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Merge branch 'develop' into features/JAL-2393customMatrices
[jalview.git] / src /
2017-03-07 kiramtJAL-2429 findColumnPosition returns 0 for cols in regio... tree | commitdiff
2017-03-07 kiramtJAL-2429 Additional fix to ColumnSelection when hidden... tree | commitdiff
2017-03-06 kiramtJAL-2388 Dependency tidy tree | commitdiff
2017-03-06 kiramtJAL-2388 Remove OverviewDimensions dependency on gui... tree | commitdiff
2017-03-06 gmungocJAL-2428 correct order of processing in joinClusters() tree | commitdiff
2017-03-06 kiramtJAL-2388 Corrected overview panel behaviour, updated... tree | commitdiff
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree... tree | commitdiff
2017-03-03 kiramtJAL-2429 Fix to ColumnSelection::findColumnPosition tree | commitdiff
2017-03-03 gmungocJAL-2428 use BitSet for clusters and done flags tree | commitdiff
2017-03-03 kiramtJAL-2388 Initial removal of hidden cols/seqs out of... tree | commitdiff
2017-03-02 gmungocJAL-2295 tweak order and wording of Superpose menu... tree | commitdiff
2017-03-02 gmungocJAL-2295 make 'Jmol' menu appear; enable/disable Superp... tree | commitdiff
2017-03-01 kiramtJAL-2388 Reverted to previous tree | commitdiff
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... tree | commitdiff
2017-03-01 kiramtJAL-2388 Preliminary refactor check-in, does not compile tree | commitdiff
2017-02-28 gmungocJAL-1632 'includeGaps' applied to FeatureDistanceModel... tree | commitdiff
2017-02-28 kiramtJAL-2426 Removal of NPE in conservation thread when... tree | commitdiff
2017-02-28 kiramtJAL-2388 First move of endRes etc out of AlignmentViewp... tree | commitdiff
2017-02-28 gmungocJAL-1632 disable parameters not applicable for score... tree | commitdiff
2017-02-28 kiramtJAL-2426 Checks on conservation thread in case we are... tree | commitdiff
2017-02-28 gmungocJAL-838 Javadoc tidy tree | commitdiff
2017-02-27 gmungocJAL-2416 seqspace.scm and PIDDistanceModel replaced... tree | commitdiff
2017-02-27 gmungocJAL-838 ScoreMatrix now respects SimilarityParams! tree | commitdiff
2017-02-27 gmungocJAL-838 tests for PID calculation with parameter options tree | commitdiff
2017-02-27 kiramtJAL-2388 Make startRes,startSeq,endRes,endSeq private... tree | commitdiff
2017-02-27 gmungocJAL-1632 dialog to calculate either Tree or PCA tree | commitdiff
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect... tree | commitdiff
2017-02-27 kiramtJAL-2388 Minor refactoring tree | commitdiff
2017-02-27 gmungocJAL-1632 add score model params to PCAModel and PCA... tree | commitdiff
2017-02-27 gmungocJAL-1632 refactored NJTree constructor to include Simil... tree | commitdiff
2017-02-27 gmungocJAL-2403 JAL-838 remove unused methods and unneeded... tree | commitdiff
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters... tree | commitdiff
2017-02-24 gmungocJAL-1403 preserve range of distance scores for similarity tree | commitdiff
2017-02-24 gmungocJAL-2403 PIDModel added (wip) tree | commitdiff
2017-02-24 gmungocJAL-2403 code tidy tree | commitdiff
2017-02-24 gmungocJAL-1483 PIDModel potential replacement for PIDDistance... tree | commitdiff
2017-02-24 gmungocJAL-838 first version of PID parameters model tree | commitdiff
2017-02-24 gmungocJAL-2403 remove unused ScoreMatrix.symmetric tree | commitdiff
2017-02-24 gmungocJAL-2403 JAL-1483 push 'reverseRange' inside Matrix tree | commitdiff
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy... tree | commitdiff
2017-02-23 gmungocJAL-2403 additional methods to support distance/similar... tree | commitdiff
2017-02-23 kiramtJAL-2388 Unit tests in progress tree | commitdiff
2017-02-21 gmungocJAL-2416 ScoreMatrix.getMatrix() returns a defensive... tree | commitdiff
2017-02-21 gmungocJAL-2416 support roundtrip print/parse of ScoreMatrix tree | commitdiff
2017-02-21 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-02-21 kiramtMerge branch 'bug/JAL-2421overviewboxflicker' into tree | commitdiff
2017-02-21 kiramtMerge branch 'develop' into features/JAL-2388OverviewWindow tree | commitdiff
2017-02-21 gmungocJAL-2416 quality calculation now only depends on loaded... tree | commitdiff
2017-02-21 kiramtJAL-2421 Unit test tree | commitdiff
2017-02-21 gmungocJAL-2416 more validation in ScoreMatrix constructor tree | commitdiff
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix... tree | commitdiff
2017-02-20 gmungocJAL-2416 replaced dependency on ResidueProperties with... tree | commitdiff
2017-02-20 Jim ProcterMerge branch 'features/JAL-2379pcaMemory' into develop tree | commitdiff
2017-02-20 gmungocJAL-2416 public constant for space gap character tree | commitdiff
2017-02-20 gmungocJAL-2416 remove unused pep, dna alphabets, unused metho... tree | commitdiff
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62... tree | commitdiff
2017-02-17 gmungocJAL-2416 BLOSUM62 removed from ResidueProperties tree | commitdiff
2017-02-17 gmungocJAL-2416 removed DNA and PAM250 matrices from ResiduePr... tree | commitdiff
2017-02-17 gmungocJAL-2416 scoreMatrices removed from ResidueProperties tree | commitdiff
2017-02-17 gmungocJAL-2413 extracted new method SetUtils.countDisjunction() tree | commitdiff
2017-02-17 gmungocJAL-2423 refactored method to build panel title for... tree | commitdiff
2017-02-17 kiramtJAL-2388 Incomplete unit tests tree | commitdiff
2017-02-17 gmungocJAL-2416 SeqSpace PCA now provided as an alternative... tree | commitdiff
2017-02-17 gmungocJAL-2416 allow space in score matrix name tree | commitdiff
2017-02-17 gmungocJAL-2416 order score models by order of addition rather... tree | commitdiff
2017-02-17 gmungocJAL-2403 redundant 'implements' removed tree | commitdiff
2017-02-17 gmungocJAL-2403 extract method refactoring of FeatureScoreMode... tree | commitdiff
2017-02-17 gmungocJAL-2403 constants for "NJ", "AV" tree | commitdiff
2017-02-17 kiramtJAL-2421 Fix to alignment panel scroll values, and... tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 JAL-2419 - TODO suspiciously redundant nested... bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu tree | commitdiff
2017-02-15 Jim Procterfix for JAL-2419 - don’t trash the current selection tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 don’t search twice for containing group to... tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 new contains methods for seq and seq,apos tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 javadoc - qualify that sequence argument to... tree | commitdiff
2017-02-14 gmungocParsing moved to (new) ScoreMatrixFile, drag and drop... tree | commitdiff
2017-02-14 gmungocJAL-2346 disable 'threshold min/max' when 'use original... tree | commitdiff
2017-02-14 gmungocJAL-2346 remove refactored fields, fix test for above... tree | commitdiff
2017-02-14 kiramtJAL-2388 Removed unnecessary CommandListener interface... tree | commitdiff
2017-02-14 gmungocMerge branch 'develop' into bug/JAL-2346annotationChoice tree | commitdiff
2017-02-13 gmungocJAL-2416 allow alphabet symbol (optional) in first... tree | commitdiff
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... tree | commitdiff
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode... tree | commitdiff
2017-02-10 gmungocJAL-2371 small move of code, typo correction tree | commitdiff
2017-02-09 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-02-09 gmungocJAL-1608 menu entry text; enable/disable Create/Remove... tree | commitdiff
2017-02-09 kiramtJAL-2388 Initial refactor of OverviewPanel tree | commitdiff
2017-02-09 Jim ProcterMerge branch 'develop' into features/JAL-2316 features/JAL-2316 tree | commitdiff
2017-02-09 gmungocJAL-2401 change 'Lower Case Colour' to checkbox with... tree | commitdiff
2017-02-09 gmungocJAL-2371 ensure some colour scheme (may be None) is... tree | commitdiff
2017-02-09 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory tree | commitdiff
2017-02-09 gmungocJAL-2371 skip upper-casing consensus as it already is tree | commitdiff
2017-02-09 gmungocJAL-2405 check for circular reference in SequenceGroup... tree | commitdiff
2017-02-09 gmungocJAL-2405 set initial selection group alignment context tree | commitdiff
2017-02-09 gmungocJAL-2405 enable nucleotide/peptide colour schemes in... tree | commitdiff
2017-02-08 gmungocJAL-2405 set context on selection group for tailored... tree | commitdiff
2017-02-08 gmungocJAL-2401 fix for NPE on selectedButtons, tweak for... tree | commitdiff
2017-02-08 gmungocJAL-2399 JAL-2400 tidy Text Colour wording, behaviour... tree | commitdiff
2017-02-08 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-02-08 Jim ProcterJAL-2366 updated default URL to jalview.org/services... tree | commitdiff
2017-02-07 Jim ProcterMerge branch 'features/JAL-2371collectionColourScheme... tree | commitdiff
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