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2015-02-05	Jim Procter	JAL-1643 jarred up the quaqua native libraries and...	commit \| commitdiff \| tree
2015-02-05	Jim Procter	JAL-1643 added quaqua filechooser and jni libraries...	commit \| commitdiff \| tree
2015-02-05	Jim Procter	JAL-1643 correct version of quaqua (8) plus THIRDPARTYLIB...	commit \| commitdiff \| tree
2015-02-05	Jim Procter	JAL-1643 renamed quaqua library to add version number	commit \| commitdiff \| tree
2014-12-03	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 update applet authors list	commit \| commitdiff \| tree
2014-12-03	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 disable desktop 'take snapshot' menu item...	commit \| commitdiff \| tree
2014-12-03	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 dropped jnlp file in help documentation in...	commit \| commitdiff \| tree
2014-12-03	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 updated library licensing info	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 release notes	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1517 typo	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1517 TOC items must be on one line for help2Website	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1602 tweak VM inclusion options	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1517 documentation for 2.8.2 release	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1602 typo in jsonsimple jar	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1602 add missing jars to install	commit \| commitdiff \| tree
2014-12-01	Jim Procter	Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-1602 upgrade to InstallAnywhere 2014 J17 runtimes	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-1199 JAL-1569 incremental patch allow non-standard...	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-1517 updating author list	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-1517 updating authors list	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-795 hack to ignore black colour in annotation element.	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-1601 ignore the JABA Jpred client in Jalview 2...	commit \| commitdiff \| tree
2014-12-01	Jim Procter	Merge branch 'bug/JAL-1610refAnnotationsInViews' into...	commit \| commitdiff \| tree
2014-12-01	Jim Procter	file for JAL-1268 jalview.io.Jalview2xmlTests.testTCoffeeScores	commit \| commitdiff \| tree
2014-11-28	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1517 first stab at release notes... lots of documentatio...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1522 output installation type to stdout	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1522 remove build/deployment details imported from...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1517 formatting	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1611 revise log level to reduce verbosity	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1583 javadoc and fix constructor signature	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1342 document argument to specify preferred JABA...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1604 formatting	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1604 revised wording and internationalised dialog	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1583 back out original fix and simply check MSAWSThread...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1583 formatting	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1583 new validInput flag set according to validity...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1583 refactored addInternalFrame to allow webservice...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1517 formatting/tidy	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-1517 svg==scalable :)	commit \| commitdiff \| tree
2014-11-27	Jim Procter	Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 add sequence associated annotation rows to...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-1177 JAL-905 cannot recover sequences from dataset...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 avoid writing \0 for chain code	commit \| commitdiff \| tree
2014-11-27	Jim Procter	Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 patch to fix bug with showing reference annotation...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 formatting	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 unused variable	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 bug in test	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 test that PDB annotation created when importing...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 patch NPE bug when test run in isolation	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 fix test properties path and add properties...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 JAL-966 new method to retrieve all views	commit \| commitdiff \| tree
2014-11-27	Jim Procter	organise imports	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-966 promote getName to an api method	commit \| commitdiff \| tree
2014-11-26	Jim Procter	Merge branch 'JAL-674_fixannotlabels' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 make RNAML-extracted secondary structure lines...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-1578 fix logic for showing score when no description...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 JAL-1578 commented code for displaying annotation...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 friendly name for PDB file included in secondary...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 employ the provided DNA/Protein matrix string...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 disable addition of PDBRESNUM annotation line	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 nicer temperature factor labelling and include...	commit \| commitdiff \| tree
2014-11-25	Jim Procter	Merge branch 'bug/JAL-689' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-25	Jim Procter	fix for JAL-689 ensure fastpainting flag set only when...	commit \| commitdiff \| tree
2014-11-25	Jim Procter	formatting	commit \| commitdiff \| tree
2014-11-25	Jim Procter	patch for JAL-1599 - annotation row constructed by...	commit \| commitdiff \| tree
2014-11-25	Jim Procter	Merge branch 'patch_JAL-689' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-25	Jim Procter	back out duplicate jfree classpath entry	commit \| commitdiff \| tree
2014-11-24	Jim Procter	Merge branch 'JAL-1569_wuss_vienna_broke' into Release_2_8_2...	commit \| commitdiff \| tree
2014-11-24	Jim Procter	JAL-1593 refactor rna helix colours to static singleton...	commit \| commitdiff \| tree
2014-11-24	Jim Procter	JAL-1264 update annotation panel dimensions before...	commit \| commitdiff \| tree
2014-11-24	Jim Procter	JAL-1595 update annotation sort on opening of the ...	commit \| commitdiff \| tree
2014-11-24	Jim Procter	JAL-1595 annotation score is total number of rna helices	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 interactive editing of secondary structure...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	Merge branch 'JAL-1569_wuss_vienna_broke' into Release_2_8_2...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	employ test and secondary structure character for determinin...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 formatting	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1593 allow per-sequence shading of RNA helix (stored...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 test for open/close RNA parenthesis character	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 formatting	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 refactoring of stockholm test	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 consistent handling of sequence and alignment...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 revise tests to count number and type of annotation...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 formatting	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 preserve input ordering for stockholm files...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 remove stdout on parsing RNA	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1152 avoid NPE on null alignment annotation vector	commit \| commitdiff \| tree
2014-11-21	Jim Procter	JAL-674 add RNA sequence associated annotation to alignment...	commit \| commitdiff \| tree
2014-11-21	Jim Procter	JAL-1569 formatting	commit \| commitdiff \| tree
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