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2015-11-13	Jim Procter	JAL-1965 alternate ‘bestMatch’ picker for word matches...	commit \| commitdiff \| tree
2015-11-13	Jim Procter	JAL-1965 test asserts no partial word matches can be...	commit \| commitdiff \| tree
2015-11-13	Jim Procter	JAL-1965 fencepost patch makes wordSplit test pass	commit \| commitdiff \| tree
2015-11-13	Jim Procter	JAL-1965 refactored SeqIdName to public class, and...	commit \| commitdiff \| tree
2015-11-13	Jim Procter	JAL-1965 formatting	commit \| commitdiff \| tree
2015-11-13	Jim Procter	JAL-1965 hang onto original string so best match (including...	commit \| commitdiff \| tree
2015-11-13	Jim Procter	JAL-1965 word based matching and explicit coping with...	commit \| commitdiff \| tree
2015-11-12	Jim Procter	JAL-1965 case insensitive & word matching SequenceIdMatcher... Signed-off-by: Jim Procter <jprocter@issues.jalview.org>	commit \| commitdiff \| tree
2015-11-12	Jim Procter	JAL-1965 tests for word and case insensitive matching	commit \| commitdiff \| tree
2015-11-12	Jim Procter	JAL-753_JAL-1427 basic test cases for SequenceIdMatcher	commit \| commitdiff \| tree
2015-10-30	Jim Procter	Merge branch 'JAL-1954_pfamformatbroke' into develop	commit \| commitdiff \| tree
2015-10-30	Jim Procter	JAL-1954 rejigged PFAMFile to split on ‘\t’ if no space...	commit \| commitdiff \| tree
2015-10-30	Jim Procter	JAL-1954 formatting	commit \| commitdiff \| tree
2015-10-28	Jim Procter	JAL-1954 test PFAM import results in AlignmentI.hasValidSequ...	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
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