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Merge branch 'JAL-895/reopen' into Release_2_8_1_Branch
2013-07-09 Jim ProcterMerge branch 'JAL-895/reopen' into Release_2_8_1_Branch
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2013-07-09 Jim ProcterJAL-895 - patch example files with correct Fe positions
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2013-07-08 Jim Proctermake sure 'example alignment' can be found in documentation
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2013-07-07 Jim ProcterMerge branch 'structures/JAL-1016' into Release_2_8_Branch
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2013-07-07 Jim ProcterJAL-1345 - set nSeconds arg for http://chemapps.stolaf...
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2013-07-07 Jim ProcterJAL-1016 Instruct user to report situations where the...
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2013-07-07 Jim ProcterJAL-1332 make SSM context discovery safer (particularly...
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2013-07-07 Jim ProcterJAL-583 refactor todo about separating code to construct...
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2013-07-07 Jim Procterfix for JAL-1016 - wait around until we have a complete...
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2013-07-07 Jim ProcterJAL-1016 - do our assertions immediatly
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2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch
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2013-06-23 Jim ProcterJAL-1230 update alignment state for annotation edits...
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2013-06-23 Jim ProcterJAL-1230 proxy method for synchronising internal AlignmentI...
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2013-06-23 Jim ProcterJAL-1230 simplify initialisation of consensus, conservation...
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2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch
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2013-06-23 Jim ProcterMerge commit '72c628b' into Release_2_8_Branch
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2013-06-22 Jim ProcterMerge branch 'feature/JAL-1330' into Release_2_8_Branch
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2013-06-22 Jim ProcterJAL-1330 pick primary seqeunce data source for authority...
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2013-06-21 Jim ProcterJAL-1230 comment unused code to avoid NPE
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2013-06-21 Jim ProcterJAL-1327 TODO
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2013-06-21 Jim ProcterJAL-1326 JAL-1327 update all graphline thresholds with...
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2013-06-21 Jim ProcterJAL-1241 - generate colour for all annotation values...
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2013-06-21 Jim ProcterMerge branch 'JAL-1294_iupredexportimport' into Release_2_8_...
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2013-06-21 Jim ProcterJAL-1325 formatting
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2013-06-21 Jim ProcterJAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF...
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2013-06-21 Jim ProcterJAL-1294 JAL-1325 store graphline for individual annotation...
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2013-06-21 Jim ProcterJAL-1294 JAL-1325 bugfix equals
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2013-06-21 Jim ProcterJAL-1294 JAL-1325 test annotation threshold line equivalence
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2013-06-21 Jim ProcterMerge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
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2013-06-21 Jim ProcterJAL-1127 set option widgets to service defaults only...
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2013-06-19 Jim ProcterJAL-1240 avoid NPE when source has no proxy available
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2013-06-19 Jim ProcterMerge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
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2013-06-18 Jim ProcterJAL-1320 ascending alphabetical order
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2013-06-18 Jim ProcterJAL-1320 preserve option/parameter order with LinkedHashMap
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2013-06-18 Jim ProcterJAL-1320 sort options and parameters according to their...
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2013-06-18 Jim Proctertypo
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2013-06-18 Jim ProcterJAL-1321 don't show a tooltip for empty strings
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2013-06-17 Jim ProcterMerge branch 'JAL-1319_jronn_npe' into Release_2_8_Branch
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2013-06-17 Jim ProcterJAL-1319 (blacklist fix) check for presence of a score...
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2013-06-17 Jim ProcterMerge branch 'JAL-1312_ambiguity_na' into Release_2_8_Branch
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2013-06-17 Jim ProcterJAL-1027 fix errors in alternative codon table
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2013-06-17 Jim ProcterJAL-1027 check that ResidueProperties.codonHash2 is...
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2013-06-17 Jim ProcterJAL-1027 use alternative codon table in ResidueProperties...
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2013-06-17 Jim ProcterJAL-1035 option to allow 'STOP' codon to translate...
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2013-06-17 Jim ProcterJAL-1312 patch for regression noticed after patch to...
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2013-06-17 Jim ProcterJAL-1312 rewrite of code for first reported exception...
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2013-06-17 Jim ProcterJAL-1312 formatting and more comprehensive test
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2013-06-17 Jim ProcterJAL-1312 remove unnecessary methods
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2013-06-17 Jim ProcterJAL-1312 more helpful error message when translation...
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2013-06-17 Jim ProcterJAL-529 - IUBMB nucleotide ambiguity codes and programmatic...
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2013-06-17 Jim ProcterJAL-1318 - route warnings to stderr (need to find a...
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2013-06-17 Jim ProcterJAL-1318 avoid failure if SequenceI objects don't have...
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2013-06-17 Jim ProcterJAL-966 avoid using java.util.Vector
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2013-06-17 Jim Proctertest for JAL-1312
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2013-06-14 Jim ProcterMerge branch 'JAL-1316' into Release_2_8_Branch
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2013-06-14 Jim ProcterJAL-1316 compact '' to '
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2013-06-14 Jim ProcterJAL-1316 recognise and extract quoted region as nodename
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2013-06-14 Jim ProcterJAL-1316 JAL-1313 newick IO test harness
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2013-06-13 Jim ProcterMerge branch 'JAL-1314_headlessFlag' into Release_2_8_Branch
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2013-06-13 Jim ProcterJAL-1314 allow 'nogui' and 'headless' as synonyms for...
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2013-06-13 Jim ProcterJAL-1314 test for common variants of -nodisplay performing...
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2013-06-13 Jim ProcterMerge branch 'JAL-1315_headlessEPS' into Release_2_8_Branch
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2013-06-13 Jim Procterfix for JAL-1315
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2013-06-13 Jim ProcterJAL-1315 test for exit and successful generation of...
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2013-06-09 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into Release_2_8_Branch
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2013-06-09 Jim Procterfix for JAL-1298
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2013-06-09 Jim ProcterJAL-715 - TODO
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2013-06-07 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into Release_2_8_Branch
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2013-06-07 Jim ProcterJAL-1309 fix broken partition computation for adding...
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2013-06-07 Jim ProcterJAL-945 uniquify prior to submission
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2013-06-07 Jim Procterformatting
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2013-06-07 Jim ProcterJAL-715 allow headless construction for testing
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2013-06-07 Jim ProcterJAL-724 JAL-715 refactor and create new test for RSBS...
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2013-06-07 Jim Procterfix for JAL-1246
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2013-06-07 Jim ProcterJAL-1307 patch to squash number format exceptions when...
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2013-06-07 Jim ProcterJAL-1300 documentation
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2013-05-31 Jim ProcterMerge branch 'JAL-1259_hotfix' into Release_2_8_Branch
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2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE
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2013-05-24 Jim ProcterMerge branch 'JAL-1161_optimisingAnnotationPanel' ...
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2013-05-24 Jim ProcterJAL-1291 reinstate fastPaint flag manipulation to make...
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2013-05-24 Jim ProcterJAL-1291 TODO: revised graphGroup model so grouped...
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2013-05-24 Jim ProcterJAL-1291 - don't touch the graphics object until after...
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2013-05-24 Jim ProcterJAL-1291 conditional output of rendering debugging...
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2013-05-24 Jim Procterpatch for JAL-1300 fixes JAL-1294: read and write COMBINE...
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2013-05-24 Jim ProcterJAL-1300 test and example data for parsing annotation...
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2013-05-24 Jim ProcterJAL-1295 test to demonstrate JAL-1294 (caused by JAL...
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2013-05-24 Jim ProcterJAL-1295 refactored Jws2 discovery bootstrap code to...
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2013-05-24 Jim ProcterJAL-1295 relaxed test for Annotation element equivalence...
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2013-05-24 Jim ProcterJAL-381 Desktop.addInternalFrame cannot be called in...
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2013-05-24 Jim ProcterJAL-1299 fix: ensure a new graphGroup is created if...
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2013-05-24 Jim ProcterJAL-1295 JAL-1296 clearer assertion failed message
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2013-05-24 Jim ProcterJAL-1295 JAL-1297 enhance test to check graph visiblity...
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2013-05-24 Jim Procterfix for JAL-1297: COMBINE output now follows specification...
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2013-05-24 Jim ProcterJAL-1296 JAL-1291 JAL-1297 JAL-1295 JAL-1294
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2013-05-24 Jim ProcterJAL-1291 JAL-1297 JAL-1295 JAL-1294 allow alignment...
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2013-05-24 Jim Procterjavadoc and formatting
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2013-05-24 Jim ProcterJAL-1297 JAL-1295 JAL-1294 sensible toString for benefit...
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2013-05-24 Jim ProcterJAL-1297 JAL-1295 JAL-1294 improve test logic for comparing...
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2013-05-24 Jim ProcterJAL-1296 reinstated tab characters so example annotation...
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2013-05-24 Jim ProcterJAL-1070 - [ not a real patch ] - include offending...
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