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JAL-2210 two pass attempt to import retrieved sequences. First pass relies on matchin...
2016-10-02 Jim ProcterJAL-2210 two pass attempt to import retrieved sequences...
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2016-10-02 Jim ProcterJAL-2210 try to merge all sequences referenced by a...
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2016-10-02 Jim ProcterJAL-2210 comments
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2016-10-02 Jim ProcterJAL-2210 discover candidate dataset sequences for an...
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2016-10-02 Jim ProcterJAL-2079 pass server name when reporting FTS ‘warning...
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2016-10-01 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_uniprot_pri...
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2016-10-01 Jim ProcterJAL-2210 factored out code for processing cross-referenced...
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2016-10-01 Jim ProcterJAL-2210 refactor code to remove from a list of dbrefs...
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2016-09-30 Jim ProcterJAL-2210 some DBRef xref/ref correspondences may add...
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2016-09-30 Jim ProcterJAL-2210 CrossRef.findInDataset should search for presence...
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2016-09-30 Jim ProcterJAL-2210 add uniprot+mapping between ENST and ENSP...
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2016-09-29 Jim ProcterJAL-2089 fix broken help link
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2016-09-29 Jim ProcterMerge branch 'patch/JAL-2236_filtercolumns_seqassoc...
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2016-09-29 Jim ProcterJAL-2236 include associated sequence id for annotation...
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2016-09-29 Jim ProcterMerge branch 'patch/JAL-2238_tcoffee_subgroups' into...
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2016-09-29 Jim ProcterJAL-2236 fix: bail if no context available for subgroup
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2016-09-28 Jim ProcterJAL-2210 patch network test for additional refs
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2016-09-28 Jim ProcterJAL-2210 JAL-2235 fix deriveSequence test for tightened...
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2016-09-28 Jim ProcterJAL-1270 read test props before manipulating config...
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2016-09-28 Jim ProcterJAL-2235 patch tests where self-reference was used...
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2016-09-28 Jim ProcterJAL-2235 implicit test to check that exception is raised...
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2016-09-28 Jim ProcterJAL-2235 raise exceptions if self reference or reference...
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2016-09-28 Jim ProcterJAL-2210 patch for when no DBRefs on sequence
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2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries
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2016-09-28 Jim ProcterJAL-2210 JAL-2232 check response code before attempting...
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2016-09-28 Jim ProcterJAL-2232 extract EMBLCDS refs from EMBL refs on Uniprot...
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2016-09-27 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_uniprot_pri...
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2016-09-27 Jim ProcterJAL-2210 formatting
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2016-09-27 Jim ProcterJAL-2210 report stack trace for unexpected exceptions
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2016-09-27 Jim ProcterJAL-2210 promote direct dbrefs from verified sources...
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2016-09-27 Jim ProcterJAL-2210 resolve todo - addDBRef adds to dataset sequence...
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2016-09-24 Jim ProcterMerge branch 'releases/Release_2_10_Branch' into develop
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2016-09-24 Jim ProcterJAL-1919 whats new link
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2016-09-23 Jim ProcterJAL-1957 JAL-1479 tweak SIFTS mappings documentation...
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2016-09-23 Jim ProcterJAL-1957 JAL-1479 mention SIFTS mappings in PDB Structure...
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2016-09-23 Jim ProcterJAL-1957 release notes
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2016-09-23 Jim ProcterJAL-1962 release notes
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2016-09-23 Jim ProcterJAL-2214 fix docs (consistent and correct base pair...
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2016-09-23 Jim ProcterMerge branch 'develop' into releases/Release_2_10_Branch
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2016-09-23 Jim ProcterJAL-2189 JAL-1479 JAL-1491 JAL-1827 release notes
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2016-09-22 Jim ProcterJAL-2275 release notes
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2016-09-22 Jim ProcterJAL-2151 release notes
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2016-09-22 Jim ProcterJAL-2168 -news release notes
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2016-09-22 Jim ProcterJAL-1557 release notes
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2016-09-22 Jim ProcterJAL-2189 bumped date to 27th September \o/
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2016-09-22 Jim ProcterJAL-2189 JAL-1812 JAL-2068 new groovy docs (new files...
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2016-09-22 Jim ProcterJAL-2189 JAL-2092 popup show/hide cols with feature...
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2016-09-22 Jim ProcterJAL-2189 JAL-2077 note about CTRL-Click to right click...
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2016-09-22 Jim ProcterJAL-2189 tidy up docs
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2016-09-22 Jim ProcterJAL-1812 JAL-1868 release notes
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2016-09-22 Jim ProcterJAL-2189 JAL-1812 JAL-2068 new groovy doc section and...
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2016-09-21 Jim ProcterJAL-2189 JAL-2171 JAL-2214 JAL-1841 JAL-2215 release...
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2016-09-21 Jim ProcterJAL-1841 JAL-2214 updated RNA Structure Consensus documentation
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2016-09-21 Jim ProcterJAL-2214 JAL-1841 compute canonical, canonicalAndWobble...
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2016-09-21 Jim ProcterJAL-1841 JAL-2215 add the ‘ignore gaps’ structure consensus...
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2016-09-21 Jim ProcterJAL-2214 test for strict Watson-Crick pairing
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2016-09-21 Jim ProcterJAL-2215 fix - trigger alignment update when ‘ignore...
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2016-09-21 Jim ProcterJAL-2189 reworked annotation docs
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2016-09-21 Jim ProcterMerge branch 'develop' into releases/Release_2_10_Branch
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2016-09-19 Jim ProcterJAL-1577 release notes
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2016-09-19 Jim ProcterJAL-2027 releasenotes
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2016-09-19 Jim ProcterJAL-1563 release notes
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2016-09-19 Jim ProcterJAL-2189 JAL-2002 revised the structure chooser documentation
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2016-09-19 Jim ProcterJAL-2189 Release notes for JAL-2079 JAL-2084 JAL-2054...
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2016-09-19 Jim ProcterJAL-2189 JAL-1369 JAL-192 expand referenceseq documentation
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2016-09-19 Jim ProcterJAL-2189 what’s new - ensembl, new structure stuff...
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2016-09-19 Jim ProcterMerge branch 'develop' of http://source.jalview.org...
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2016-09-19 Jim ProcterJAL-2175 JAL-2170 fix sense for assertEquals
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2016-09-19 Jim ProcterMerge branch 'develop' of http://source.jalview.org...
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2016-09-18 Jim ProcterJAL-1795 JAL-2206 prevent NPE when no data returned...
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2016-09-16 Jim ProcterJAL-2189 clear out old what’s new and add ensembl and...
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2016-09-16 Jim ProcterJAL-2189 JAL-1705 JAL-1795 ensembl fetching docs
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2016-09-16 Jim ProcterJAL-2089 tidied docs for sequence fetcher

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2016-09-16 Jim ProcterJAL-2089 release notes
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2016-09-16 Jim ProcterJAL-2089 zero day for 2.10 - 20th Sep 2016
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2016-09-16 Jim ProcterMerge branch 'patch/JAL-2164_updatesRESNUMtests' into...
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2016-09-16 Jim ProcterJAL-2164 update asserts for padded residue numbers...
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2016-09-14 Jim ProcterJAL-2164 create RESNUM features with padding the same...
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2016-09-14 Jim ProcterJAL-2168 simpler help text re -nonews
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2016-09-13 Jim ProcterJAL-2119 keeping gmungoc happy by not running linkcheck...
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2016-09-12 Jim ProcterMerge branch 'patch/JAL-2068_JAL-2169_multiviewannotworker...
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2016-09-09 Jim ProcterJAL-2119 links must match case on Linux systems
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2016-09-08 Jim ProcterJAL-2119 pass/resolve real help dir in link checker
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2016-09-08 Jim ProcterMerge branch 'feature/JAL-2119_helplinkchecker' into...
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2016-09-08 Jim ProcterJAL-1551 formatting
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2016-09-08 Jim ProcterJAL-2119 build fails if invalid links are present
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2016-09-08 Jim ProcterJAL-2119 non-zero exit if any invalid links
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2016-09-08 Jim ProcterJAL-2119 count and report total invalid anchor links
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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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