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Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
[jalview.git]
/
src
/
2013-07-11
Jim Procter
JAL-1347 refactor logic for setting display flags for...
tree
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commitdiff
2013-07-11
Jim Procter
JAL-1347 make it efficient to call getConsensus to...
tree
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commitdiff
2013-07-07
Jim Procter
JAL-1345 - set nSeconds arg for chemapps.stolaf.edu...
tree
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commitdiff
2013-07-07
Jim Procter
JAL-1016 Instruct user to report situations where the...
tree
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commitdiff
2013-07-07
Jim Procter
JAL-1332 make SSM context discovery safer (particularly...
tree
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commitdiff
2013-07-07
Jim Procter
JAL-583 refactor todo about separating code to construc...
tree
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commitdiff
2013-07-07
Jim Procter
fix for JAL-1016 - wait around until we have a complete...
tree
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commitdiff
2013-07-07
Jim Procter
JAL-1016 - do our assertions immediatly
tree
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commitdiff
2013-06-23
Jim Procter
Merge branch 'bug/JAL-1230' into Release_2_8_Branch
tree
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commitdiff
2013-06-23
Jim Procter
JAL-1230 update alignment state for annotation edits...
tree
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commitdiff
2013-06-23
Jim Procter
JAL-1230 proxy method for synchronising internal Alignm...
tree
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commitdiff
2013-06-23
Jim Procter
JAL-1230 simplify initialisation of consensus, conserva...
tree
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commitdiff
2013-06-23
Jim Procter
Merge branch 'bug/JAL-1230' into Release_2_8_Branch
tree
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commitdiff
2013-06-23
Jim Procter
Merge commit '72c628b' into Release_2_8_Branch
tree
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commitdiff
2013-06-22
Jim Procter
JAL-1330 pick primary seqeunce data source for authorit...
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1230 comment unused code to avoid NPE
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1327 TODO
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1326 JAL-1327 update all graphline thresholds with...
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1241 - generate colour for all annotation values...
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF...
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1294 JAL-1325 store graphline for individual annota...
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1294 JAL-1325 bugfix equals
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1294 JAL-1325 test annotation threshold line equiva...
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1127 set option widgets to service defaults only...
tree
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commitdiff
2013-06-19
Jim Procter
JAL-1240 avoid NPE when source has no proxy available
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
2013-06-17
Jim Procter
JAL-1319 (blacklist fix) check for presence of a score...
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
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
JAL-1314 allow 'nogui' and 'headless' as synonyms for...
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
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
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
2013-05-31
Jim Procter
JAL-1259 patch to avoid NPE
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
2013-05-13
Jim Procter
Merge branch 'JAL-1289_initCallBack' into Release_2_8_B...
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
2013-02-06
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...
tree
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commitdiff
2013-02-06
jprocter
JAL-1199 refactored stockholm test code from main class...
tree
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commitdiff
2013-02-05
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
tree
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commitdiff
2013-02-05
jprocter
formatting
tree
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commitdiff
2013-02-05
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
tree
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commitdiff
2013-01-18
jprocter
JAL-1238 order to place primary sources before lower...
tree
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commitdiff
2013-01-18
jprocter
JAL-1238 method to test if DAS source is a primary...
tree
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commitdiff
2013-01-18
jprocter
JAL-1238 tier index indicating distance of a source...
tree
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commitdiff
2013-01-18
jprocter
JAL-1255 don't show 'Right click to add annotations...
tree
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commitdiff
2013-01-18
jprocter
JAL-1254 patch for NPE in annotation renderer when...
tree
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commitdiff
2012-12-17
Natasha
test for output a file in Stockholm format
tree
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commitdiff
2012-12-12
Natasha
Output accession number for file in stockholm format
tree
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commitdiff
2012-12-11
jprocter
JAL-1217 check and avoid NPE if no datastore object...
tree
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commitdiff
2012-12-11
jprocter
JAL-1217 report exception for service when no datastore...
tree
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commitdiff
2012-11-23
Natasha
stockholm file output code developed by Natasha Sherstneva
tree
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commitdiff
2012-11-15
Paolo Di Tommaso
Fixed T-Coffee file scores parser to support extended...
tree
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commitdiff
2012-11-09
jprocter
constructor takes settings from any existing feature...
tree
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commitdiff
2012-11-08
jprocter
JAL-1193 ensure the 'loadedComplete' method gets called...
tree
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commitdiff
2012-11-08
jprocter
remember to close input file!
tree
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commitdiff
2012-11-08
jprocter
tidy imports
tree
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commitdiff
next