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2016-04-12	Jim Procter	Merge branch 'develop' into trialmerge/JAL-1950_hmmer3client	commit \| commitdiff \| tree
2016-04-08	Jim Procter	Merge branch 'feature/JAL-2050_intronhidden' into develop	commit \| commitdiff \| tree
2016-04-08	Jim Procter	JAL-2050 JAL-1722 new getSelectedRange() method to...	commit \| commitdiff \| tree
2016-04-08	Jim Procter	JAL-2053 fix erratic hidden column marker display	commit \| commitdiff \| tree
2016-04-08	Jim Procter	JAL-2053 JAL-1551 javadoc and simpler code	commit \| commitdiff \| tree
2016-04-07	Jim Procter	JAL-1722 fix: don’t draw visible regions outside viewport...	commit \| commitdiff \| tree
2016-04-04	Jim Procter	Merge branch 'optimisation/JAL-2001' into develop	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2001 drop isSelected(int) in favour of original...	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2001 catch -ve column values	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2001 TODO for new ColumnSelection API	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2001 - note about possible side effect on JalviewLite...	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2010 refactoring todo	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2001 use fast column selection test	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-969 refactor columnselection operation (during...	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2001 faster check for a column being selected	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2001 javadoc	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2001 faster getMax/getMin selected column, with...	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2001 JAL-1722 - store selection as ArrayList and...	commit \| commitdiff \| tree
2016-01-21	Jim Procter	JAL-1995 remove jalviewApplet.jar from tree and added...	commit \| commitdiff \| tree
2015-12-09	Jim Procter	JAL-1982 hotfix to prevent NPE with applet launch on...	commit \| commitdiff \| tree
2015-11-30	Jim Procter	JAL-1950 optionally just delete any redundant sequences...	commit \| commitdiff \| tree
2015-11-17	Jim Procter	JAL-1950 represent duplicate sequences by their representati...	commit \| commitdiff \| tree
2015-11-16	Jim Procter	JAL-1950 group hits by architecture	commit \| commitdiff \| tree
2015-11-16	Jim Procter	JAL-1950 formatting	commit \| commitdiff \| tree
2015-11-16	Jim Procter	JAL-1958 modulate per-sequence shading with local score...	commit \| commitdiff \| tree
2015-11-16	Jim Procter	JAL-1950 add domain architecture feature	commit \| commitdiff \| tree
2015-11-10	Jim Procter	JAL-653 added missing pragma string to processing filter	commit \| commitdiff \| tree
2015-11-10	Jim Procter	Merge branch 'features/JAL-1705_ensembl' of http:/...	commit \| commitdiff \| tree
2015-11-09	Jim Procter	JAL-1950 JAL-1958 bitscore is more effective for shading...	commit \| commitdiff \| tree
2015-11-09	Jim Procter	JAL-1950 - JAL-1958 hardwired hack to explore shading...	commit \| commitdiff \| tree
2015-11-09	Jim Procter	JAL-1950 transfer posterior probability onto hit sequences	commit \| commitdiff \| tree
2015-11-09	Jim Procter	JAL-1950 magic keys for different parts of the JSON...	commit \| commitdiff \| tree
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
2015-10-30	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
2015-10-28	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-653 JAL-1766 merge 290b1 - fix erroneous conflicts...	commit \| commitdiff \| tree
2015-10-15	Jim Procter	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2015-10-15	Jim Procter	Merge branch 'develop' into features/JAL-1705_ensembl	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
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