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JAL-4059 fix that boolean for non-value query string args
[jalview.git]
/
src
/
jalview
/
analysis
/
scoremodels
/
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
tree
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commitdiff
2019-03-11
gmungoc
JAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test...
tree
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commitdiff
2019-03-03
gmungoc
JAL-3205 faster calculation with symmetric score matrix
tree
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commitdiff
2019-01-21
gmungoc
JAL-3187 (hacked up) show complement features on struct...
tree
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commitdiff
2018-05-07
gmungoc
JAL-1767 unit test for save and restore PCA
features/JAL-1767pcaInProject
tree
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commitdiff
2018-04-26
gmungoc
JAL-2962 remove Change Parameters menu from PCA panel
tree
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commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
tree
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
tree
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commitdiff
2017-06-01
gmungoc
JAL-2754 Sequence.findFeatures(fromCol, toCol)
features/JAL-2754findFeaturesByColumn
tree
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commitdiff
2017-05-16
gmungoc
JAL-2403 simplify instantiation / configuration of...
tree
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commitdiff
2017-05-02
gmungoc
JAL-2499 JAL-2403 push 'configure for view' inside...
tree
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commitdiff
2017-04-12
gmungoc
JAL-2403 public static methods to convert distance...
tree
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commitdiff
2017-04-11
gmungoc
JAL-2403 improved ScoreModelI hierarchy as per Kira...
tree
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commitdiff
2017-03-29
gmungoc
JAL-2416 revert to '*' not '-' in score matrix, handle...
tree
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commitdiff
2017-03-29
gmungoc
JAL-2416 explicit constant for unknown/unknown identity...
tree
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commitdiff
2017-03-28
gmungoc
JAL-2403 JAL-2416 pairwise score unexpected symbols...
tree
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commitdiff
2017-03-28
gmungoc
JAL-2403 further test coverage for ScoreMatrix, min...
tree
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commitdiff
2017-03-27
gmungoc
JAL-2416 parse score matrices in either NCBI or AAindex...
tree
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commitdiff
2017-03-27
gmungoc
JAL-2416 tidy up after switch from ' ' to '-' in score...
tree
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commitdiff
2017-03-27
gmungoc
JAL-2416 score matrix gap symbol (if any) dynamically...
tree
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commitdiff
2017-03-27
gmungoc
JAL-2416 add score model description field for tooltip...
tree
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commitdiff
2017-03-27
gmungoc
JAL-2403 SWDistanceModel now SmithWatermanModel - a...
tree
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commitdiff
2017-03-27
gmungoc
JAL-2416 use '-' not space for gap in score matrices
tree
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commitdiff
2017-03-27
gmungoc
JAL-2403 PIDDistanceModel deleted as superseded by...
tree
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commitdiff
2017-03-24
gmungoc
JAL-838 move two callers off Comparison.PID and depreca...
tree
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commitdiff
2017-03-23
gmungoc
JAL-838 class javadoc added
tree
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commitdiff
2017-03-23
gmungoc
JAL-2393 code tidy and comments, PIDDistanceModel depre...
tree
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commitdiff
2017-02-28
gmungoc
JAL-1632 'includeGaps' applied to FeatureDistanceModel...
tree
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commitdiff
2017-02-27
gmungoc
JAL-2416 seqspace.scm and PIDDistanceModel replaced...
tree
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commitdiff
2017-02-27
gmungoc
JAL-838 ScoreMatrix now respects SimilarityParams!
tree
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commitdiff
2017-02-27
gmungoc
JAL-838 tests for PID calculation with parameter options
tree
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commitdiff
2017-02-27
gmungoc
JAL-1632 similarity options on TreeChooser panel affect...
tree
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commitdiff
2017-02-24
gmungoc
JAL-838 added 'SeqSpace' PID mode, added parameters...
tree
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commitdiff
2017-02-24
gmungoc
JAL-2403 PIDModel added (wip)
tree
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commitdiff
2017-02-24
gmungoc
JAL-1483 PIDModel potential replacement for PIDDistance...
tree
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commitdiff
2017-02-24
gmungoc
JAL-838 first version of PID parameters model
tree
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commitdiff
2017-02-24
gmungoc
JAL-2403 remove unused ScoreMatrix.symmetric
tree
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commitdiff
2017-02-23
gmungoc
JAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
tree
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commitdiff
2017-02-21
gmungoc
JAL-2416 ScoreMatrix.getMatrix() returns a defensive...
tree
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commitdiff
2017-02-21
gmungoc
JAL-2416 support roundtrip print/parse of ScoreMatrix
tree
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commitdiff
2017-02-21
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-02-21
gmungoc
JAL-2416 more validation in ScoreMatrix constructor
tree
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commitdiff
2017-02-20
gmungoc
JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
tree
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commitdiff
2017-02-18
gmungoc
JAL-2416 better encapsulated 'constants' for BLOSUM62...
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 scoreMatrices removed from ResidueProperties
tree
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commitdiff
2017-02-17
gmungoc
JAL-2413 extracted new method SetUtils.countDisjunction()
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 order score models by order of addition rather...
tree
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commitdiff
2017-02-17
gmungoc
JAL-2403 redundant 'implements' removed
tree
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commitdiff
2017-02-17
gmungoc
JAL-2403 extract method refactoring of FeatureScoreMode...
tree
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commitdiff
2017-02-14
gmungoc
Parsing moved to (new) ScoreMatrixFile, drag and drop...
tree
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commitdiff
2017-02-13
gmungoc
JAL-2416 allow alphabet symbol (optional) in first...
tree
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commitdiff
2017-02-13
gmungoc
JAL-1632 JAL-2416 load score matrices from file, as...
tree
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commitdiff
2017-02-13
gmungoc
JAL-1632 first cut of Tree chooser dialog and ScoreMode...
tree
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commitdiff
2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
tree
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commitdiff
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
tree
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commitdiff
2016-04-23
Jim Procter
JAL-2075 fix: use AlignmentView.getVisibleContigs and...
tree
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commitdiff
2016-02-12
gmungoc
JAL-2008 avoid unnecessary repaints; signatures changed...
tree
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commitdiff
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
tree
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commitdiff
2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 licencing for new files in src
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
tree
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commitdiff
2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
tree
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commitdiff
2015-03-06
Jim Procter
Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
tree
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commitdiff
2015-01-07
Jim Procter
JAL-1483 patches to make test case pass: hamming distan...
tree
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commitdiff
2015-01-07
Jim Procter
JAL-1483 organise imports
tree
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commitdiff
2014-12-15
Jim Procter
JAL-1620 version bump and release notes
tree
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commitdiff
2014-08-08
j.procter@dundee...
JAL-1483 reformatting and use new feature renderer...
tree
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commitdiff
2014-06-13
Jim Procter
Merge branch 'Release_2_8_2_Branch' into JAL-1483_featu...
tree
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commitdiff
2014-06-06
Jim Procter
JAL-1517 source formatting
tree
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commitdiff
2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1483 cut and paste from SW score model to allow...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1473 refactor score matrices and tree score calcula...
tree
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commitdiff