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2015-09-10	Jim Procter	JAL-1645 licencing for groovy files	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 licencing for new files in test and utils	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 licencing for new files in src	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1684 updated example to just a fragment of the...	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 add reference seq docs to index/etc	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 formatting and updated release date	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 formatting	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-736 JAL-1645 brief documentation about physicochemical...	commit \| commitdiff \| tree
2015-09-10	Jim Procter	Merge branch 'develop' into release/2_9_documentation	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 typo	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 JAL-1595 sort by RNA helices docs	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 more cross-links and fixing menu entries	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 links from whats New page	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 yet more documentation tweaks	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1370 correct i18n message for reference sequence...	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1370 detect any type of gap character in reference...	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1370 mark Jpred query sequence as reference sequence	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 rejig annotation selection dialog box	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 rejig biojson/biojsmsa docs	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 documentation tweaks	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 rejig bioJSON, export and whats new	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 relocate developer info about BioJS MSA templates...	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 update 2.9 docs	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 JAL-1667 revised PDB sequence fetcher docs	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 update TOC for 2.9 what’s new	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 update release note link to v2.9	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1684 use Muscle protein alignment as guide for...	commit \| commitdiff \| tree
2015-09-09	Jim Procter	Merge branch 'release/2_9_documentation' into develop	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1684 clarification of which alignment will be used...	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1684 aligned proteins and citation for for Estrogen...	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1645 formatting tree distance docs	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1483 more explicit description of feature similarity...	commit \| commitdiff \| tree
2015-09-09	Jim Procter	JAL-1483 description of the sequence feature based...	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1645 Merge branch 'release/2_9_documentation' into...	commit \| commitdiff \| tree
2015-09-08	Jim Procter	Merge branch 'develop' into release/2_9_documentation	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1645 defictionalising release notes	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1645 first stab at R2.9 “What’s new”	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1645 JAL-1701 fix up split frame docs and add a...	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1645 incorrect internal doc link	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1645 update appletParameters docs for 2.9	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1695 make enableSplitFrame applet parameter true...	commit \| commitdiff \| tree
2015-09-08	Jim Procter	Merge branch 'develop' into release/2_9_documentation	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1626 added missing gap character and fixed typo...	commit \| commitdiff \| tree
2015-09-08	Jim Procter	Merge branch 'develop' into release/2_9_documentation	commit \| commitdiff \| tree
2015-09-08	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2015-09-08	Jim Procter	Merge branch 'develop' into release/2_9_documentation	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1551 crlf change	commit \| commitdiff \| tree
2015-09-08	Jim Procter	Merge branch 'develop' into release/2_9_documentation	commit \| commitdiff \| tree
2015-09-08	Jim Procter	JAL-1645 draft release notes for v2.9...	commit \| commitdiff \| tree
2015-09-07	Jim Procter	Merge branch 'features/JAL-857_dynamic-example-files...	commit \| commitdiff \| tree
2015-09-07	Jim Procter	Merge branch 'features/JAL-857_dynamic-example-files...	commit \| commitdiff \| tree
2015-09-07	Jim Procter	JAL-1522 report commit id and branch in installation...	commit \| commitdiff \| tree
2015-09-07	Jim Procter	JAL-1522 make installation default 'applet' for the...	commit \| commitdiff \| tree
2015-09-07	Jim Procter	JAL-1701 added links to example files. will probably...	commit \| commitdiff \| tree
2015-09-06	Jim Procter	JAL-1655 transfer setting option only displayed in...	commit \| commitdiff \| tree
2015-09-06	Jim Procter	JAL-1368 JAL-1863 JAL-1304 reformatting and revision...	commit \| commitdiff \| tree
2015-09-06	Jim Procter	JAL-1368 JAL-1628 revise documentation in line with...	commit \| commitdiff \| tree
2015-09-06	Jim Procter	JAL-1645 JAL-1355 UI/i18n: added missing messages,...	commit \| commitdiff \| tree
2015-09-05	Jim Procter	JAL-1871 JAL-1553 don’t modify selection/view colour...	commit \| commitdiff \| tree
2015-09-05	Jim Procter	JAL-1871 choose a new RNA Helices palette when annotation...	commit \| commitdiff \| tree
2015-09-05	Jim Procter	JAL-1871 don’t change the palette every time an edit...	commit \| commitdiff \| tree
2015-09-05	Jim Procter	JAL-1871 reinstate random generation of palette when...	commit \| commitdiff \| tree
2015-09-05	Jim Procter	JAL-1869 make per-sequence RNA helix colours each time...	commit \| commitdiff \| tree
2015-09-05	Jim Procter	Merge branch 'bugfix/JAL-841_JAL-1081' into develop	commit \| commitdiff \| tree
2015-09-05	Jim Procter	JAL-1805 move misassigned test from Functional to Network	commit \| commitdiff \| tree
2015-09-05	Jim Procter	JAL-1233 tidy up and use same RNA helix colours in...	commit \| commitdiff \| tree
2015-09-05	Jim Procter	JAL-1081 JAL-891 don’t overwrite global colour scheme...	commit \| commitdiff \| tree
2015-09-05	Jim Procter	JAL-1081 JAL-841 JAL-1053 JAL-1081 use same selection...	commit \| commitdiff \| tree
2015-09-04	Jim Procter	JAL-1847 Merge branch 'thiago' into develop	commit \| commitdiff \| tree
2015-09-04	Jim Procter	JAL-1847 added AUTOSUPERIMPOSE property which can be...	commit \| commitdiff \| tree
2015-09-03	Jim Procter	JAL-1863 allow RNA secondary structure rows exported...	commit \| commitdiff \| tree
2015-09-03	Jim Procter	JAL-961 efficiency TODO: decouple overview updates...	commit \| commitdiff \| tree
2015-09-03	Jim Procter	JAL-1680 JAL-1576 JAL-1233 all conservation and consensus...	commit \| commitdiff \| tree
2015-09-03	Jim Procter	JAL-1576 fix: trigger broadcast of colour change with...	commit \| commitdiff \| tree
2015-09-03	Jim Procter	JAL-961 TODO use workers for calculations supporting...	commit \| commitdiff \| tree
2015-09-03	Jim Procter	JAL-1551 source tidy	commit \| commitdiff \| tree
2015-09-03	Jim Procter	JAL-1550 JAL-1551 formatting	commit \| commitdiff \| tree
2015-09-03	Jim Procter	JAL-1233 JAL-1576 copy constructor to propagate helix...	commit \| commitdiff \| tree
2015-09-02	Jim Procter	JAL-1853 add test to list for ant task	commit \| commitdiff \| tree
2015-09-02	Jim Procter	JAL-535 todo: refactor logic to desktop controller...	commit \| commitdiff \| tree
2015-09-02	Jim Procter	JAL-1772 non-functional test added. not doing any more...	commit \| commitdiff \| tree
2015-09-01	Jim Procter	Merge branch 'bug/JAL-1853_gapchar_output' into develop	commit \| commitdiff \| tree
2015-09-01	Jim Procter	JAL-1853 add test to Functional group	commit \| commitdiff \| tree
2015-09-01	Jim Procter	JAL-1853 make getVisibleSeqs more memory efficient...	commit \| commitdiff \| tree
2015-09-01	Jim Procter	JAL-1853 refactor clip routine from getSequenceStrings	commit \| commitdiff \| tree
2015-09-01	Jim Procter	patch for JAL-1853 - use given gap character to reconstruct...	commit \| commitdiff \| tree
2015-09-01	Jim Procter	JAL-1853 test origin of gapChar bug in AlignView method	commit \| commitdiff \| tree
2015-09-01	Jim Procter	JAL-1853 test demonstrating bug	commit \| commitdiff \| tree
2015-08-27	Jim Procter	JAL-1844 adding more missing jars - jersey, other json...	commit \| commitdiff \| tree
2015-08-27	Jim Procter	fix for JAL-1844 add jersey-core,json,client-1.19 to...	commit \| commitdiff \| tree
2015-08-10	Jim Procter	JAL-1645 updated final release date for version 2.9	commit \| commitdiff \| tree
2015-08-10	Jim Procter	Merge branch 'release/2_9_documentation' into develop	commit \| commitdiff \| tree
2015-08-10	Jim Procter	JAL-736 relocate group associated conservation symbols...	commit \| commitdiff \| tree
2015-08-10	Jim Procter	JAL-736 source formatting	commit \| commitdiff \| tree
2015-08-05	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2015-08-05	Jim Procter	JAL-1821 formatting	commit \| commitdiff \| tree
2015-08-05	Jim Procter	JAL-1821 launch the structure view in a separate thread...	commit \| commitdiff \| tree
2015-08-05	Jim Procter	JAL-1822 create dataset sequences if they aren’t already...	commit \| commitdiff \| tree
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