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2016-10-02	Jim Procter	JAL-2079 pass server name when reporting FTS ‘warning...	commit \| commitdiff \| tree
2016-10-01	Jim Procter	Merge branch 'develop' into bug/JAL-2210_ensembl_uniprot_pri...	commit \| commitdiff \| tree
2016-10-01	Jim Procter	JAL-2210 factored out code for processing cross-referenced...	commit \| commitdiff \| tree
2016-10-01	Jim Procter	JAL-2210 refactor code to remove from a list of dbrefs...	commit \| commitdiff \| tree
2016-09-30	Jim Procter	JAL-2210 some DBRef xref/ref correspondences may add...	commit \| commitdiff \| tree
2016-09-30	Jim Procter	JAL-2210 CrossRef.findInDataset should search for presence...	commit \| commitdiff \| tree
2016-09-30	Jim Procter	JAL-2210 add uniprot+mapping between ENST and ENSP...	commit \| commitdiff \| tree
2016-09-29	Jim Procter	JAL-2089 fix broken help link	commit \| commitdiff \| tree
2016-09-29	Jim Procter	Merge branch 'patch/JAL-2236_filtercolumns_seqassoc...	commit \| commitdiff \| tree
2016-09-29	Jim Procter	JAL-2236 include associated sequence id for annotation...	commit \| commitdiff \| tree
2016-09-29	Jim Procter	Merge branch 'patch/JAL-2238_tcoffee_subgroups' into...	commit \| commitdiff \| tree
2016-09-29	Jim Procter	JAL-2236 fix: bail if no context available for subgroup	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 patch network test for additional refs	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 JAL-2235 fix deriveSequence test for tightened...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-1270 read test props before manipulating config...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2235 patch tests where self-reference was used...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2235 implicit test to check that exception is raised...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2235 raise exceptions if self reference or reference...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 patch for when no DBRefs on sequence	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 instrument setDBRefs to call ensurePrimaries	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2210 JAL-2232 check response code before attempting...	commit \| commitdiff \| tree
2016-09-28	Jim Procter	JAL-2232 extract EMBLCDS refs from EMBL refs on Uniprot...	commit \| commitdiff \| tree
2016-09-27	Jim Procter	Merge branch 'develop' into bug/JAL-2210_ensembl_uniprot_pri...	commit \| commitdiff \| tree
2016-09-27	Jim Procter	JAL-2210 formatting	commit \| commitdiff \| tree
2016-09-27	Jim Procter	JAL-2210 report stack trace for unexpected exceptions	commit \| commitdiff \| tree
2016-09-27	Jim Procter	JAL-2210 promote direct dbrefs from verified sources...	commit \| commitdiff \| tree
2016-09-27	Jim Procter	JAL-2210 resolve todo - addDBRef adds to dataset sequence...	commit \| commitdiff \| tree
2016-09-24	Jim Procter	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-09-24	Jim Procter	JAL-1919 whats new link	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-1957 JAL-1479 tweak SIFTS mappings documentation...	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-1957 JAL-1479 mention SIFTS mappings in PDB Structure...	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-1957 release notes	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-1962 release notes	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-2214 fix docs (consistent and correct base pair...	commit \| commitdiff \| tree
2016-09-23	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-09-23	Jim Procter	JAL-2189 JAL-1479 JAL-1491 JAL-1827 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2275 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2151 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2168 -news release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-1557 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 bumped date to 27th September \o/	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 JAL-1812 JAL-2068 new groovy docs (new files...	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 JAL-2092 popup show/hide cols with feature...	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 JAL-2077 note about CTRL-Click to right click...	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 tidy up docs	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-1812 JAL-1868 release notes	commit \| commitdiff \| tree
2016-09-22	Jim Procter	JAL-2189 JAL-1812 JAL-2068 new groovy doc section and...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2189 JAL-2171 JAL-2214 JAL-1841 JAL-2215 release...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-1841 JAL-2214 updated RNA Structure Consensus documentation	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2214 JAL-1841 compute canonical, canonicalAndWobble...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-1841 JAL-2215 add the ‘ignore gaps’ structure consensus...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2214 test for strict Watson-Crick pairing	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2215 fix - trigger alignment update when ‘ignore...	commit \| commitdiff \| tree
2016-09-21	Jim Procter	JAL-2189 reworked annotation docs	commit \| commitdiff \| tree
2016-09-21	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-09-19	Jim Procter	JAL-1577 release notes	commit \| commitdiff \| tree
2016-09-19	Jim Procter	JAL-2027 releasenotes	commit \| commitdiff \| tree
2016-09-19	Jim Procter	JAL-1563 release notes	commit \| commitdiff \| tree
2016-09-19	Jim Procter	JAL-2189 JAL-2002 revised the structure chooser documentation	commit \| commitdiff \| tree
2016-09-19	Jim Procter	JAL-2189 Release notes for JAL-2079 JAL-2084 JAL-2054...	commit \| commitdiff \| tree
2016-09-19	Jim Procter	JAL-2189 JAL-1369 JAL-192 expand referenceseq documentation	commit \| commitdiff \| tree
2016-09-19	Jim Procter	JAL-2189 what’s new - ensembl, new structure stuff...	commit \| commitdiff \| tree
2016-09-19	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-09-19	Jim Procter	JAL-2175 JAL-2170 fix sense for assertEquals	commit \| commitdiff \| tree
2016-09-19	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-09-18	Jim Procter	JAL-1795 JAL-2206 prevent NPE when no data returned...	commit \| commitdiff \| tree
2016-09-16	Jim Procter	JAL-2189 clear out old what’s new and add ensembl and...	commit \| commitdiff \| tree
2016-09-16	Jim Procter	JAL-2189 JAL-1705 JAL-1795 ensembl fetching docs	commit \| commitdiff \| tree
2016-09-16	Jim Procter	JAL-2089 tidied docs for sequence fetcher	commit \| commitdiff \| tree
2016-09-16	Jim Procter	JAL-2089 release notes	commit \| commitdiff \| tree
2016-09-16	Jim Procter	JAL-2089 zero day for 2.10 - 20th Sep 2016	commit \| commitdiff \| tree
2016-09-16	Jim Procter	Merge branch 'patch/JAL-2164_updatesRESNUMtests' into...	commit \| commitdiff \| tree
2016-09-16	Jim Procter	JAL-2164 update asserts for padded residue numbers...	commit \| commitdiff \| tree
2016-09-14	Jim Procter	JAL-2164 create RESNUM features with padding the same...	commit \| commitdiff \| tree
2016-09-14	Jim Procter	JAL-2168 simpler help text re -nonews	commit \| commitdiff \| tree
2016-09-13	Jim Procter	JAL-2119 keeping gmungoc happy by not running linkcheck...	commit \| commitdiff \| tree
2016-09-12	Jim Procter	Merge branch 'patch/JAL-2068_JAL-2169_multiviewannotworker...	commit \| commitdiff \| tree
2016-09-09	Jim Procter	JAL-2119 links must match case on Linux systems	commit \| commitdiff \| tree
2016-09-08	Jim Procter	JAL-2119 pass/resolve real help dir in link checker	commit \| commitdiff \| tree
2016-09-08	Jim Procter	Merge branch 'feature/JAL-2119_helplinkchecker' into...	commit \| commitdiff \| tree
2016-09-08	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2016-09-08	Jim Procter	JAL-2119 build fails if invalid links are present	commit \| commitdiff \| tree
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
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