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