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Merge branch 'develop' into trialMerge
[jalview.git] / src / jalview / analysis /
2016-11-22 Jim ProcterMerge branch 'features/JAL-1738_JAL-345_selectionfromhi... tree | commitdiff
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns tree | commitdiff
2016-11-08 tcofoegbuJAL-2292 updated method calls tree | commitdiff
2016-11-04 tcofoegbuJAL-2292 fix for wrong mapping output in sequence mappi... tree | commitdiff
2016-11-03 gmungocJAL-2310 don't double-count sequence matches; code... tree | commitdiff
2016-11-02 Jim ProcterJAL-1738 JAL-345 fix for JAL-2302 only report Matches... tree | commitdiff
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold... tree | commitdiff
2016-11-02 gmungocJAL-98 ProfileI interface for Profile tree | commitdiff
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis... tree | commitdiff
2016-11-02 gmungocJAL-98 wording "negatively conserved" now "absence... tree | commitdiff
2016-11-01 gmungocConservation now using ResidueCount; tests added tree | commitdiff
2016-11-01 gmungocJAL-98 typo in javadoc tree | commitdiff
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults... tree | commitdiff
2016-10-25 gmungocJAL-98 javadoc corrected tree | commitdiff
2016-10-25 gmungocJAL-98 javadoc added tree | commitdiff
2016-10-25 gmungocJAL-98 minor fixes to / tests for annotation derivation tree | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch tree | commitdiff
2016-10-25 gmungocJAL-98 small efficiency fix + commenting tree | commitdiff
2016-10-25 gmungocJAL-98 javadoc / comments updated tree | commitdiff
2016-10-24 gmungocJAL-98 fixme comment removed - nothing to do tree | commitdiff
2016-10-24 gmungocJAL-98 ResidueCount 100% test coverage (and bug fixes!) tree | commitdiff
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory tree | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... tree | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting tree | commitdiff
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount... tree | commitdiff
2016-10-03 Jim ProcterJAL-2210 hack to remove EMBL from Protein crossrefs... tree | commitdiff
2016-10-03 Jim ProcterJAL-2210 explicit ‘doNotAdd’ list to prevent sequences... tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 two pass attempt to import retrieved sequences... tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 try to merge all sequences referenced by a... tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 comments tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 discover candidate dataset sequences for an... tree | commitdiff
2016-10-01 Jim ProcterJAL-2210 factored out code for processing cross-referen... tree | commitdiff
2016-10-01 Jim ProcterJAL-2210 refactor code to remove from a list of dbrefs... tree | commitdiff
2016-09-30 Jim ProcterJAL-2210 some DBRef xref/ref correspondences may add... tree | commitdiff
2016-09-30 Jim ProcterJAL-2210 CrossRef.findInDataset should search for prese... tree | commitdiff
2016-09-30 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory tree | commitdiff
2016-09-27 gmungocJAL-2230 use correct mapping to transfer features to... tree | commitdiff
2016-09-26 gmungocJAL-98 bug fix, string optimisation, sorted AA properties tree | commitdiff
2016-09-26 gmungocJAL-98 don't include gaps in maxResidue! tree | commitdiff
2016-09-23 gmungocJAL-98 performance tweaks to use of SparseIntArray tree | commitdiff
2016-09-23 Jim ProcterJAL-2214 fix docs (consistent and correct base pair... tree | commitdiff
2016-09-23 gmungocJAL-98 first working version tree | commitdiff
2016-09-23 gmungocJAL-2214 Javadoc tree | commitdiff
2016-09-23 gmungocJAL-98 use SparseIntArray (wip) tree | commitdiff
2016-09-22 gmungocJAL-1421 use declared type of ResidueProperties.propHash tree | commitdiff
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176... tree | commitdiff
2016-09-21 Jim ProcterJAL-2214 JAL-1841 compute canonical, canonicalAndWobble... tree | commitdiff
2016-09-21 Jim ProcterJAL-1841 JAL-2215 add the ‘ignore gaps’ structure conse... tree | commitdiff
2016-09-21 Jim ProcterJAL-2214 test for strict Watson-Crick pairing tree | commitdiff
2016-09-20 gmungocJAL-1306 calculate Quality also when Conservation not... tree | commitdiff
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157 tree | commitdiff
2016-09-01 gmungocJAL-1421 add generics to NJTree, refactor recursive... tree | commitdiff
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... tree | commitdiff
2016-08-29 Jim ProcterJAL-2154 don’t synthesise multiple CDS|<Acc> sequences... tree | commitdiff
2016-08-29 Jim ProcterJAL-2154 filter out dbrefs that already match primary... tree | commitdiff
2016-08-29 Jim ProcterJAL-2154 refactor if (for easier breakpoint) and formatting tree | commitdiff
2016-08-29 gmungocJAL-1841 robustness fix bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-26 Jim ProcterJAL-2154 check that xref is a coding xref before adding... tree | commitdiff
2016-08-26 Jim ProcterJAL-2154 don’t add any remaining xrefed sequences of... tree | commitdiff
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ... tree | commitdiff
2016-08-25 Jim ProcterJAL-2154 JAL-2106 transfer primary refs to CDS for... tree | commitdiff
2016-08-25 Jim ProcterJAL-2154 copy and paste error tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'trailm' into trial_fixMakeCDSDBRefPropagation tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision... tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... tree | commitdiff
2016-08-23 Jim ProcterJAL-2154 propagate from contig to CDS after constructin... tree | commitdiff
2016-08-23 Jim ProcterJAL-2154 should only add mappings between dataset sequences tree | commitdiff
2016-08-23 Jim ProcterJAL-2154 - only copy DBRef from contig to new CDS seque... tree | commitdiff
2016-08-23 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings tree | commitdiff
2016-08-22 Jim ProcterJAL-2154 verify recovered xref sequence not already... tree | commitdiff
2016-08-22 Jim ProcterJAL-2154 regression warning - should never recover... tree | commitdiff
2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test tree | commitdiff
2016-08-18 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-17 gmungocJAL-2172 reverted to not sorting column selection tree | commitdiff
2016-08-17 gmungocJAL-2172 handle case where column selection is not... tree | commitdiff
2016-08-16 Jim ProcterJAL-2154 make sure any new sequences via DBRefEntry... tree | commitdiff
2016-08-16 Jim ProcterJAL-2154 always resolve dataset sequences when creating... tree | commitdiff
2016-08-16 gmungocJAL-2171 matching bracket default character for rna... tree | commitdiff
2016-08-12 gmungocJAL-1841 count (logo height) is valid pairs only; detec... tree | commitdiff
2016-08-12 gmungocJAL-1841, bug fix in rna SS consensus, additions to... tree | commitdiff
2016-08-04 Jim ProcterJAL-2154 make sure codon mappings between sequences... tree | commitdiff
2016-08-04 Jim ProcterJAL-2154 todo tree | commitdiff
2016-08-04 Jim ProcterJAL-2154 use convenience method tree | commitdiff
2016-07-20 gmungocJAL-2023 JAL-1681 fixed bug in computing '+' for co... tree | commitdiff
2016-07-19 gmungocJAL-391 corrected handling of gapped sequences tree | commitdiff
2016-07-18 Jim ProcterJAL-2145 improvement: ensure conservation calculation... tree | commitdiff
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr... tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple... tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 javadoc tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 scalability todo tree | commitdiff
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO tree | commitdiff
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct... tree | commitdiff
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack tree | commitdiff
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented tree | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds tree | commitdiff
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment... tree | commitdiff
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when... tree | commitdiff
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying... tree | commitdiff
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