jalview.git
2013-08-30 Jim ProcterJAL-1367 allow reference sequence to be shown in bold...
2013-08-30 Jim ProcterJAL-1370 JAL-1371 flags for display and colour of view...
2013-08-30 Jim ProcterJAL-1367 promote the existing representative sequence...
2013-08-27 Jim ProcterMerge branch 'JAL-1359_patch' into Release_2_8_1_Branch
2013-08-27 Jim ProcterJAL-1359 simpler logic for deciding if all threads...
2013-08-27 Jim ProcterMerge branch 'JAL-1332_regression' into Release_2_8_1_B...
2013-08-27 Jim ProcterJAL-1332 regression from 7ce72ca7fadf35a249427ecb836b22...
2013-08-27 Jim ProcterJAL-1332 - defer SSM provision to root provider for...
2013-08-20 Jim ProcterMerge branch 'JAL-1353-bugdemo' into Release_2_8_1_Branch
2013-08-20 Jim ProcterJAL-1353 test demonstrating the freeze with minimal...
2013-07-12 Jim ProcterMerge branch 'JAL-1347' into Release_2_8_1_Branch
2013-07-12 Jim ProcterJAL-1347 RNA Structure consensus follows the alignment...
2013-07-12 Jim ProcterJAL-1347 flow control for display of profile data is...
2013-07-11 Jim ProcterMerge branch 'JAL-1347' into Release_2_8_1_Branch
2013-07-11 Jim ProcterJAL-1347 identify and set rendering settings for consen...
2013-07-11 Jim ProcterJAL-1347 refactor logic for setting display flags for...
2013-07-11 Jim ProcterJAL-1347 make it efficient to call getConsensus to...
2013-07-09 Jim ProcterMerge branch 'JAL-895/reopen' into Release_2_8_1_Branch
2013-07-09 Jim ProcterJAL-895 - patch example files with correct Fe positions
2013-07-08 Jim ProcterMerge branch 'Release_2_8_1_Branch' into Release_2_8_Branch
2013-07-08 Jim Proctermake sure 'example alignment' can be found in documentation
2013-07-07 Jim ProcterMerge branch 'structures/JAL-1016' into Release_2_8_Branch
2013-07-07 Jim ProcterJAL-1345 - set nSeconds arg for chemapps.stolaf.edu...
2013-07-07 Jim ProcterJAL-1016 Instruct user to report situations where the...
2013-07-07 Jim ProcterJAL-1332 make SSM context discovery safer (particularly...
2013-07-07 Jim ProcterJAL-583 refactor todo about separating code to construc...
2013-07-07 Jim Procterfix for JAL-1016 - wait around until we have a complete...
2013-07-07 Jim ProcterJAL-1016 - do our assertions immediatly
2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch
2013-06-23 Jim ProcterJAL-1230 update alignment state for annotation edits...
2013-06-23 Jim ProcterJAL-1230 proxy method for synchronising internal Alignm...
2013-06-23 Jim ProcterJAL-1230 simplify initialisation of consensus, conserva...
2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch
2013-06-23 Jim ProcterMerge commit '72c628b' into Release_2_8_Branch
2013-06-22 Jim ProcterMerge branch 'feature/JAL-1330' into Release_2_8_Branch
2013-06-22 Jim ProcterJAL-1330 pick primary seqeunce data source for authorit...
2013-06-21 Jim ProcterJAL-1230 comment unused code to avoid NPE
2013-06-21 Jim ProcterJAL-1327 TODO
2013-06-21 Jim ProcterJAL-1326 JAL-1327 update all graphline thresholds with...
2013-06-21 Jim ProcterJAL-1241 - generate colour for all annotation values...
2013-06-21 Jim ProcterMerge branch 'JAL-1294_iupredexportimport' into Release...
2013-06-21 Jim ProcterJAL-1325 formatting
2013-06-21 Jim ProcterJAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF...
2013-06-21 Jim ProcterJAL-1294 JAL-1325 store graphline for individual annota...
2013-06-21 Jim ProcterJAL-1294 JAL-1325 bugfix equals
2013-06-21 Jim ProcterJAL-1294 JAL-1325 test annotation threshold line equiva...
2013-06-21 Jim ProcterMerge branch 'JAL-1321_jws2_tooltips' into Release_2_8_...
2013-06-21 Jim ProcterJAL-1127 set option widgets to service defaults only...
2013-06-19 Jim ProcterJAL-1240 avoid NPE when source has no proxy available
2013-06-19 Jim ProcterMerge branch 'JAL-1321_jws2_tooltips' into Release_2_8_...
2013-06-18 Jim ProcterJAL-1320 ascending alphabetical order
2013-06-18 Jim ProcterJAL-1320 preserve option/parameter order with LinkedHashMap
2013-06-18 Jim ProcterJAL-1320 sort options and parameters according to their...
2013-06-18 Jim Proctertypo
2013-06-18 Jim ProcterJAL-1321 don't show a tooltip for empty strings
2013-06-17 Jim ProcterMerge branch 'JAL-1319_jronn_npe' into Release_2_8_Branch
2013-06-17 Jim ProcterJAL-1319 (blacklist fix) check for presence of a score...
2013-06-17 Jim ProcterMerge branch 'JAL-1312_ambiguity_na' into Release_2_8_B...
2013-06-17 Jim ProcterJAL-1027 fix errors in alternative codon table
2013-06-17 Jim ProcterJAL-1027 check that ResidueProperties.codonHash2 is...
2013-06-17 Jim ProcterJAL-1027 use alternative codon table in ResidueProperti...
2013-06-17 Jim ProcterJAL-1035 option to allow 'STOP' codon to translate...
2013-06-17 Jim ProcterJAL-1312 patch for regression noticed after patch to...
2013-06-17 Jim ProcterJAL-1312 rewrite of code for first reported exception...
2013-06-17 Jim ProcterJAL-1312 formatting and more comprehensive test
2013-06-17 Jim ProcterJAL-1312 remove unnecessary methods
2013-06-17 Jim ProcterJAL-1312 more helpful error message when translation...
2013-06-17 Jim ProcterJAL-529 - IUBMB nucleotide ambiguity codes and programm...
2013-06-17 Jim ProcterJAL-1318 - route warnings to stderr (need to find a...
2013-06-17 Jim ProcterJAL-1318 avoid failure if SequenceI objects don't have...
2013-06-17 Jim ProcterJAL-966 avoid using java.util.Vector
2013-06-17 Jim Proctertest for JAL-1312
2013-06-14 Jim ProcterMerge branch 'JAL-1316' into Release_2_8_Branch
2013-06-14 Jim ProcterJAL-1316 compact '' to '
2013-06-14 Jim ProcterJAL-1316 recognise and extract quoted region as nodename
2013-06-14 Jim ProcterJAL-1316 JAL-1313 newick IO test harness
2013-06-13 Jim ProcterMerge branch 'JAL-1314_headlessFlag' into Release_2_8_B...
2013-06-13 Jim ProcterJAL-1314 allow 'nogui' and 'headless' as synonyms for...
2013-06-13 Jim ProcterJAL-1314 test for common variants of -nodisplay perform...
2013-06-13 Jim ProcterMerge branch 'JAL-1315_headlessEPS' into Release_2_8_Branch
2013-06-13 Jim Procterfix for JAL-1315
2013-06-13 Jim ProcterJAL-1315 test for exit and successful generation of...
2013-06-09 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into Release_2_...
2013-06-09 Jim Procterfix for JAL-1298
2013-06-09 Jim ProcterJAL-715 - TODO
2013-06-07 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into Release_2_...
2013-06-07 Jim ProcterJAL-1309 fix broken partition computation for adding...
2013-06-07 Jim ProcterJAL-945 uniquify prior to submission
2013-06-07 Jim Procterformatting
2013-06-07 Jim ProcterJAL-715 allow headless construction for testing
2013-06-07 Jim ProcterJAL-724 JAL-715 refactor and create new test for RSBS...
2013-06-07 Jim Procterfix for JAL-1246
2013-06-07 Jim ProcterJAL-1307 patch to squash number format exceptions when...
2013-06-07 Jim ProcterJAL-1300 documentation
2013-05-31 Jim ProcterMerge branch 'JAL-1259_hotfix' into Release_2_8_Branch
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE
2013-05-24 Jim ProcterMerge branch 'JAL-1161_optimisingAnnotationPanel' ...
2013-05-24 Jim ProcterJAL-1291 reinstate fastPaint flag manipulation to make...
2013-05-24 Jim ProcterJAL-1291 TODO: revised graphGroup model so grouped...
2013-05-24 Jim ProcterJAL-1291 - don't touch the graphics object until after...
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