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