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2015-11-09	Jim Procter	JAL-1950 javadoc: clarify AlignmentAnnotation.createSequence...	commit \| commitdiff \| tree
2015-11-09	Jim Procter	JAL-1950 test positioning of posterior probability...	commit \| commitdiff \| tree
2015-11-04	Jim Procter	JAL-1950 hook up JSON result dump parser to hmmerClient	commit \| commitdiff \| tree
2015-11-04	Jim Procter	JAL-1950 first stab at Hmmer3 JSON parser and alignment...	commit \| commitdiff \| tree
2015-11-04	Jim Procter	JAL-1950 - cache URL as a local file (needs a test...	commit \| commitdiff \| tree
2015-11-02	Jim Procter	JAL-1950 keys for hmm search score file parser. not...	commit \| commitdiff \| tree
2015-11-02	Jim Procter	JAL-1950 structuring methods and note on parsing flat...	commit \| commitdiff \| tree
2015-11-02	Jim Procter	JAL-1934 conditional evaluation structure not needed	commit \| commitdiff \| tree
2015-11-02	Jim Procter	JAL-1934 new preference to disable gap character normalisati...	commit \| commitdiff \| tree
2015-10-28	Jim Procter	JAL-1950 JAL-715 fall through for 201 ‘CREATED’ codes...	commit \| commitdiff \| tree
2015-10-28	Jim Procter	JAL-1950 extremely rough prototype submission/poll...	commit \| commitdiff \| tree
2015-10-28	Jim Procter	JAL-715 tidy up the job poll loop ready to adapt for...	commit \| commitdiff \| tree
2015-10-28	Jim Procter	JAL-715 JAL-724 refactored multi harmony definition...	commit \| commitdiff \| tree
2015-10-16	Jim Procter	JAL-1925 version change	commit \| commitdiff \| tree
2015-10-16	Jim Procter	JAL-1925 update what's new and release notes	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1791 remove blanket sign of examples/*.jar	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1791 id rather than name attrib	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1791 sign the applet with/out timestamps	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1791 add explicit proxy for benefit of jalview...	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1791 fix ant target dependencies	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1791 make timestamping optional using -Dtimestamp	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1791 add jalview.tsaurl for specifying timestamp...	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1791 add jalview.tsaurl for specifying timestamp...	commit \| commitdiff \| tree
2015-10-15	Jim Procter	Merge branch 'bug/JAL-1923_290b2_group_annots' into...	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1923 formatting	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1923 add groups to codon-complement and notify...	commit \| commitdiff \| tree
2015-10-15	Jim Procter	JAL-1923 fix: don’t add group twice	commit \| commitdiff \| tree
2015-10-08	Jim Procter	JAL-1684 updated fragment alignment for example and...	commit \| commitdiff \| tree
2015-10-08	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2015-10-08	Jim Procter	JAL-1894 add licensing	commit \| commitdiff \| tree
2015-10-08	Jim Procter	JAL-1894 update what's new	commit \| commitdiff \| tree
2015-10-08	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2015-10-08	Jim Procter	JAL-1894 formatting	commit \| commitdiff \| tree
2015-10-08	Jim Procter	JAL-1894 organise imports	commit \| commitdiff \| tree
2015-10-07	Jim Procter	JAL-1894 source formatting	commit \| commitdiff \| tree
2015-10-07	Jim Procter	JAL-1894 organise imports	commit \| commitdiff \| tree
2015-10-07	Jim Procter	JAL-1894 update release date	commit \| commitdiff \| tree
2015-10-07	Jim Procter	JAL-1912 formatting	commit \| commitdiff \| tree
2015-10-07	Jim Procter	JAL-1912 javadoc for adjustForAlignment stating current...	commit \| commitdiff \| tree
2015-10-07	Jim Procter	JAL-1912 efficiency: look up sequenceMapping once per...	commit \| commitdiff \| tree
2015-10-07	Jim Procter	Merge branch 'features/JAL-1912_biojson-per-sequence...	commit \| commitdiff \| tree
2015-10-05	Jim Procter	Merge branch 'develop' into features/JAL-1912_biojson...	commit \| commitdiff \| tree
2015-10-05	Jim Procter	JAL-1894 note about menu option bugfix JAL-1865 JAL...	commit \| commitdiff \| tree
2015-10-05	Jim Procter	JAL-1894 update release notes for JAL-1815 JAL-1860	commit \| commitdiff \| tree
2015-10-05	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2015-10-05	Jim Procter	JAL-1684 trimmed proteins to just those sequences that...	commit \| commitdiff \| tree
2015-10-02	Jim Procter	JAL-1900 JAL-1625 disable iconify button for internal...	commit \| commitdiff \| tree
2015-10-01	Jim Procter	JAL-1894 release notes update and 6th October release...	commit \| commitdiff \| tree
2015-09-30	Jim Procter	fix for JAL-1883	commit \| commitdiff \| tree
2015-09-22	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2015-09-22	Jim Procter	JAL-1894 update RELEASE for 2.9.0b1 release	commit \| commitdiff \| tree
2015-09-18	Jim Procter	JAL-1889 wrong clean for buildTest!	commit \| commitdiff \| tree
2015-09-18	Jim Procter	JAL-1270 JAL-1889 move the stevesoft test back into...	commit \| commitdiff \| tree
2015-09-18	Jim Procter	JAL-1889 remove non-UTF8 characters so we can build...	commit \| commitdiff \| tree
2015-09-18	Jim Procter	JAL-1888 updated documentation for unit testing in...	commit \| commitdiff \| tree
2015-09-18	Jim Procter	JAL-1888 set verbosity and exclude the 'parallel' attribute...	commit \| commitdiff \| tree
2015-09-18	Jim Procter	JAL-1888 JAL-1551 format XML file (2 spaces, no tabs...	commit \| commitdiff \| tree
2015-09-18	Jim Procter	JAL-1888 compile tests to separate directory and pass...	commit \| commitdiff \| tree
2015-09-18	Jim Procter	JAL-1888 documentation for testing target	commit \| commitdiff \| tree
2015-09-18	Jim Procter	JAL-1888 property to specify which testng groups should...	commit \| commitdiff \| tree
2015-09-16	Jim Procter	Merge branch 'JAL-1612_JAL-1439_JAL-1845_osx_icons_signing_i...	commit \| commitdiff \| tree
2015-09-16	Jim Procter	JAL-1612 JAL-1439 JAL-1845 OSX Installers set Xdock...	commit \| commitdiff \| tree
2015-09-11	Jim Procter	JAL-1884 add the JNLP template to jalview_jnlp_vm.jar	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 fix broken link in docs	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 reformat help html - 2 spaces indents, no...	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 licencing for help html	commit \| commitdiff \| tree
2015-09-10	Jim Procter	JAL-1645 licencing for doc directory files	commit \| commitdiff \| tree
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
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