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2013-06-17 Jim ProcterMerge branch 'JAL-1319_jronn_npe' into develop 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 develop 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 develop 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 develop 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 develop 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
2013-06-11 Jim Procterchange to release version of VARNA-3-9 commit | commitdiff | tree | snapshot
2013-06-09 Jim ProcterJAL-674 avoid runtime dependency on annotate3d webservi... commit | commitdiff | tree | snapshot
2013-06-09 Jim ProcterJAL-674 - update applet build dependency on VARNA commit | commitdiff | tree | snapshot
2013-06-09 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into develop 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 develop 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
2013-06-07 Jim ProcterMerge branch 'JAL-1161_optimisingAnnotationPanel' into... commit | commitdiff | tree | snapshot
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE 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-???? notes on summarisation and analysis of annotat... 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
2013-05-24 Jim Procterjavadoc and formatting commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1297 JAL-1295 JAL-1294 sensible toString for benefi... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1297 JAL-1295 JAL-1294 improve test logic for compa... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1296 reinstated tab characters so example annotatio... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1070 - [ not a real patch ] - include offending... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-966 paintrefresher should be abstract [ Merge branc... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1161 conditional parameters for controlling clipping commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1292 avoid exception by using bitset of arbitrary... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1161 changed signature to allow clipping bounds... commit | commitdiff | tree | snapshot
2013-05-24 Jim Procterformatting commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1161 only trigger an annotation repaint in unwrappe... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1161 enable fastPaint for nudges from scroll bars... commit | commitdiff | tree | snapshot
2013-05-24 Jim ProcterJAL-1161 stick to api commit | commitdiff | tree | snapshot
2013-05-24 Jim Proctertypo commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-05-21 Jim Proctersplit test for general Stockholm IO consistency (JAL... JAL-1199-Stk_writing commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterJAL-1199 JAL-1272 remove main() method from test class commit | commitdiff | tree | snapshot
2013-05-21 Jim Procterformatting commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterJAL-1199 JAL-1272 refactored Natasha's test to a generi... commit | commitdiff | tree | snapshot
2013-05-13 Jim ProcterJAL-1286 URL stream reader tries to use a GZIPInputStre... commit | commitdiff | tree | snapshot
2013-05-13 Jim ProcterMerge branch 'JAL-1289_initCallBack' into Release_2_8_B... commit | commitdiff | tree | snapshot
2013-05-13 Jim ProcterMerge branch 'JAL-1289_initCallBack' into develop commit | commitdiff | tree | snapshot
2013-05-13 Jim ProcterJAL-1289 call oninit callback even if no alignment... commit | commitdiff | tree | snapshot
2013-04-12 Jim ProcterMerge branch 'JAL-1286_gzip' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-04-12 Jim ProcterJAL-1286 URL stream reader tries to use a GZIPInputStre... commit | commitdiff | tree | snapshot
2013-02-06 jprocterMerge branch 'Release_2_8_Branch' into JAL-1199-Stk_writing commit | commitdiff | tree | snapshot
2013-02-06 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-02-06 jprocterJAL-1265 basic support for parsing database accessions... commit | commitdiff | tree | snapshot
2013-02-06 jprocterJAL-1199 added test for Rfam Stockholm file example commit | commitdiff | tree | snapshot
2013-02-06 jprocterJAL-1199 refactored stockholm test code from main class... commit | commitdiff | tree | snapshot
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