JAL-2629 fix expected length error for hmmbuild by uniquifying sequences
[jalview.git] / test / jalview / analysis /
2017-08-09 TZVanaaltenJAL-2629 disable AAFrequencyTest compilation error
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder...
2017-07-12 TZVanaaltentest HMM annotaTION
2017-05-22 gmungocJAL-2544 unit tests for sort by feature score
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
2017-05-02 Jim ProcterJAL-2424 fixme’s removed
2017-05-02 Jim ProcterJAL-2424 update assert to correct width for normalising...
2017-05-02 Jim ProcterJAL-2424 resolved, assert updated to pass (1f != 1d)
2017-05-02 gmungocJAL-2499 JAL-2403 push 'configure for view' inside...
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection...
2017-04-11 gmungocJAL-2403 improved ScoreModelI hierarchy as per Kira...
2017-04-10 gmungocJAL-2403 unit tests for PCA.computeSimilarity, signatur...
2017-04-10 gmungocJAL-2416 test updated for reinstatement of '*' row...
2017-03-29 gmungocJAL-2416 revert to '*' not '-' in score matrix, handle...
2017-03-28 gmungocJAL-2403 JAL-2416 pairwise score unexpected symbols...
2017-03-28 gmungocJAL-2403 further test coverage for ScoreMatrix, min...
2017-03-27 gmungocJAL-2416 tidy up after switch from ' ' to '-' in score...
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically...
2017-03-27 gmungocJAL-2416 add score model description field for tooltip...
2017-03-27 gmungocJAL-2416 use '-' not space for gap in score matrices
2017-03-24 gmungocJAL-2416 tests added for ScoreMatrix
2017-03-23 gmungocJAL-2393 updated test for removal of PIDDistanceModel
2017-02-28 gmungocJAL-1632 'includeGaps' applied to FeatureDistanceModel...
2017-02-27 gmungocJAL-2416 seqspace.scm and PIDDistanceModel replaced...
2017-02-27 gmungocJAL-838 ScoreMatrix now respects SimilarityParams!
2017-02-27 gmungocJAL-838 tests for PID calculation with parameter options
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters...
2017-02-24 gmungocJAL-2403 PIDModel added (wip)
2017-02-24 gmungocJAL-1483 PIDModel potential replacement for PIDDistance...
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
2017-02-21 gmungocJAL-2416 typo
2017-02-21 gmungocJAL-2416 ScoreMatrix.getMatrix() returns a defensive...
2017-02-21 gmungocJAL-2416 support roundtrip print/parse of ScoreMatrix
2017-02-21 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-02-21 gmungocJAL-2416 more validation in ScoreMatrix constructor
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
2017-02-20 gmungocJAL-2416 replaced dependency on ResidueProperties with...
2017-02-17 gmungocJAL-2416 score models now held in order added
2017-02-17 gmungocJAL-2403 extract method refactoring of FeatureScoreMode...
2017-02-14 gmungocParsing moved to (new) ScoreMatrixFile, drag and drop...
2017-02-13 gmungocJAL-2416 allow alphabet symbol (optional) in first...
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as...
2017-02-06 gmungocJAL-2379 computePairwiseScores() moved to ScoreMatrix
2017-02-03 gmungocJAL-2379 'direct' pairwise score calculation for PCA...
2017-01-16 gmungocJAL-1270 class renamed
2017-01-16 gmungocJAL-1270 tweaks to AlignmentGenerator / client class
2017-01-12 gmungocJAL-1270 renamed AlignmentGenerator, and added peptide...
2016-11-28 gmungocMerge branch 'develop' into trialMerge
2016-11-28 tcofoegbuMerge branch 'features/JAL-2326_JOptionPane-refactoring...
2016-11-25 gmungocMerge branch 'develop' into trialMerge
2016-11-24 tcofoegbuJAL-2326 added setup method for JvOptionPane in all... features/JAL-2326_JOptionPane-refactoring
2016-11-24 Jim ProcterJAL-2325 apply license to new source files
2016-11-23 Jim ProcterMerge branch 'bug/JAL-2323disulfideOverview' into develop
2016-11-22 Jim ProcterMerge branch 'features/JAL-1738_JAL-345_selectionfromhi...
2016-11-21 Jim ProcterJAL-2335 failing test for FeatureRendererModel.findFeat...
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns
2016-11-04 gmungocJAL-966 JAL-1854 removed redundant methods / modifiers...
2016-11-04 gmungocJAL-2302 unit tests added for Finder
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold...
2016-11-02 gmungocJAL-98 ProfileI interface for Profile
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis...
2016-11-01 gmungocConservation now using ResidueCount; tests added
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
2016-10-25 gmungocJAL-98 minor fixes to / tests for annotation derivation
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-24 gmungocJAL-98 ResidueCount 100% test coverage (and bug fixes!)
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 apply license
2016-10-05 Jim ProcterJAL-2189 format tests
2016-10-04 gmungocJAL-2232 some fix / partial fix of failing tests bug/JAL-2210_hack_for_Release_2_10
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount...
2016-10-02 Jim ProcterJAL-2210 first pass at attempting to fix CrossRef tests...
2016-09-27 gmungocJAL-2230 JAL-2049 added sequence feature transfer to
2016-09-21 Jim ProcterJAL-2214 test for strict Watson-Crick pairing
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p...
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum
2016-08-29 gmungocJAL-1841 robustness fix bug/JAL-1841rnaSecStr
2016-08-26 Jim ProcterJAL-2154 patch regression on DbRefFetcher due to PDB...
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ...
2016-08-25 Jim ProcterJAL-2106 JAL-2154 fix test for additional reference...
2016-08-25 Jim ProcterMerge branch 'trailm' into trial_fixMakeCDSDBRefPropagation
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-24 Jim ProcterJAL-2106 FIXME for test failure
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-23 Jim ProcterJAL-2154 updated testMakeCDSAlignment for expected...
2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test
2016-08-18 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
2016-08-17 gmungocJAL-2172 reverted to not sorting column selection
2016-08-17 gmungocJAL-2172 handle case where column selection is not...
2016-08-16 gmungocJAL-2171 matching bracket default character for rna...
2016-08-12 gmungocJAL-1841, bug fix in rna SS consensus, additions to...
2016-08-04 Jim ProcterJAL-2110 comment on failing test (consider skipping...
2016-07-19 gmungocJAL-391 corrected handling of gapped sequences
2016-07-18 gmungocfileFormat enum wip changes
2016-07-12 Jim ProcterJAL-2110 note about use case for when alignAsSameSequen...
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple...
2016-07-11 gmungocfile format enum wip changes
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct...
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