jalview.git
2016-09-06 gmungocJAL-2147 additional test coverage for findMappingsForSe...
2016-09-05 gmungocJAL-2154 made Java 7 compatible
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs
2016-09-05 gmungocJAL-2106 corrections to DBRefEntry.isPrimary code and...
2016-09-04 Jim ProcterJAL-1919 preserve filename on restore of project so...
2016-09-04 Jim ProcterJAL-1803 JAL-2106 patch tests for tighter PDB Primary...
2016-09-04 Jim ProcterJAL-2148 JAL-1803 JAL-1919 resolve type for mmCIF loade...
2016-09-04 Jim ProcterJAL-1803 recover type field faithfully for mmCIF/PDB...
2016-09-04 Jim ProcterJAL-1803 restore property array for a sequence’s associ...
2016-09-04 Jim ProcterJAL-1803 chainCode moved onto property hashtable as...
2016-09-04 Jim ProcterJAL-1803 patch test: PDBEntry.getFile() will always...
2016-09-01 Jim ProcterJAL-1803 JAL-2188 experimental:
2016-08-31 Jim ProcterJAL-1926 JAL-2106 source DB refs come from SequenceI...
2016-08-31 Jim ProcterJAL-1926 JAL-2106 resolve source DB refs using canonica...
2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:...
2016-08-31 Jim ProcterJAL-2157 JAL-2154 simplify CanshowProducts code to...
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... merge/develop_bug/JAL-2154projectMappings
2016-08-30 Jim ProcterJAL-2154 doc & AssertError trap for known failure case...
2016-08-30 Jim ProcterJAL-2154 always compare canonicalised DBRefEntry source...
2016-08-30 Jim ProcterJAL-2154 simplify expression
2016-08-30 gmungocJAL-2183 defensive check for openFrameCount < 0 (should...
2016-08-30 gmungocJAL-2183 simplified database tree actionPerformed,...
2016-08-30 gmungocJAL-2183 revised change (= no change)
2016-08-30 gmungocJAL-2183 formatter added @Override (only)
2016-08-30 gmungocJAL-2183 removed redundant (overriden) add panel to...
2016-08-30 Jim ProcterJAL-2154 javadoc, fix underloaded version of assertData...
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 Jim ProcterJAL-2154 canonical dbsources are lowercased before...
2016-08-29 Jim ProcterJAL-2154 ENA specific Ensembl canonical db prefixes
2016-08-29 Jim ProcterJAL-2154 endless loop fixed (hopefully :) )
2016-08-29 gmungocJAL-1854 tweaks to rules and README
2016-08-29 Jim ProcterJAL-2154 catch insertion of duplicate CDS after retriev...
2016-08-29 Jim ProcterJAL-2154 Optional message parameter for assertDatasetNo...
2016-08-29 Jim ProcterJAL-2154 new assertDatasetIsNormalised to trivially...
2016-08-29 Jim ProcterJAL-2154 additional test that removing a duplicate...
2016-08-29 gmungocJAL-1854 checkstyle relocated to /utils, newlines to...
2016-08-29 gmungocMerge branch 'bug/JAL-1841rnaSecStr' into develop
2016-08-29 gmungocJAL-1448 updated unit test for last change
2016-08-29 gmungocJAL-1841 robustness fix bug/JAL-1841rnaSecStr
2016-08-29 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
2016-08-26 gmungocJAL-1854 two more rules, readme notes
2016-08-26 Jim ProcterJAL-2154 patch regression on DbRefFetcher due to PDB...
2016-08-26 Jim ProcterMerge branch 'bug/JAL-2154projectMappings' into merge...
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings
2016-08-26 Jim ProcterJAL-2154 ENSEMBL and Uniprot tests
2016-08-26 Jim ProcterJAL-2154 report any db fetch failures as a fail at end
2016-08-26 Jim ProcterJAL-2154 ensure pass increments actually result in...
2016-08-26 Jim ProcterJAL-2154 catch and report a failures when xrefed projec...
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-1854 commented FallThrough rule
2016-08-26 gmungocJAL-1854 corrected nested package rule
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ...
2016-08-26 Jim ProcterJAL-2154 drop PDB from Protein db list to remove from...
2016-08-26 Jim ProcterJAL-2154 Defer failing cross-ref combinations that...
2016-08-26 Jim ProcterJAL-2154 check that CDS panel is only nucleotide, and...
2016-08-26 gmungocJAL-1854 comment switch case fallthrough
2016-08-25 Jim ProcterJAL-2106 JAL-2154 fix test for additional reference...
2016-08-25 Jim ProcterJAL-2106 JAL-2154 cross-refs from Ensembl should verify...
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB
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 gmungocJAL-1854 missing case break statements added
2016-08-25 gmungocJAL-1854 initial checkstyle config
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 bug/JAL-2154projectMappings
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-25 gmungocJAL-2178 remove duplicate Uniprot db source
2016-08-25 gmungocJAL-1424 duplicate key removed
2016-08-24 Jim ProcterJAL-2106 FIXME for test failure
2016-08-24 Jim ProcterJAL-2106 TODO - verify Embl primary refs get added
2016-08-24 Jim ProcterJAL-2106 tidy up and comments for DBRefFetcher
2016-08-24 Jim ProcterJAL-2106 javadoc for sifts mapping method
2016-08-24 Jim ProcterJAL-2106 prevent SIFTS mappings for sequences that...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-24 Jim ProcterJAL-2106 stricter check for 1:1 mapping (same numbering...
2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that...
2016-08-24 Jim ProcterJAL-2106 formatting
2016-08-24 Jim ProcterJAL-2106 DBRefEntry.isPrimary() minimal test & implemen...
2016-08-24 Jim ProcterJAL-2106 convenience method to find all dbsource names...
2016-08-24 gmungocJAL-1355 correct 'thereshold' to 'threshold' in message...
2016-08-24 gmungocJAL-1424 removed unused and duplicated message keys
2016-08-24 gmungocJAL-1424 tidy / recode MessageManager calls to support...
2016-08-24 gmungocJAL-1854 removed pointless method override
2016-08-24 gmungocJAL-1424 removed two redundant (overwritten) setText...
2016-08-24 gmungocJAL-1424 corrected Message bundle lookup key
2016-08-24 gmungocJAL-1424 undo i18n of exception message
2016-08-24 gmungocJAL-1854 declare immutable class as final
2016-08-24 gmungocJAL-1424 recode calls to MessageManager to allow code...
2016-08-24 gmungocJAL-2151 port fix to applet
2016-08-24 gmungocJAL-1424 enhanced for cleaner reporting, checks calls...
2016-08-24 gmungocJAL-1424 also report (obsolete) keys in translated...
2016-08-23 Jim ProcterJAL-2154 updated testMakeCDSAlignment for expected...
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
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