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JAL-2089 JAL-2119 help link fixups
2016-09-08 Jim ProcterJAL-2089 JAL-2119 help link fixups
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2016-09-08 Jim ProcterJAL-2119 linkcheck target. runs before build indices
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2016-09-07 Jim ProcterMerge branch 'bug/JAL-1803_JAL-2157' into develop
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2016-09-07 Jim ProcterJAL-1670 groundhog day: fix FeaturesFileTest by redacting...
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2016-09-07 Jim ProcterMerge branch 'bug/JAL-1803_JAL-2157' into develop
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2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157
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2016-09-07 Jim ProcterJAL-2192 TODO
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2016-09-07 Jim ProcterJAL-2191 comments re chimera view code redundancy and...
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2016-09-07 Jim ProcterJAL-282 TODO - Sequence name from PDB had redundant...
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2016-09-07 Jim ProcterJAL-1803 transfer mapped chain’s PDBEntry to the *dataset...
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2016-09-07 Jim ProcterJAL-1803 JAL-1919 set type when structure file is parsed
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2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry
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2016-09-07 Jim ProcterJAL-1803 switched so ‘expected’ is constant in assert
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2016-09-06 Jim ProcterMerge branch 'releases/Release_2_10_Branch' into develop
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2016-09-05 Jim ProcterJAL-1563 UniProt FTS doc revisions
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2016-09-05 Jim ProcterJAL-2089 reworked and formatted doc for
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2016-09-05 Jim ProcterJAL-2089 reworked and formatted doc for
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2016-09-05 Jim ProcterJAL-2089 update Uniprot to UniProt in help docs.
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2016-09-05 Jim ProcterJAL-2089 drop MCView documentation from contents.
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2016-09-05 Jim ProcterJAL-1919 revised mmCIF documentation
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2016-09-05 Jim ProcterJAL-2089 bump release date for 2.10
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2016-09-04 Jim ProcterJAL-1919 preserve filename on restore of project so...
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2016-09-04 Jim ProcterJAL-1803 JAL-2106 patch tests for tighter PDB Primary...
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2016-09-04 Jim ProcterJAL-2148 JAL-1803 JAL-1919 resolve type for mmCIF loaded...
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2016-09-04 Jim ProcterJAL-1803 recover type field faithfully for mmCIF/PDB...
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2016-09-04 Jim ProcterJAL-1803 restore property array for a sequence’s associated...
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2016-09-04 Jim ProcterJAL-1803 chainCode moved onto property hashtable as...
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2016-09-04 Jim ProcterJAL-1803 patch test: PDBEntry.getFile() will always...
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2016-09-01 Jim ProcterMerge branch 'bug/JAL-2034_fix' into develop
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2016-09-01 Jim ProcterJAL-2034 - remember to reset needsOverviewUpdate at...
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2016-09-01 Jim ProcterJAL-2034 check context of selection group to catch...
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2016-09-01 Jim ProcterJAL-1803 JAL-2188 experimental:
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2016-08-31 Jim ProcterJAL-1926 JAL-2106 source DB refs come from SequenceI...
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2016-08-31 Jim ProcterJAL-1926 JAL-2106 resolve source DB refs using canonical...
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2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:...
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2016-08-31 Jim ProcterJAL-2157 JAL-2154 simplify CanshowProducts code to...
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2016-08-31 Jim ProcterJAL-2034 fix logic so recalcConservation(true) returns...
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2016-08-31 Jim ProcterJAL-2034 moved ‘isDefinedGroup’ flag to a test method...
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2016-08-31 Jim ProcterJAL-2034 remove todo - answer is yes!
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2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154projec...
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2016-08-30 Jim ProcterJAL-2154 doc & AssertError trap for known failure case...
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2016-08-30 Jim ProcterJAL-2154 always compare canonicalised DBRefEntry source...
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2016-08-30 Jim ProcterJAL-2154 simplify expression
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2016-08-30 Jim ProcterJAL-2154 javadoc, fix underloaded version of assertDatasetIs...
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2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154projec...
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2016-08-29 Jim ProcterJAL-2154 don’t synthesise multiple CDS|<Acc> sequences...
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2016-08-29 Jim ProcterJAL-2154 filter out dbrefs that already match primary...
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2016-08-29 Jim ProcterJAL-2154 refactor if (for easier breakpoint) and formatting
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2016-08-29 Jim ProcterJAL-2154 canonical dbsources are lowercased before...
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2016-08-29 Jim ProcterJAL-2154 ENA specific Ensembl canonical db prefixes
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2016-08-29 Jim ProcterJAL-2154 endless loop fixed (hopefully :) )
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2016-08-29 Jim ProcterJAL-2154 catch insertion of duplicate CDS after retrieve...
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2016-08-29 Jim ProcterJAL-2154 Optional message parameter for assertDatasetNormalised
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2016-08-29 Jim ProcterJAL-2154 new assertDatasetIsNormalised to trivially...
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2016-08-29 Jim ProcterJAL-2154 additional test that removing a duplicate...
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2016-08-26 Jim ProcterJAL-2154 patch regression on DbRefFetcher due to PDB...
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2016-08-26 Jim ProcterMerge branch 'bug/JAL-2154projectMappings' into merge...
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2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRef...
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2016-08-26 Jim ProcterJAL-2154 ENSEMBL and Uniprot tests
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2016-08-26 Jim ProcterJAL-2154 report any db fetch failures as a fail at end
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2016-08-26 Jim ProcterJAL-2154 ensure pass increments actually result in...
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2016-08-26 Jim ProcterJAL-2154 catch and report a failures when xrefed project...
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2016-08-26 Jim ProcterJAL-2154 check that xref is a coding xref before adding...
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2016-08-26 Jim ProcterJAL-2154 don’t add any remaining xrefed sequences of...
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2016-08-26 Jim ProcterJAL-2154 drop PDB from Protein db list to remove from...
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2016-08-26 Jim ProcterJAL-2154 Defer failing cross-ref combinations that...
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2016-08-26 Jim ProcterJAL-2154 check that CDS panel is only nucleotide, and...
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2016-08-25 Jim ProcterJAL-2106 JAL-2154 fix test for additional reference...
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2016-08-25 Jim ProcterJAL-2106 JAL-2154 cross-refs from Ensembl should verify...
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2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB
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2016-08-25 Jim ProcterJAL-2154 JAL-2106 transfer primary refs to CDS for...
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2016-08-25 Jim ProcterJAL-2154 copy and paste error
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2016-08-25 Jim ProcterMerge branch 'trailm' into trial_fixMakeCDSDBRefPropagation
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2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision...
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2016-08-25 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings
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2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbRef_re...
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2016-08-24 Jim ProcterJAL-2106 FIXME for test failure
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2016-08-24 Jim ProcterJAL-2106 TODO - verify Embl primary refs get added
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2016-08-24 Jim ProcterJAL-2106 tidy up and comments for DBRefFetcher
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2016-08-24 Jim ProcterJAL-2106 javadoc for sifts mapping method
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2016-08-24 Jim ProcterJAL-2106 prevent SIFTS mappings for sequences that...
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2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRef...
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2016-08-24 Jim ProcterJAL-2106 stricter check for 1:1 mapping (same numbering...
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2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that...
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2016-08-24 Jim ProcterJAL-2106 formatting
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2016-08-24 Jim ProcterJAL-2106 DBRefEntry.isPrimary() minimal test & implementation
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2016-08-24 Jim ProcterJAL-2106 convenience method to find all dbsource names...
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2016-08-23 Jim ProcterJAL-2154 updated testMakeCDSAlignment for expected...
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2016-08-23 Jim ProcterJAL-2154 propagate from contig to CDS after constructing...
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2016-08-23 Jim ProcterJAL-2154 should only add mappings between dataset sequences
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2016-08-23 Jim ProcterJAL-2154 - only copy DBRef from contig to new CDS sequence...
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2016-08-23 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings
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2016-08-22 Jim ProcterJAL-2154 - rejig test pass code for breadth-first ...
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2016-08-22 Jim ProcterJAL-2154 verify recovered xref sequence not already...
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2016-08-22 Jim ProcterJAL-2154 regression warning - should never recover...
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2016-08-22 Jim ProcterJAL-2154 always check dataset sequence for sequence...
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2016-08-22 Jim ProcterJAL-2154 patch verifyAlignment so it fails for duplicate...
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2016-08-22 Jim ProcterJAL-2154 tidy assert messages and fix test to verify...
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2016-08-22 Jim ProcterJAL-2154 test that verifyAlignment fails for duplicate...
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2016-08-19 Jim ProcterJAL-2154 - possible patch .. but leads to new stringify...
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