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