jalview.git
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 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...
2016-08-25 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 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
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
2016-08-23 gmungocJAL-2176 unused field / methods removed
2016-08-23 gmungocJAL-2174 markColumns() refactored inside ColumnSelection
2016-08-22 Jim ProcterJAL-2154 - rejig test pass code for breadth-first ...
2016-08-22 gmungocJAL-1448 corrected for backwards compatibility for...
2016-08-22 gmungocJAL-2175 code tidying
2016-08-22 gmungocJAL-2175 code/test fixes/tidy for PFAM/MSF/JSON roundtrip
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 Jim ProcterJAL-2154 always check dataset sequence for sequence...
2016-08-22 Jim ProcterJAL-2154 patch verifyAlignment so it fails for duplicat...
2016-08-22 Jim ProcterJAL-2154 tidy assert messages and fix test to verify...
2016-08-22 Jim ProcterJAL-2154 test that verifyAlignment fails for duplicate...
2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test
2016-08-19 gmungocJAL-2174 bug fixes + refactoring to allow + unit tests
2016-08-19 Jim ProcterJAL-2154 - possible patch .. but leads to new stringify...
2016-08-19 Jim ProcterJAL-2154 major rejigging of test looping again
2016-08-19 Jim ProcterJAL-2154 disable DAS sources for Jalview2XML tests
2016-08-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-08-19 tcofoegbuJAL-1803 unit test for PDB chainCode save/restore from...
2016-08-19 Jim ProcterJAL-2154 fix looping structure so for a particular...
2016-08-19 Jim ProcterJAL-2154 drop unused hashes
2016-08-19 Jim ProcterJAL-2154 testNG like assertAlignmentDatasetRefs static...
2016-08-19 Jim ProcterJAL-2154 reorder the dataset sequences according to...
2016-08-19 Jim ProcterJAL-2154 belt-and-braces patch:
2016-08-19 Jim ProcterJAL-2154 verify mapping’s sequenceI ref has been resolv...
2016-08-19 Jim ProcterJAL-2154 use right reference string for recovering...
2016-08-19 Jim ProcterJAL-2154 refactor setSequenceAt to replaceSequenceAt...
2016-08-18 gmungocJAL-2077 using Platform method to check for Ctrl-down
2016-08-18 gmungocJAL-1445 status message '...not containing...' for...
2016-08-18 gmungocJAL-1693 show warning dialog if unable to make CDS...
2016-08-18 gmungocJAL-1855 fail gracefully if XML has no <sequence> element
2016-08-18 gmungocJAL-2077 handling Cmd-click in scale panel for Mac...
2016-08-18 gmungocJAL-2001 return copy of selection in getSelected()
2016-08-17 gmungocJAL-2146 status message now with formatted residue...
2016-08-17 gmungocJAL-2173 don't remove annotation from hidden columns
2016-08-17 gmungocJAL-2172 reverted to not sorting column selection
2016-08-17 gmungocJAL-2105 rest versions updated to 4.6, change log link...
2016-08-17 gmungocJAL-2172 handle case where column selection is not...
2016-08-16 Jim ProcterJAL-2154 verify sequenceI/dataset refs for codonmappings
2016-08-16 Jim ProcterJAL-2154 make sure any new sequences via DBRefEntry...
2016-08-16 Jim ProcterJAL-2154 check alignment isn’t null before validating
2016-08-16 Jim ProcterJAL-2154 always resolve dataset sequences when creating...
2016-08-16 Jim ProcterJAL-2154 [test] verify reference integrity for alignmen...
2016-08-16 gmungocJAL-2172 unit test added
2016-08-16 Jim ProcterJAL-2154 formatting
2016-08-16 Jim ProcterJAL-2154 new assert to check reference integrity for...
2016-08-16 Jim ProcterJAL-2154 xref test harness - test fails if there are...
2016-08-15 tcofoegbuJAL-1128 fix for truncated bottom boarder pixels in...
2016-08-15 tcofoegbuJAL-1128 fix for truncated bottom boarder pixels in...
2016-08-15 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
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