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2016-10-24	Jim Procter	JAL-2197 refactored jnet target in help to jpred	commit \| commitdiff \| tree
2016-10-24	Jim Procter	JAL-2197 add jpredfile as alternative form of jnetfile...	commit \| commitdiff \| tree
2016-10-24	Jim Procter	Merge branch 'develop' into releases/Release_2_10_0_Branch	commit \| commitdiff \| tree
2016-10-24	Jim Procter	JAL-2089 JAL-2195 release notes	commit \| commitdiff \| tree
2016-10-24	Jim Procter	JAL-2089 JAL-2283 release notes	commit \| commitdiff \| tree
2016-10-24	Jim Procter	Merge branch 'bug/JAL-2283consColourEnabled' into develop	commit \| commitdiff \| tree
2016-10-24	Jim Procter	JAL-2044 documentation	commit \| commitdiff \| tree
2016-10-20	Jim Procter	Merge branch 'releases/Release_2_10_Branch' into releases...	commit \| commitdiff \| tree
2016-10-20	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-10-20	Jim Procter	JAL-2089 update release date for 2.10.0b1 to Tuesday...	commit \| commitdiff \| tree
2016-10-20	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-10-19	Jim Procter	JAL-2269 JAL-2195 review and revised test	commit \| commitdiff \| tree
2016-10-19	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-10-19	Jim Procter	JAL-2089 update 2.10.0b1 release date	commit \| commitdiff \| tree
2016-10-18	Jim Procter	JAL-2089 release notes and new known defects	commit \| commitdiff \| tree
2016-10-18	Jim Procter	JAL-2039 release notes	commit \| commitdiff \| tree
2016-10-18	Jim Procter	JAL-2245 release notes	commit \| commitdiff \| tree
2016-10-18	Jim Procter	JAL-2089 2.10.0b1 release notes	commit \| commitdiff \| tree
2016-10-18	Jim Procter	JAL-2039 rejig instructions for Structure Chooser and...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 update year in author.props	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 CITATION file and reorder authors: 2.10: JBP...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2252 workaround for link checker not recognising...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 updated third party licenses	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2036 rebuild menus for each panel before adding...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 tidy up release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 tweak ensembl release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 formatting and release notes	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 license header	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 apply license	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 format help	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 format tests	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 formatting and GPL	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 source formatting	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Revert "JAL-2245 Castor mapping and code changes for...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 release notes/whats new	commit \| commitdiff \| tree
2016-10-05	Jim Procter	JAL-2189 JAL-2152 Chimera 1.11.1 minimum version requirement	commit \| commitdiff \| tree
2016-10-04	Jim Procter	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2189 link to feature sorting documentation	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2189 JAL-2005 mention alignment order preservation...	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-04	Jim Procter	JAL-2005 JAL-599 test alignment and features for checking...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2189 update RELEASE file	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2189 more release notes	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2189 ensembl sequence fetching, locus view and...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2189 release notes	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 use addDBRef to ensure normalisation (just...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 need to add both transcript and product, and...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 JAL-2232 remove version number from ENACDS...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 hack to remove EMBL from Protein crossrefs...	commit \| commitdiff \| tree
2016-10-03	Jim Procter	JAL-2210 explicit ‘doNotAdd’ list to prevent sequences...	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 first pass at attempting to fix CrossRef tests...	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 remove ENSEMBL from protein DB list:	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 two pass attempt to import retrieved sequences...	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 try to merge all sequences referenced by a...	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 comments	commit \| commitdiff \| tree
2016-10-02	Jim Procter	JAL-2210 discover candidate dataset sequences for an...	commit \| commitdiff \| tree
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
2016-09-30	Jim Procter	JAL-2238 release notes	commit \| commitdiff \| tree
2016-09-30	Jim Procter	JAL-2236 release notes and additional docs	commit \| commitdiff \| tree
2016-09-30	Jim Procter	Merge branch 'develop' into releases/Release_2_10_Branch	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
2016-09-26	Jim Procter	JAL-2148 release notes	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
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