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Merge branch 'develop' into develop_m2_8_1_2
[jalview.git] / src /
2013-06-19 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-19 Jim ProcterMerge branch 'JAL-1321_jws2_tooltips' into develop tree | commitdiff
2013-06-18 Jim ProcterJAL-1320 ascending alphabetical order tree | commitdiff
2013-06-18 Jim ProcterJAL-1320 preserve option/parameter order with LinkedHashMap tree | commitdiff
2013-06-18 Jim ProcterJAL-1320 sort options and parameters according to their... tree | commitdiff
2013-06-18 Jim Proctertypo tree | commitdiff
2013-06-18 Jim ProcterJAL-1321 don't show a tooltip for empty strings tree | commitdiff
2013-06-18 Jim ProcterJAL-674 fix the mapping generation algorithm tree | commitdiff
2013-06-18 Jim ProcterMerge branch 'menard' into develop_m2_8_1_2 tree | commitdiff
2013-06-18 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-18 Jim ProcterJAL-674 - avoid java.util.ConcurrentModificationExcepti... tree | commitdiff
2013-06-17 Jim ProcterMerge branch 'JAL-1319_jronn_npe' into develop tree | commitdiff
2013-06-17 Jim ProcterJAL-1319 (blacklist fix) check for presence of a score... tree | commitdiff
2013-06-17 Jim ProcterMerge branch 'JAL-1312_ambiguity_na' into develop tree | commitdiff
2013-06-17 Jim ProcterJAL-1027 fix errors in alternative codon table tree | commitdiff
2013-06-17 Jim ProcterJAL-1027 use alternative codon table in ResidueProperti... tree | commitdiff
2013-06-17 Jim ProcterJAL-1035 option to allow 'STOP' codon to translate... tree | commitdiff
2013-06-17 Jim ProcterJAL-1312 patch for regression noticed after patch to... tree | commitdiff
2013-06-17 Jim ProcterJAL-1312 rewrite of code for first reported exception... tree | commitdiff
2013-06-17 Jim ProcterJAL-1312 more helpful error message when translation... tree | commitdiff
2013-06-17 Jim ProcterJAL-529 - IUBMB nucleotide ambiguity codes and programm... tree | commitdiff
2013-06-17 Jim ProcterJAL-1318 - route warnings to stderr (need to find a... tree | commitdiff
2013-06-17 Jim ProcterJAL-1318 avoid failure if SequenceI objects don't have... tree | commitdiff
2013-06-17 Jim ProcterJAL-966 avoid using java.util.Vector tree | commitdiff
2013-06-14 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-14 Jim ProcterMerge branch 'JAL-1316' into develop tree | commitdiff
2013-06-14 Jim ProcterJAL-1316 compact '' to ' tree | commitdiff
2013-06-14 Jim ProcterJAL-1316 recognise and extract quoted region as nodename tree | commitdiff
2013-06-13 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-13 Jim ProcterMerge branch 'JAL-1314_headlessFlag' into develop tree | commitdiff
2013-06-13 Jim ProcterJAL-1314 allow 'nogui' and 'headless' as synonyms for... tree | commitdiff
2013-06-13 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-13 Jim ProcterMerge branch 'JAL-1315_headlessEPS' into develop tree | commitdiff
2013-06-13 Jim Procterfix for JAL-1315 tree | commitdiff
2013-06-09 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-09 Jim ProcterJAL-674 avoid runtime dependency on annotate3d webservi... tree | commitdiff
2013-06-09 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-09 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into develop tree | commitdiff
2013-06-09 Jim Procterfix for JAL-1298 tree | commitdiff
2013-06-09 Jim ProcterJAL-715 - TODO tree | commitdiff
2013-06-07 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-07 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into develop tree | commitdiff
2013-06-07 Jim ProcterJAL-1309 fix broken partition computation for adding... tree | commitdiff
2013-06-07 Jim ProcterJAL-945 uniquify prior to submission tree | commitdiff
2013-06-07 Jim Procterformatting tree | commitdiff
2013-06-07 Jim ProcterJAL-715 allow headless construction for testing tree | commitdiff
2013-06-07 Jim ProcterJAL-724 JAL-715 refactor and create new test for RSBS... tree | commitdiff
2013-06-07 Jim Procterfix for JAL-1246 tree | commitdiff
2013-06-07 Jim ProcterJAL-1307 patch to squash number format exceptions when... tree | commitdiff
2013-06-07 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-07 Jim ProcterMerge branch 'JAL-1161_optimisingAnnotationPanel' into... tree | commitdiff
2013-05-31 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE tree | commitdiff
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE tree | commitdiff
2013-05-26 Jim ProcterJAL-1269 RNAML returned directly from Annotate3d rather... tree | commitdiff
2013-05-24 Jim ProcterMerge branch 'menard' into develop_m2_8_1_2 tree | commitdiff
2013-05-24 Jim ProcterJAL-1291 reinstate fastPaint flag manipulation to make... tree | commitdiff
2013-05-24 Jim ProcterJAL-1291 TODO: revised graphGroup model so grouped... tree | commitdiff
2013-05-24 Jim ProcterJAL-1291 - don't touch the graphics object until after... tree | commitdiff
2013-05-24 Jim ProcterJAL-1291 conditional output of rendering debugging... tree | commitdiff
2013-05-24 Jim Procterpatch for JAL-1300 fixes JAL-1294: read and write COMBI... tree | commitdiff
2013-05-24 Jim ProcterJAL-1295 relaxed test for Annotation element equivalenc... tree | commitdiff
2013-05-24 Jim ProcterJAL-381 Desktop.addInternalFrame cannot be called in... tree | commitdiff
2013-05-24 Jim ProcterJAL-1299 fix: ensure a new graphGroup is created if... tree | commitdiff
2013-05-24 Jim Procterfix for JAL-1297: COMBINE output now follows specificat... tree | commitdiff
2013-05-24 Jim Procterjavadoc and formatting tree | commitdiff
2013-05-24 Jim ProcterJAL-1297 JAL-1295 JAL-1294 sensible toString for benefi... tree | commitdiff
2013-05-24 Jim ProcterJAL-1070 - [ not a real patch ] - include offending... tree | commitdiff
2013-05-24 Jim ProcterJAL-966 paintrefresher should be abstract [ Merge branc... tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 conditional parameters for controlling clipping tree | commitdiff
2013-05-24 Jim ProcterJAL-1292 avoid exception by using bitset of arbitrary... tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 changed signature to allow clipping bounds... tree | commitdiff
2013-05-24 Jim Procterformatting tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 only trigger an annotation repaint in unwrappe... tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 enable fastPaint for nudges from scroll bars... tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 stick to api tree | commitdiff
2013-05-24 Jim Proctertypo tree | commitdiff
2013-05-21 Jim ProcterJAL-1140 JAL-674 process with annotate3d and Jmol to... tree | commitdiff
2013-05-21 Jim ProcterJAL-674 ensure annotation is properly annotated tree | commitdiff
2013-05-21 Jim ProcterJAL-1231 add chain ID tree | commitdiff
2013-05-21 Jim ProcterJAL-1231 allow Jmol file handler to read from a stream tree | commitdiff
2013-05-13 Jim ProcterJAL-1286 URL stream reader tries to use a GZIPInputStre... tree | commitdiff
2013-05-13 Jim ProcterMerge branch 'JAL-1289_initCallBack' into Release_2_8_B... tree | commitdiff
2013-05-13 Jim ProcterMerge branch 'JAL-1289_initCallBack' into develop tree | commitdiff
2013-05-13 Jim ProcterJAL-1289 call oninit callback even if no alignment... tree | commitdiff
2013-04-12 Jim ProcterJAL-1286 URL stream reader tries to use a GZIPInputStre... tree | commitdiff
2013-02-14 Jim ProcterMerge branch 'JAL-1199-Stk_writing' into rnaml_test tree | commitdiff
2013-02-14 Jim ProcterJAL-1140 reinstate the simpler version of parsing code... tree | commitdiff
2013-02-14 Jim Procterpatch for bizarre ConcurrentModificationException that... tree | commitdiff
2013-02-13 Jim ProcterMerge branch 'jims_annotate3d_update' into menard_final... tree | commitdiff
2013-02-13 jprocterfix merge conflicts for finess on JAL-1140 (introduced... tree | commitdiff
2013-02-13 jprocterJAL-1216 switch to official release of VARNA 3.9 tree | commitdiff
2013-02-13 jprocterJAL-1214 todo tree | commitdiff
2013-02-13 jprocterJAL-1213 JAL-674 - import a PDB file using Jmol data... tree | commitdiff
2013-02-13 jprocterJAL-674 commented out annotate3d calling code for Jmol... tree | commitdiff
2013-02-13 jprocterJAL-1028 JAL-674 hooks to call external processing... tree | commitdiff
2013-02-11 jprocterpatch for 'This parser does not support specification... tree | commitdiff
2013-02-11 jprocterupgrade to latest paradise services model using JSon... tree | commitdiff
2013-02-06 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch tree | commitdiff
2013-02-06 jprocterJAL-1265 basic support for parsing database accessions... tree | commitdiff
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