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2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 don’t synthesise multiple CDS|<Acc> sequences... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 filter out dbrefs that already match primary... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 refactor if (for easier breakpoint) and formatting commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 canonical dbsources are lowercased before... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 ENA specific Ensembl canonical db prefixes commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 endless loop fixed (hopefully :) ) commit | commitdiff | tree | snapshot
2016-08-29 gmungocJAL-1854 tweaks to rules and README commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 catch insertion of duplicate CDS after retriev... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 Optional message parameter for assertDatasetNo... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 new assertDatasetIsNormalised to trivially... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 additional test that removing a duplicate... commit | commitdiff | tree | snapshot
2016-08-29 gmungocJAL-1854 checkstyle relocated to /utils, newlines to... commit | commitdiff | tree | snapshot
2016-08-29 gmungocMerge branch 'bug/JAL-1841rnaSecStr' into develop commit | commitdiff | tree | snapshot
2016-08-29 gmungocJAL-1448 updated unit test for last change commit | commitdiff | tree | snapshot
2016-08-29 gmungocJAL-1841 robustness fix bug/JAL-1841rnaSecStr commit | commitdiff | tree | snapshot
2016-08-29 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr commit | commitdiff | tree | snapshot
2016-08-26 gmungocJAL-1854 two more rules, readme notes commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 patch regression on DbRefFetcher due to PDB... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterMerge branch 'bug/JAL-2154projectMappings' into merge... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 ENSEMBL and Uniprot tests commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 report any db fetch failures as a fail at end commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 ensure pass increments actually result in... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 catch and report a failures when xrefed projec... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 check that xref is a coding xref before adding... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 don’t add any remaining xrefed sequences of... commit | commitdiff | tree | snapshot
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr commit | commitdiff | tree | snapshot
2016-08-26 gmungocJAL-1854 commented FallThrough rule commit | commitdiff | tree | snapshot
2016-08-26 gmungocJAL-1854 corrected nested package rule commit | commitdiff | tree | snapshot
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 drop PDB from Protein db list to remove from... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 Defer failing cross-ref combinations that... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 check that CDS panel is only nucleotide, and... commit | commitdiff | tree | snapshot
2016-08-26 gmungocJAL-1854 comment switch case fallthrough commit | commitdiff | tree | snapshot
2016-08-25 Jim ProcterJAL-2106 JAL-2154 fix test for additional reference... commit | commitdiff | tree | snapshot
2016-08-25 Jim ProcterJAL-2106 JAL-2154 cross-refs from Ensembl should verify... commit | commitdiff | tree | snapshot
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB commit | commitdiff | tree | snapshot
2016-08-25 Jim ProcterJAL-2154 JAL-2106 transfer primary refs to CDS for... commit | commitdiff | tree | snapshot
2016-08-25 Jim ProcterJAL-2154 copy and paste error commit | commitdiff | tree | snapshot
2016-08-25 gmungocJAL-1854 missing case break statements added commit | commitdiff | tree | snapshot
2016-08-25 gmungocJAL-1854 initial checkstyle config commit | commitdiff | tree | snapshot
2016-08-25 Jim ProcterMerge branch 'trailm' into trial_fixMakeCDSDBRefPropagation commit | commitdiff | tree | snapshot
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision... commit | commitdiff | tree | snapshot
2016-08-25 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings commit | commitdiff | tree | snapshot
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR... commit | commitdiff | tree | snapshot
2016-08-25 gmungocJAL-2178 remove duplicate Uniprot db source commit | commitdiff | tree | snapshot
2016-08-25 gmungocJAL-1424 duplicate key removed commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 FIXME for test failure commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 TODO - verify Embl primary refs get added commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 tidy up and comments for DBRefFetcher commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 javadoc for sifts mapping method commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 prevent SIFTS mappings for sequences that... commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 stricter check for 1:1 mapping (same numbering... commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that... commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 formatting commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 DBRefEntry.isPrimary() minimal test & implemen... commit | commitdiff | tree | snapshot
2016-08-24 Jim ProcterJAL-2106 convenience method to find all dbsource names... commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1355 correct 'thereshold' to 'threshold' in message... commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1424 removed unused and duplicated message keys commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1424 tidy / recode MessageManager calls to support... commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1854 removed pointless method override commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1424 removed two redundant (overwritten) setText... commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1424 corrected Message bundle lookup key commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1424 undo i18n of exception message commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1854 declare immutable class as final commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1424 recode calls to MessageManager to allow code... commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-2151 port fix to applet commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1424 enhanced for cleaner reporting, checks calls... commit | commitdiff | tree | snapshot
2016-08-24 gmungocJAL-1424 also report (obsolete) keys in translated... commit | commitdiff | tree | snapshot
2016-08-23 Jim ProcterJAL-2154 updated testMakeCDSAlignment for expected... commit | commitdiff | tree | snapshot
2016-08-23 Jim ProcterJAL-2154 propagate from contig to CDS after constructin... commit | commitdiff | tree | snapshot
2016-08-23 Jim ProcterJAL-2154 should only add mappings between dataset sequences commit | commitdiff | tree | snapshot
2016-08-23 Jim ProcterJAL-2154 - only copy DBRef from contig to new CDS seque... commit | commitdiff | tree | snapshot
2016-08-23 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings commit | commitdiff | tree | snapshot
2016-08-23 gmungocJAL-2176 unused field / methods removed commit | commitdiff | tree | snapshot
2016-08-23 gmungocJAL-2174 markColumns() refactored inside ColumnSelection commit | commitdiff | tree | snapshot
2016-08-22 Jim ProcterJAL-2154 - rejig test pass code for breadth-first ... commit | commitdiff | tree | snapshot
2016-08-22 gmungocJAL-1448 corrected for backwards compatibility for... commit | commitdiff | tree | snapshot
2016-08-22 gmungocJAL-2175 code tidying commit | commitdiff | tree | snapshot
2016-08-22 gmungocJAL-2175 code/test fixes/tidy for PFAM/MSF/JSON roundtrip commit | commitdiff | tree | snapshot
2016-08-22 Jim ProcterJAL-2154 verify recovered xref sequence not already... commit | commitdiff | tree | snapshot
2016-08-22 Jim ProcterJAL-2154 regression warning - should never recover... commit | commitdiff | tree | snapshot
2016-08-22 Jim ProcterJAL-2154 always check dataset sequence for sequence... commit | commitdiff | tree | snapshot
2016-08-22 Jim ProcterJAL-2154 patch verifyAlignment so it fails for duplicat... commit | commitdiff | tree | snapshot
2016-08-22 Jim ProcterJAL-2154 tidy assert messages and fix test to verify... commit | commitdiff | tree | snapshot
2016-08-22 Jim ProcterJAL-2154 test that verifyAlignment fails for duplicate... commit | commitdiff | tree | snapshot
2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test commit | commitdiff | tree | snapshot
2016-08-19 gmungocJAL-2174 bug fixes + refactoring to allow + unit tests commit | commitdiff | tree | snapshot
2016-08-19 Jim ProcterJAL-2154 - possible patch .. but leads to new stringify... commit | commitdiff | tree | snapshot
2016-08-19 Jim ProcterJAL-2154 major rejigging of test looping again commit | commitdiff | tree | snapshot
2016-08-19 Jim ProcterJAL-2154 disable DAS sources for Jalview2XML tests commit | commitdiff | tree | snapshot
2016-08-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-08-19 tcofoegbuJAL-1803 unit test for PDB chainCode save/restore from... commit | commitdiff | tree | snapshot
2016-08-19 Jim ProcterJAL-2154 fix looping structure so for a particular... commit | commitdiff | tree | snapshot
2016-08-19 Jim ProcterJAL-2154 drop unused hashes commit | commitdiff | tree | snapshot
2016-08-19 Jim ProcterJAL-2154 testNG like assertAlignmentDatasetRefs static... commit | commitdiff | tree | snapshot
2016-08-19 Jim ProcterJAL-2154 reorder the dataset sequences according to... commit | commitdiff | tree | snapshot
2016-08-19 Jim ProcterJAL-2154 belt-and-braces patch: commit | commitdiff | tree | snapshot
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