Merge branch 'develop' into releases/Release_2_11_Branch
[jalview.git] / src / jalview / analysis /
2016-10-24 gmungocJAL-98 fixme comment removed - nothing to do
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 source formatting
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount...
2016-10-03 Jim ProcterJAL-2210 hack to remove EMBL from Protein crossrefs...
2016-10-03 Jim ProcterJAL-2210 explicit ‘doNotAdd’ list to prevent sequences...
2016-10-02 Jim ProcterJAL-2210 two pass attempt to import retrieved sequences...
2016-10-02 Jim ProcterJAL-2210 try to merge all sequences referenced by a...
2016-10-02 Jim ProcterJAL-2210 comments
2016-10-02 Jim ProcterJAL-2210 discover candidate dataset sequences for an...
2016-10-01 Jim ProcterJAL-2210 factored out code for processing cross-referen...
2016-10-01 Jim ProcterJAL-2210 refactor code to remove from a list of dbrefs...
2016-09-30 Jim ProcterJAL-2210 some DBRef xref/ref correspondences may add...
2016-09-30 Jim ProcterJAL-2210 CrossRef.findInDataset should search for prese...
2016-09-30 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-09-27 gmungocJAL-2230 use correct mapping to transfer features to...
2016-09-26 gmungocJAL-98 bug fix, string optimisation, sorted AA properties
2016-09-26 gmungocJAL-98 don't include gaps in maxResidue!
2016-09-23 gmungocJAL-98 performance tweaks to use of SparseIntArray
2016-09-23 Jim ProcterJAL-2214 fix docs (consistent and correct base pair...
2016-09-23 gmungocJAL-98 first working version
2016-09-23 gmungocJAL-2214 Javadoc
2016-09-23 gmungocJAL-98 use SparseIntArray (wip)
2016-09-22 gmungocJAL-1421 use declared type of ResidueProperties.propHash
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176...
2016-09-21 Jim ProcterJAL-2214 JAL-1841 compute canonical, canonicalAndWobble...
2016-09-21 Jim ProcterJAL-1841 JAL-2215 add the ‘ignore gaps’ structure conse...
2016-09-21 Jim ProcterJAL-2214 test for strict Watson-Crick pairing
2016-09-20 gmungocJAL-1306 calculate Quality also when Conservation not...
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157
2016-09-01 gmungocJAL-1421 add generics to NJTree, refactor recursive...
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p...
2016-08-29 Jim ProcterJAL-2154 don’t synthesise multiple CDS|<Acc> sequences...
2016-08-29 Jim ProcterJAL-2154 filter out dbrefs that already match primary...
2016-08-29 Jim ProcterJAL-2154 refactor if (for easier breakpoint) and formatting
2016-08-29 gmungocJAL-1841 robustness fix bug/JAL-1841rnaSecStr
2016-08-26 Jim ProcterJAL-2154 check that xref is a coding xref before adding...
2016-08-26 Jim ProcterJAL-2154 don’t add any remaining xrefed sequences of...
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-2154 JAL-2106 transfer primary refs to CDS for...
2016-08-25 Jim ProcterJAL-2154 copy and paste error
2016-08-25 Jim ProcterMerge branch 'trailm' into trial_fixMakeCDSDBRefPropagation
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision...
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-23 Jim ProcterJAL-2154 propagate from contig to CDS after constructin...
2016-08-23 Jim ProcterJAL-2154 should only add mappings between dataset sequences
2016-08-23 Jim ProcterJAL-2154 - only copy DBRef from contig to new CDS seque...
2016-08-23 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings
2016-08-22 Jim ProcterJAL-2154 verify recovered xref sequence not already...
2016-08-22 Jim ProcterJAL-2154 regression warning - should never recover...
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 Jim ProcterJAL-2154 make sure any new sequences via DBRefEntry...
2016-08-16 Jim ProcterJAL-2154 always resolve dataset sequences when creating...
2016-08-16 gmungocJAL-2171 matching bracket default character for rna...
2016-08-12 gmungocJAL-1841 count (logo height) is valid pairs only; detec...
2016-08-12 gmungocJAL-1841, bug fix in rna SS consensus, additions to...
2016-08-04 Jim ProcterJAL-2154 make sure codon mappings between sequences...
2016-08-04 Jim ProcterJAL-2154 todo
2016-08-04 Jim ProcterJAL-2154 use convenience method
2016-07-20 gmungocJAL-2023 JAL-1681 fixed bug in computing '+' for co...
2016-07-19 gmungocJAL-391 corrected handling of gapped sequences
2016-07-18 Jim ProcterJAL-2145 improvement: ensure conservation calculation...
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr...
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple...
2016-07-12 Jim ProcterJAL-2110 javadoc
2016-07-12 Jim ProcterJAL-2110 scalability todo
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct...
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment...
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 bug fixing and tidying for get cross-refs
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results...
2016-06-23 Jim ProcterMerge branch 'develop' into merge_JAL-2110
2016-06-23 Jim ProcterJAL-2110 make indirect xref searches work by not filter...
2016-06-23 Jim ProcterJAL-2110 warning message when routine finds non-ds...
2016-06-23 Jim ProcterJAL-2110 clarify javadoc
2016-06-23 Jim ProcterJAL-2110 refactor to split SequenceFetcher from x-ref...
2016-06-23 Jim ProcterJAL-2110 use SequenceI.isProtein()
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array
2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context...
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
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 ensure bare Strings are lowercased before...
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame...
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