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2013-11-07	Jim Procter	Merge branch 'JAL-1286' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-07	Jim Procter	JAL-1286 additional tests to ensure that non-GZ files...	commit \| commitdiff \| tree
2013-11-07	Jim Procter	JAL-1286 check if local file ends with .gz and opens...	commit \| commitdiff \| tree
2013-11-07	Jim Procter	JAL-1286 test input of gzip stream from local file	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 found a fix for the sandbox exception - need...	commit \| commitdiff \| tree
2013-11-05	Jim Procter	experiment with reinstating the sandbox permissions	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 try putting explicit domain for jalviewLite...	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 Always create indices for jar before signing	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 sign everything !	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 explicit security settings for applet	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 explicit security permissions for Desktop	commit \| commitdiff \| tree
2013-10-11	Jim Procter	Merge branch 'JAL-1164_disorderforselection' into Release_2_...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1164 regression on JAL-1292 use bitset to mark...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1164 scope bySequence analysis methods to start...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1114 javadoc	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1114 promote start/end attributes to gettable fields...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1114 API javadoc	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1164 only predict on currently selected sequences...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1385 expose core view model methods in interface	commit \| commitdiff \| tree
2013-07-12	Jim Procter	Merge branch 'JAL-1347' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-07-12	Jim Procter	JAL-1347 RNA Structure consensus follows the alignment...	commit \| commitdiff \| tree
2013-07-12	Jim Procter	JAL-1347 flow control for display of profile data is...	commit \| commitdiff \| tree
2013-07-11	Jim Procter	Merge branch 'JAL-1347' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-07-11	Jim Procter	JAL-1347 identify and set rendering settings for consensus...	commit \| commitdiff \| tree
2013-07-11	Jim Procter	JAL-1347 refactor logic for setting display flags for...	commit \| commitdiff \| tree
2013-07-11	Jim Procter	JAL-1347 make it efficient to call getConsensus to...	commit \| commitdiff \| tree
2013-07-08	Jim Procter	Merge branch 'Release_2_8_1_Branch' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-07-08	Jim Procter	make sure 'example alignment' can be found in documentation	commit \| commitdiff \| tree
2013-07-07	Jim Procter	Merge branch 'structures/JAL-1016' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-07-07	Jim Procter	JAL-1345 - set nSeconds arg for http://chemapps.stolaf...	commit \| commitdiff \| tree
2013-07-07	Jim Procter	JAL-1016 Instruct user to report situations where the...	commit \| commitdiff \| tree
2013-07-07	Jim Procter	JAL-1332 make SSM context discovery safer (particularly...	commit \| commitdiff \| tree
2013-07-07	Jim Procter	JAL-583 refactor todo about separating code to construct...	commit \| commitdiff \| tree
2013-07-07	Jim Procter	fix for JAL-1016 - wait around until we have a complete...	commit \| commitdiff \| tree
2013-07-07	Jim Procter	JAL-1016 - do our assertions immediatly	commit \| commitdiff \| tree
2013-06-23	Jim Procter	Merge branch 'bug/JAL-1230' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-23	Jim Procter	JAL-1230 update alignment state for annotation edits...	commit \| commitdiff \| tree
2013-06-23	Jim Procter	JAL-1230 proxy method for synchronising internal AlignmentI...	commit \| commitdiff \| tree
2013-06-23	Jim Procter	JAL-1230 simplify initialisation of consensus, conservation...	commit \| commitdiff \| tree
2013-06-23	Jim Procter	Merge branch 'bug/JAL-1230' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-23	Jim Procter	Merge commit '72c628b' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-22	Jim Procter	Merge branch 'feature/JAL-1330' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-22	Jim Procter	JAL-1330 pick primary seqeunce data source for authority...	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1230 comment unused code to avoid NPE	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1327 TODO	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1326 JAL-1327 update all graphline thresholds with...	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1241 - generate colour for all annotation values...	commit \| commitdiff \| tree
2013-06-21	Jim Procter	Merge branch 'JAL-1294_iupredexportimport' into Release_2_8_...	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1325 formatting	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF...	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1294 JAL-1325 store graphline for individual annotation...	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1294 JAL-1325 bugfix equals	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1294 JAL-1325 test annotation threshold line equivalence	commit \| commitdiff \| tree
2013-06-21	Jim Procter	Merge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-21	Jim Procter	JAL-1127 set option widgets to service defaults only...	commit \| commitdiff \| tree
2013-06-19	Jim Procter	JAL-1240 avoid NPE when source has no proxy available	commit \| commitdiff \| tree
2013-06-19	Jim Procter	Merge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-18	Jim Procter	JAL-1320 ascending alphabetical order	commit \| commitdiff \| tree
2013-06-18	Jim Procter	JAL-1320 preserve option/parameter order with LinkedHashMap	commit \| commitdiff \| tree
2013-06-18	Jim Procter	JAL-1320 sort options and parameters according to their...	commit \| commitdiff \| tree
2013-06-18	Jim Procter	typo	commit \| commitdiff \| tree
2013-06-18	Jim Procter	JAL-1321 don't show a tooltip for empty strings	commit \| commitdiff \| tree
2013-06-17	Jim Procter	Merge branch 'JAL-1319_jronn_npe' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1319 (blacklist fix) check for presence of a score...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	Merge branch 'JAL-1312_ambiguity_na' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1027 fix errors in alternative codon table	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1027 check that ResidueProperties.codonHash2 is...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1027 use alternative codon table in ResidueProperties...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1035 option to allow 'STOP' codon to translate...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1312 patch for regression noticed after patch to...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1312 rewrite of code for first reported exception...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1312 formatting and more comprehensive test	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1312 remove unnecessary methods	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1312 more helpful error message when translation...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-529 - IUBMB nucleotide ambiguity codes and programmatic...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1318 - route warnings to stderr (need to find a...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-1318 avoid failure if SequenceI objects don't have...	commit \| commitdiff \| tree
2013-06-17	Jim Procter	JAL-966 avoid using java.util.Vector	commit \| commitdiff \| tree
2013-06-17	Jim Procter	test for JAL-1312	commit \| commitdiff \| tree
2013-06-14	Jim Procter	Merge branch 'JAL-1316' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-14	Jim Procter	JAL-1316 compact '' to '	commit \| commitdiff \| tree
2013-06-14	Jim Procter	JAL-1316 recognise and extract quoted region as nodename	commit \| commitdiff \| tree
2013-06-14	Jim Procter	JAL-1316 JAL-1313 newick IO test harness	commit \| commitdiff \| tree
2013-06-13	Jim Procter	Merge branch 'JAL-1314_headlessFlag' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-13	Jim Procter	JAL-1314 allow 'nogui' and 'headless' as synonyms for...	commit \| commitdiff \| tree
2013-06-13	Jim Procter	JAL-1314 test for common variants of -nodisplay performing...	commit \| commitdiff \| tree
2013-06-13	Jim Procter	Merge branch 'JAL-1315_headlessEPS' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-13	Jim Procter	fix for JAL-1315	commit \| commitdiff \| tree
2013-06-13	Jim Procter	JAL-1315 test for exit and successful generation of...	commit \| commitdiff \| tree
2013-06-09	Jim Procter	Merge branch '2_8_1_patch_multiharmony' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-09	Jim Procter	fix for JAL-1298	commit \| commitdiff \| tree
2013-06-09	Jim Procter	JAL-715 - TODO	commit \| commitdiff \| tree
2013-06-07	Jim Procter	Merge branch '2_8_1_patch_multiharmony' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-1309 fix broken partition computation for adding...	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-945 uniquify prior to submission	commit \| commitdiff \| tree
2013-06-07	Jim Procter	formatting	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-715 allow headless construction for testing	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-724 JAL-715 refactor and create new test for RSBS...	commit \| commitdiff \| tree
2013-06-07	Jim Procter	fix for JAL-1246	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-1307 patch to squash number format exceptions when...	commit \| commitdiff \| tree
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