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2013-07-11 Jim ProcterMerge branch 'JAL-1347' into Release_2_8_1_Branch commit | commitdiff | tree | snapshot
2013-07-11 Jim ProcterJAL-1347 identify and set rendering settings for consen... commit | commitdiff | tree | snapshot
2013-07-11 Jim ProcterJAL-1347 refactor logic for setting display flags for... commit | commitdiff | tree | snapshot
2013-07-11 Jim ProcterJAL-1347 make it efficient to call getConsensus to... commit | commitdiff | tree | snapshot
2013-07-09 Jim ProcterMerge branch 'JAL-895/reopen' into Release_2_8_1_Branch commit | commitdiff | tree | snapshot
2013-07-09 Jim ProcterJAL-895 - patch example files with correct Fe positions commit | commitdiff | tree | snapshot
2013-07-08 Jim ProcterMerge branch 'Release_2_8_1_Branch' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-07-08 Jim Proctermake sure 'example alignment' can be found in documentation commit | commitdiff | tree | snapshot
2013-07-07 Jim ProcterMerge branch 'structures/JAL-1016' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-07-07 Jim ProcterJAL-1345 - set nSeconds arg for chemapps.stolaf.edu... commit | commitdiff | tree | snapshot
2013-07-07 Jim ProcterJAL-1016 Instruct user to report situations where the... commit | commitdiff | tree | snapshot
2013-07-07 Jim ProcterJAL-1332 make SSM context discovery safer (particularly... commit | commitdiff | tree | snapshot
2013-07-07 Jim ProcterJAL-583 refactor todo about separating code to construc... commit | commitdiff | tree | snapshot
2013-07-07 Jim Procterfix for JAL-1016 - wait around until we have a complete... commit | commitdiff | tree | snapshot
2013-07-07 Jim ProcterJAL-1016 - do our assertions immediatly commit | commitdiff | tree | snapshot
2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-06-23 Jim ProcterJAL-1230 update alignment state for annotation edits... commit | commitdiff | tree | snapshot
2013-06-23 Jim ProcterJAL-1230 proxy method for synchronising internal Alignm... commit | commitdiff | tree | snapshot
2013-06-23 Jim ProcterJAL-1230 simplify initialisation of consensus, conserva... commit | commitdiff | tree | snapshot
2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-06-23 Jim ProcterMerge commit '72c628b' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-06-22 Jim ProcterMerge branch 'feature/JAL-1330' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-06-22 Jim ProcterJAL-1330 pick primary seqeunce data source for authorit... commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1230 comment unused code to avoid NPE commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1327 TODO commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1326 JAL-1327 update all graphline thresholds with... commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1241 - generate colour for all annotation values... commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterMerge branch 'JAL-1294_iupredexportimport' into Release... commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1325 formatting commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF... commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1294 JAL-1325 store graphline for individual annota... commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1294 JAL-1325 bugfix equals commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1294 JAL-1325 test annotation threshold line equiva... commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterMerge branch 'JAL-1321_jws2_tooltips' into Release_2_8_... commit | commitdiff | tree | snapshot
2013-06-21 Jim ProcterJAL-1127 set option widgets to service defaults only... commit | commitdiff | tree | snapshot
2013-06-19 Jim ProcterJAL-1240 avoid NPE when source has no proxy available commit | commitdiff | tree | snapshot
2013-06-19 Jim ProcterMerge branch 'JAL-1321_jws2_tooltips' into Release_2_8_... commit | commitdiff | tree | snapshot
2013-06-18 Jim ProcterJAL-1320 ascending alphabetical order commit | commitdiff | tree | snapshot
2013-06-18 Jim ProcterJAL-1320 preserve option/parameter order with LinkedHashMap commit | commitdiff | tree | snapshot
2013-06-18 Jim ProcterJAL-1320 sort options and parameters according to their... commit | commitdiff | tree | snapshot
2013-06-18 Jim Proctertypo commit | commitdiff | tree | snapshot
2013-06-18 Jim ProcterJAL-1321 don't show a tooltip for empty strings commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterMerge branch 'JAL-1319_jronn_npe' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1319 (blacklist fix) check for presence of a score... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterMerge branch 'JAL-1312_ambiguity_na' into Release_2_8_B... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1027 fix errors in alternative codon table commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1027 check that ResidueProperties.codonHash2 is... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1027 use alternative codon table in ResidueProperti... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1035 option to allow 'STOP' codon to translate... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1312 patch for regression noticed after patch to... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1312 rewrite of code for first reported exception... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1312 formatting and more comprehensive test commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1312 remove unnecessary methods commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1312 more helpful error message when translation... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-529 - IUBMB nucleotide ambiguity codes and programm... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1318 - route warnings to stderr (need to find a... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-1318 avoid failure if SequenceI objects don't have... commit | commitdiff | tree | snapshot
2013-06-17 Jim ProcterJAL-966 avoid using java.util.Vector commit | commitdiff | tree | snapshot
2013-06-17 Jim Proctertest for JAL-1312 commit | commitdiff | tree | snapshot
2013-06-14 Jim ProcterMerge branch 'JAL-1316' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-06-14 Jim ProcterJAL-1316 compact '' to ' commit | commitdiff | tree | snapshot
2013-06-14 Jim ProcterJAL-1316 recognise and extract quoted region as nodename commit | commitdiff | tree | snapshot
2013-06-14 Jim ProcterJAL-1316 JAL-1313 newick IO test harness commit | commitdiff | tree | snapshot
2013-06-13 Jim ProcterMerge branch 'JAL-1314_headlessFlag' into Release_2_8_B... commit | commitdiff | tree | snapshot
2013-06-13 Jim ProcterJAL-1314 allow 'nogui' and 'headless' as synonyms for... commit | commitdiff | tree | snapshot
2013-06-13 Jim ProcterJAL-1314 test for common variants of -nodisplay perform... commit | commitdiff | tree | snapshot
2013-06-13 Jim ProcterMerge branch 'JAL-1315_headlessEPS' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-06-13 Jim Procterfix for JAL-1315 commit | commitdiff | tree | snapshot
2013-06-13 Jim ProcterJAL-1315 test for exit and successful generation of... commit | commitdiff | tree | snapshot
2013-06-09 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into Release_2_... commit | commitdiff | tree | snapshot
2013-06-09 Jim Procterfix for JAL-1298 commit | commitdiff | tree | snapshot
2013-06-09 Jim ProcterJAL-715 - TODO commit | commitdiff | tree | snapshot
2013-06-07 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into Release_2_... commit | commitdiff | tree | snapshot
2013-06-07 Jim ProcterJAL-1309 fix broken partition computation for adding... commit | commitdiff | tree | snapshot
2013-06-07 Jim ProcterJAL-945 uniquify prior to submission commit | commitdiff | tree | snapshot
2013-06-07 Jim Procterformatting commit | commitdiff | tree | snapshot
2013-06-07 Jim ProcterJAL-715 allow headless construction for testing commit | commitdiff | tree | snapshot
2013-06-07 Jim ProcterJAL-724 JAL-715 refactor and create new test for RSBS... commit | commitdiff | tree | snapshot
2013-06-07 Jim Procterfix for JAL-1246 commit | commitdiff | tree | snapshot
2013-06-07 Jim ProcterJAL-1307 patch to squash number format exceptions when... commit | commitdiff | tree | snapshot
2013-06-07 Jim ProcterJAL-1300 documentation commit | commitdiff | tree | snapshot
2013-05-31 Jim ProcterMerge branch 'JAL-1259_hotfix' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterMerge branch 'JAL-1161_optimisingAnnotationPanel' ... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1291 reinstate fastPaint flag manipulation to make... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1291 TODO: revised graphGroup model so grouped... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1291 - don't touch the graphics object until after... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1291 conditional output of rendering debugging... commit | commitdiff | tree | snapshot
2013-05-24 Jim Procterpatch for JAL-1300 fixes JAL-1294: read and write COMBI... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1300 test and example data for parsing annotation... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1295 test to demonstrate JAL-1294 (caused by JAL... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1295 refactored Jws2 discovery bootstrap code to... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1295 relaxed test for Annotation element equivalenc... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-381 Desktop.addInternalFrame cannot be called in... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1299 fix: ensure a new graphGroup is created if... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1295 JAL-1296 clearer assertion failed message commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1295 JAL-1297 enhance test to check graph visiblity... commit | commitdiff | tree | snapshot
2013-05-24 Jim Procterfix for JAL-1297: COMBINE output now follows specificat... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1296 JAL-1291 JAL-1297 JAL-1295 JAL-1294 commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1291 JAL-1297 JAL-1295 JAL-1294 allow alignment... commit | commitdiff | tree | snapshot
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