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2016-04-25	Jim Procter	JAL-2074 disable security manager at start up re: http...	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 removed xerces to explore wierdness	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 reinstate upgrade to groovy 2.8.4-indy	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 reinstate upgrade to groovy 2.8.4-indy	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 add the groovy 1.8.2 library back to classpath	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 backed out groovy upgrade - back to 1.8.2	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 groovy-all didn’t get added :q	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 switch to non-indy groovy to see if class...	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-1551 JAL-2077 formatting	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-2077 - reinstate popups on osx	commit \| commitdiff \| tree
2016-04-24	Jim Procter	Merge branch 'JAL-2075_features_hiddeng' into develop	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-2075 test showing hidden columns bug in feature...	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-2075 refactor FeatureScoreModel to native testNG...	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-2075 make GroovyConsole a singleton so tests requiring...	commit \| commitdiff \| tree
2016-04-23	Jim Procter	JAL-2075 fix: use AlignmentView.getVisibleContigs and...	commit \| commitdiff \| tree
2016-04-23	Jim Procter	JAL-2075 findPosition for SeqCigar (with test)	commit \| commitdiff \| tree
2016-04-23	Jim Procter	JAL-2075 formatting	commit \| commitdiff \| tree
2016-04-20	Jim Procter	Merge branch 'groovy/JAL-2074_upgradeto2.4.4' into...	commit \| commitdiff \| tree
2016-04-20	Jim Procter	JAL-2074 updated URLs and removed 'how to get groovy...	commit \| commitdiff \| tree
2016-04-20	Jim Procter	JAL-2074 updated groovy-all to 2.4.6-indy	commit \| commitdiff \| tree
2016-04-20	Jim Procter	fix for JAL-2072	commit \| commitdiff \| tree
2016-04-13	Jim Procter	JAL-2046 fix: patched SeqsetUtils so sequence features...	commit \| commitdiff \| tree
2016-04-13	Jim Procter	JAL-2046 test to demonstrate feature duplication bug	commit \| commitdiff \| tree
2016-04-13	Jim Procter	Merge branch 'bug/JAL-2046_ds_sharing_features_broken...	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
2016-04-05	Jim Procter	JAL-2046 RFC about cyclic dataset sequence references...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 revise test for ambiguous case	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 ambiguous test for addSequenceFeature when...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 RFC on addSequenceFeature behaviour after...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 test behaviour of copy constructor in different...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 add/delete SequenceFeature operate on dataset...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 setSequenceFeature contract implementation...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 explicit contract for get/set SequenceFeatures...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 remove javadoc	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 simpler deriveSequence - promote to dataset...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 clarify contract for copy constructor and...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 explicitly copy char[] when cloning sequence...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 safer createDatasetSequence manipulates private...	commit \| commitdiff \| tree
2016-04-04	Jim Procter	JAL-2046 basic test to make sure any derived sequence...	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
2015-11-10	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
2015-10-30	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-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
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