Bamboo test#12 adding flushEvents()
[jalview.git] / test / jalview / analysis /
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...
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when...
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying...
2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings...
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results...
2016-06-23 Jim ProcterJAL-2110 JAL-1551 formatting
2016-06-23 Jim ProcterJAL-2110 enable and fix failing tests
2016-06-23 Jim ProcterJAL-2110 enable and fix test
2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context...
2016-06-21 gmungocJAL-2110 updated unit test to match code changes
2016-06-20 Jim ProcterJAL-2110 pass dataset to makeCDSalignment
2016-06-16 Jim ProcterJAL-2110 change test for desired behaviour of getCodonF...
2016-06-16 Jim ProcterJAL-2110 throw implementation error if not given a...
2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use...
2016-06-09 gmungocJAL-2110 work in progress
2016-06-03 gmungocJAL-2110 random stuff
2016-06-02 gmungocMerge branch 'develop' into features/JAL-2110_makeSense...
2016-06-01 Jim ProcterJAL-2038 fix tests for case insensitive eSequenceIdMatcher
2016-05-25 gmungocJAL-2110 wip CrossRefs rewrite of CrossRef
2016-05-20 gmungocJAL-2110 unit tests for and minor refactoring of CrossRef
2016-05-20 gmungocJAL-2049 unit test updated for HGVS syntax, feature...
2016-04-24 Jim ProcterJAL-2075 test showing hidden columns bug in feature...
2016-04-24 Jim ProcterJAL-2075 refactor FeatureScoreModel to native testNG...
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib...
2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer...
2016-04-13 Jim ProcterJAL-2046 test to demonstrate feature duplication bug
2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ...
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align...
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
2016-03-11 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h...
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