
gmungoc | JAL-1632 suppress PID parameter options in Tree/PCA...
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commit | commitdiff | tree |
| 2017-03-23 |
gmungoc | JAL-838 class javadoc added
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commit | commitdiff | tree |
| 2017-03-23 |
gmungoc | JAL-2464 fix cancel tree print behaviour
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commit | commitdiff | tree |
| 2017-03-23 |
gmungoc | JAL-2393 code tidy and comments, PIDDistanceModel deprecated
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commit | commitdiff | tree |
| 2017-03-23 |
gmungoc | JAL-2393 updated test for removal of PIDDistanceModel
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commit | commitdiff | tree |
| 2017-03-23 |
gmungoc | Merge branch 'develop' into features/JAL-2393customMatrices
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commit | commitdiff | tree |
| 2017-03-22 |
gmungoc | JAL-2311 suppress autocalc'd annotation to isolate...
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commit | commitdiff | tree |
| 2017-03-21 |
gmungoc | JAL-2306 assert no DAS sources
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commit | commitdiff | tree |
| 2017-03-21 |
gmungoc | JAL-2438 removed (non-functional) lastSeq, lastSequenceFeatures
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commit | commitdiff | tree |
| 2017-03-21 |
gmungoc | JAL-2243 update discovered features on opening structure...
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commit | commitdiff | tree |
| 2017-03-21 |
gmungoc | JAL-2438 check for null FeatureRenderer
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commit | commitdiff | tree |
| 2017-03-15 |
gmungoc | JAL-2443 push getResidueBoxColour inside getResidueColour
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commit | commitdiff | tree |
| 2017-03-15 |
gmungoc | JAL-2438 corrected getFeatureRenderer()
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commit | commitdiff | tree |
| 2017-03-15 |
gmungoc | JAL-2442 applet feature transparency also on overview...
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commit | commitdiff | tree |
| 2017-03-15 |
gmungoc | JAL-2438 handle null FeatureRenderer in FeatureColourFinder
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commit | commitdiff | tree |
| 2017-03-15 |
gmungoc | JAL-2438 refactored checks for 'no features displayed'
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commit | commitdiff | tree |
| 2017-03-15 |
gmungoc | JAL-2438 clarify code and javadoc, reinstate updateFeatures...
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commit | commitdiff | tree |
| 2017-03-15 |
gmungoc | Merge branch 'develop' into bug/JAL-2436featureRendererThreading
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commit | commitdiff | tree |
| 2017-03-14 |
gmungoc | JAL-2438 unit test, fixes, Javadoc updates
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commit | commitdiff | tree |
| 2017-03-14 |
gmungoc | JAL-2438 unit tests for FeatureColourFinder (transparency...
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commit | commitdiff | tree |
| 2017-03-14 |
gmungoc | JAL-2438 Javadoc updates
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commit | commitdiff | tree |
| 2017-03-14 |
gmungoc | JAL-2438 comment/Javadoc tidies
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commit | commitdiff | tree |
| 2017-03-13 |
gmungoc | JAL-2438 corrected handling of default colour
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commit | commitdiff | tree |
| 2017-03-13 |
gmungoc | JAL-2438 FeatureColourFinder refactored from FeatureRenderer...
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commit | commitdiff | tree |
| 2017-03-08 |
gmungoc | JAL-2430 colour columns hidden in alignment gray on...
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commit | commitdiff | tree |
| 2017-03-08 |
gmungoc | JAL-2295 avoid quotes breaking attribute value parsing
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commit | commitdiff | tree |
| 2017-03-07 |
gmungoc | JAL-2295 status messages for Chimera attributes set...
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commit | commitdiff | tree |
| 2017-03-06 |
gmungoc | JAL-2428 correct order of processing in joinClusters()
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commit | commitdiff | tree |
| 2017-03-06 |
gmungoc | JAL-2428 separate TreeModel from TreeBuilder/NJTree...
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commit | commitdiff | tree |
| 2017-03-03 |
gmungoc | JAL-2428 use BitSet for clusters and done flags
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commit | commitdiff | tree |
| 2017-03-02 |
gmungoc | JAL-2295 tweak order and wording of Superpose menu...
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commit | commitdiff | tree |
| 2017-03-02 |
gmungoc | JAL-2295 make 'Jmol' menu appear; enable/disable Superpose...
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commit | commitdiff | tree |
| 2017-03-01 |
gmungoc | JAL-1264 smarter way to skip autocalc'd annotations...
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commit | commitdiff | tree |
| 2017-03-01 |
gmungoc | Merge branch 'features/JAL-2295setChimeraAttributes...
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commit | commitdiff | tree |
| 2017-02-28 |
gmungoc | JAL-1632 'includeGaps' applied to FeatureDistanceModel...
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commit | commitdiff | tree |
| 2017-02-28 |
gmungoc | JAL-1632 disable parameters not applicable for score...
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commit | commitdiff | tree |
| 2017-02-28 |
gmungoc | JAL-838 Javadoc tidy
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commit | commitdiff | tree |
| 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 |
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