JAL-2446 optimised new method to find feature colour for overview
[jalview.git] / src / jalview / analysis /
2017-03-16 Jim ProcterJAL-1933 refactor parameter for code clarity
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes...
2017-02-09 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory
2017-02-07 gmungocJAL-2379 removed unused commented code
2017-02-06 gmungocJAL-2379 computePairwiseScores() moved to ScoreMatrix
2017-02-03 gmungocJAL-2379 'direct' pairwise score calculation for PCA...
2017-01-26 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit...
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2360colourSche...
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory
2017-01-26 gmungocJAL-2380 code tidy after review
2017-01-17 gmungocJAL-2379 use SparseMatrix for encoded sequences, tidy...
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI
2016-12-16 gmungocJAL-1705 JAL-98 use SortedMap as more accurate type...
2016-12-05 gmungocMerge branch 'features/JAL-1933_occupancy' into feature...
2016-12-04 Jim ProcterJAL-1933 show occupancy count as a tooltip
2016-12-04 Jim ProcterJAL-1933 switch from gap count to occupancy
2016-12-02 gmungocMerge branch 'features/JAL-1933_occupancy' into feature...
2016-12-02 gmungocJAL-1933 gap value as description; minor formatting
2016-12-01 Jim ProcterJAL-1933 update the bounds for the Gap annotation row...
2016-12-01 Jim ProcterJAL-1933 basic hack to get gap counts shown as an annot...
2016-11-23 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-11-22 Jim ProcterMerge branch 'features/JAL-1738_JAL-345_selectionfromhi...
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns
2016-11-11 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-11-08 gmungocJAL-2295 make RangeComparator a top level class for...
2016-11-08 tcofoegbuJAL-2292 updated method calls
2016-11-04 tcofoegbuJAL-2292 fix for wrong mapping output in sequence mappi...
2016-11-03 gmungocJAL-2310 don't double-count sequence matches; code...
2016-11-02 Jim ProcterJAL-1738 JAL-345 fix for JAL-2302 only report Matches...
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...
2016-11-02 gmungocJAL-98 wording "negatively conserved" now "absence...
2016-11-01 gmungocConservation now using ResidueCount; tests added
2016-11-01 gmungocJAL-98 typo in javadoc
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
2016-10-25 gmungocJAL-98 javadoc corrected
2016-10-25 gmungocJAL-98 javadoc added
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
2016-10-25 gmungocJAL-98 small efficiency fix + commenting
2016-10-25 gmungocJAL-98 javadoc / comments updated
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...
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