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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
2015-08-05	Jim Procter	JAL-1821 JAL-1759 make sure we wait around until the...	commit \| commitdiff \| tree
2015-08-05	Jim Procter	JAL-1821 patch for completeness - first model number...	commit \| commitdiff \| tree
2015-08-03	Jim Procter	JAL-1821 JAL-1759 reinstate rotation speed configuration...	commit \| commitdiff \| tree
2015-08-03	Jim Procter	JAL-1821 JAL-1759 updated Jmol has different model...	commit \| commitdiff \| tree
2015-08-03	Jim Procter	JAL-1821 avoid race condition when multiple structures...	commit \| commitdiff \| tree
2015-07-23	Jim Procter	Merge branch 'features/JAL-1759jmolUpdate' into develop	commit \| commitdiff \| tree
2015-07-23	Jim Procter	JAL-1759 formatting	commit \| commitdiff \| tree
2015-07-23	Jim Procter	JAL-1759 reinstate changes from bdfde6ef989da0702cef90f03858...	commit \| commitdiff \| tree
2015-07-23	Jim Procter	JAL-1759 formatting	commit \| commitdiff \| tree
2015-07-23	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2015-07-23	Jim Procter	Merge branch 'task/JAL-1794_jettyExamplesServer' into...	commit \| commitdiff \| tree
2015-07-23	Jim Procter	Merge branch 'bug/JAL-1819_isNaN' into develop	commit \| commitdiff \| tree
2015-07-23	Jim Procter	JAL-1819 commented out debugging message to stderr	commit \| commitdiff \| tree
2015-07-23	Jim Procter	JAL-1551 JAL-1819 formatting/imports	commit \| commitdiff \| tree
2015-07-23	Jim Procter	JAL-1819 use Float.isNaN() to check for NaNs!	commit \| commitdiff \| tree
2015-07-22	Jim Procter	JAL-1805 add group spec to the BeforeMethod setup ...	commit \| commitdiff \| tree
2015-07-22	Jim Procter	JAL-1782 added summary test report for Release_2_9_Branch...	commit \| commitdiff \| tree
2015-07-21	Jim Procter	Merge branch 'ismb/2015_demo' into develop	commit \| commitdiff \| tree
2015-07-16	Jim Procter	revision for JAL-1749 - ensure view 2D structure menu...	commit \| commitdiff \| tree
2015-07-16	Jim Procter	fix for JAL-1776 renamed popup menu entry	commit \| commitdiff \| tree
2015-06-30	Jim Procter	JAL-1682 JAL-1645 remove references to 2.8.3	commit \| commitdiff \| tree
2015-06-30	Jim Procter	JAL-1645 update release history for 2.8.2b1	commit \| commitdiff \| tree
2015-06-25	Jim Procter	JAL-1794 simple file server class - configured for...	commit \| commitdiff \| tree
2015-06-25	Jim Procter	JAL-1691 avoid NPE when original split frame has been...	commit \| commitdiff \| tree
2015-06-25	Jim Procter	JAL-1780 JAL-653 JAL-1892 brackets in wrong place broke...	commit \| commitdiff \| tree
2015-06-24	Jim Procter	Merge branch 'features/JAL-1370_patchshowunconserved...	commit \| commitdiff \| tree
2015-06-24	Jim Procter	JAL-1790 fix: javac.source=1.7 and javac.target=1.7...	commit \| commitdiff \| tree
2015-06-24	Jim Procter	JAL-653 JAL-1780 JAL-1892 fix jalviewLite compilation	commit \| commitdiff \| tree
2015-06-24	Jim Procter	Merge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892...	commit \| commitdiff \| tree
2015-06-23	Jim Procter	JAL-1780 JAL-653 jim forgot to put the conditional...	commit \| commitdiff \| tree
2015-06-23	Jim Procter	JAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refactored...	commit \| commitdiff \| tree
2015-06-22	Jim Procter	JAL-1270 fix logic in stockholm test allowing annotation...	commit \| commitdiff \| tree
2015-06-22	Jim Procter	JAL-653 JAL-1780 JAL-1140 added RNAML example alignment...	commit \| commitdiff \| tree
2015-06-22	Jim Procter	JAL-653 JAL-1780 dropped unnecessary refs	commit \| commitdiff \| tree
2015-06-22	Jim Procter	JAL-1780 JAL-653 Format/AppletFormat import and export...	commit \| commitdiff \| tree
2015-06-22	Jim Procter	JAL-653 JAL-1780 reorder imports	commit \| commitdiff \| tree
2015-06-19	Jim Procter	JAL-653 JAL-1780 refactor getGroups so HTMLfile/JSONfile...	commit \| commitdiff \| tree
2015-06-19	Jim Procter	JAL-1780 JAL-653 organise imports	commit \| commitdiff \| tree
2015-06-19	Jim Procter	JAL-653 JAL-1780 minimise call rate now av.hasHiddenRows...	commit \| commitdiff \| tree
2015-06-19	Jim Procter	JAL-653 JAL-1780 dropped av.setHasHiddenRows() and...	commit \| commitdiff \| tree
2015-06-19	Jim Procter	JAL-1780 JAL-653 organise imports	commit \| commitdiff \| tree
2015-06-18	Jim Procter	JAL-653 patch broken test code - test still not passing	commit \| commitdiff \| tree
2015-06-18	Jim Procter	JAL-653 JAL-1780 JAL-1543 javadoc and comment about...	commit \| commitdiff \| tree
2015-06-18	Jim Procter	JAL-653 JAL-1780 javadoc for FeatureRenderer prior...	commit \| commitdiff \| tree
2015-06-18	Jim Procter	JAL-1780 JAL-653 moved AlignExportSettings reference...	commit \| commitdiff \| tree
2015-06-17	Jim Procter	JAL-1784 minimise data duplication, and report out...	commit \| commitdiff \| tree
2015-06-17	Jim Procter	JAL-1784 refactor parse method to directly parse FileParser...	commit \| commitdiff \| tree
2015-06-17	Jim Procter	Merge branch 'features/JAL-653_gffalignments' into...	commit \| commitdiff \| tree
2015-06-17	Jim Procter	Merge branch 'develop' into features/JAL-653_gffalignments	commit \| commitdiff \| tree
2015-06-17	Jim Procter	Merge branch 'develop' into features/JAL-1780_export...	commit \| commitdiff \| tree
2015-06-17	Jim Procter	JAL-1783 add java 1.7 and 1.8 class numbers	commit \| commitdiff \| tree
2015-06-17	Jim Procter	Merge branch 'develop' into features/JAL-1780_export...	commit \| commitdiff \| tree
2015-06-15	Jim Procter	Merge branch 'bug/JAL-1775' into develop	commit \| commitdiff \| tree
2015-06-15	Jim Procter	JAL-1665 patch for regression: failing jalview.ws.jabaws...	commit \| commitdiff \| tree
2015-06-15	Jim Procter	JAL-1775 patch for regression from Anne Menard’s pseudo...	commit \| commitdiff \| tree
2015-06-15	Jim Procter	Merge branch 'bug/JAL-1775' into develop	commit \| commitdiff \| tree
2015-06-15	Jim Procter	JAL-1775 patch regression bug when displayChar is null...	commit \| commitdiff \| tree
2015-06-15	Jim Procter	Merge branch 'bug/JAL-1775' into develop	commit \| commitdiff \| tree
2015-06-15	Jim Procter	fix for JAL-1775 (and reorganise imports)	commit \| commitdiff \| tree
2015-06-15	Jim Procter	Merge branch 'bug/JAL-1775' into develop	commit \| commitdiff \| tree
2015-06-15	Jim Procter	JAL-1775 test demonstrating bug	commit \| commitdiff \| tree
2015-06-15	Jim Procter	JAL-1775 FileLoader javadoc	commit \| commitdiff \| tree
2015-06-15	Jim Procter	JAL-1775 fix regression from commit 70f9c4700f20a8fa57ed7eb9...	commit \| commitdiff \| tree
2015-06-15	Jim Procter	Merge branch 'develop' into bug/JAL-1775	commit \| commitdiff \| tree
2015-06-15	Jim Procter	JAL-1775 fix broken test due to missing file (RF0031_unfolded).	commit \| commitdiff \| tree
2015-06-10	Jim Procter	JAL-1764 add structure view type attribute to project...	commit \| commitdiff \| tree
2015-06-07	Jim Procter	JAL-429 remove pointless code from phylip parser	commit \| commitdiff \| tree
2015-06-07	Jim Procter	JAL-653 test for GFF file recognition and alignment...	commit \| commitdiff \| tree
2015-06-07	Jim Procter	JAL-653 GFF recognition for identifyFile and format...	commit \| commitdiff \| tree
2015-06-07	Jim Procter	JAL-653 basic GFF3 alignment import wrapper class	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 make sure dummy sequences created during GFF...	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 first stab at parsing GFF3 pragmas to support...	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 gff version number field	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 test and testdata for importing GFF3 file with...	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 missing imports after rebase	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 test for SequenceDummy methods	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 allow a dummy sequence to take on attributes...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	Merge branch 'develop' into features/JAL-653_gffalignments	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 abstract sequence model to support file backed...	commit \| commitdiff \| tree
2015-06-01	Jim Procter	JAL-1370 group and alignment reference sequences are...	commit \| commitdiff \| tree
2015-05-29	Jim Procter	Merge branch 'JAL-1755_npe_groupconsensus' into develop	commit \| commitdiff \| tree
2015-05-29	Jim Procter	JAL-1755 fix for NPE when setting up temporary variables	commit \| commitdiff \| tree
2015-05-07	Jim Procter	JAL-1731 fix JPred4 citation in legacy client code	commit \| commitdiff \| tree
2015-05-07	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2015-05-07	Jim Procter	JAL-1601 migrated the JABAWS 2.1 jpred burial representation...	commit \| commitdiff \| tree
2015-04-27	Jim Procter	JAL-1645 Release_2_9 branch build tag	commit \| commitdiff \| tree
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