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Merge branch 'JAL-957_jbake' into Release_2_8_Branch
[jalview.git]
/
src
/
jalview
/
2014-01-27
Jim Procter
JAL-1430 mfa added as a known extension for FASTA files
tree
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commitdiff
2014-01-13
Jim Procter
Merge branch 'JAL-1422_srs' into Release_2_8_Branch
tree
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commitdiff
2014-01-13
Jim Procter
JAL-1422 update any existing configuration to replace...
tree
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commitdiff
2014-01-13
Jim Procter
JAL-1422 change default link to EMBL-EBI Search
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commitdiff
2014-01-07
Jim Procter
JAL-1423 - console error reporting and graceful handlin...
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commitdiff
2013-11-07
Jim Procter
JAL-1286 check if local file ends with .gz and opens...
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1164 regression on JAL-1292 use bitset to mark...
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commitdiff
2013-10-11
Jim Procter
JAL-1164 scope bySequence analysis methods to start...
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commitdiff
2013-10-11
Jim Procter
JAL-1114 javadoc
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commitdiff
2013-10-11
Jim Procter
JAL-1114 promote start/end attributes to gettable field...
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commitdiff
2013-10-11
Jim Procter
JAL-1114 API javadoc
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commitdiff
2013-10-11
Jim Procter
JAL-1164 only predict on currently selected sequences...
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commitdiff
2013-10-11
Jim Procter
JAL-1385 expose core view model methods in interface
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commitdiff
2013-07-12
Jim Procter
JAL-1347 RNA Structure consensus follows the alignment...
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commitdiff
2013-07-12
Jim Procter
JAL-1347 flow control for display of profile data is...
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commitdiff
2013-07-11
Jim Procter
JAL-1347 identify and set rendering settings for consen...
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commitdiff
2013-07-11
Jim Procter
JAL-1347 refactor logic for setting display flags for...
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commitdiff
2013-07-11
Jim Procter
JAL-1347 make it efficient to call getConsensus to...
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commitdiff
2013-07-07
Jim Procter
JAL-1345 - set nSeconds arg for chemapps.stolaf.edu...
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commitdiff
2013-07-07
Jim Procter
JAL-1016 Instruct user to report situations where the...
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commitdiff
2013-07-07
Jim Procter
JAL-1332 make SSM context discovery safer (particularly...
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commitdiff
2013-07-07
Jim Procter
JAL-583 refactor todo about separating code to construc...
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commitdiff
2013-07-07
Jim Procter
fix for JAL-1016 - wait around until we have a complete...
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commitdiff
2013-07-07
Jim Procter
JAL-1016 - do our assertions immediatly
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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...
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commitdiff
2013-06-23
Jim Procter
JAL-1230 proxy method for synchronising internal Alignm...
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commitdiff
2013-06-23
Jim Procter
JAL-1230 simplify initialisation of consensus, conserva...
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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...
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commitdiff
2013-06-21
Jim Procter
JAL-1230 comment unused code to avoid NPE
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commitdiff
2013-06-21
Jim Procter
JAL-1327 TODO
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commitdiff
2013-06-21
Jim Procter
JAL-1326 JAL-1327 update all graphline thresholds with...
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commitdiff
2013-06-21
Jim Procter
JAL-1241 - generate colour for all annotation values...
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commitdiff
2013-06-21
Jim Procter
JAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF...
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commitdiff
2013-06-21
Jim Procter
JAL-1294 JAL-1325 store graphline for individual annota...
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commitdiff
2013-06-21
Jim Procter
JAL-1294 JAL-1325 bugfix equals
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commitdiff
2013-06-21
Jim Procter
JAL-1294 JAL-1325 test annotation threshold line equiva...
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commitdiff
2013-06-21
Jim Procter
JAL-1127 set option widgets to service defaults only...
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commitdiff
2013-06-19
Jim Procter
JAL-1240 avoid NPE when source has no proxy available
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commitdiff
2013-06-18
Jim Procter
JAL-1320 ascending alphabetical order
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commitdiff
2013-06-18
Jim Procter
JAL-1320 preserve option/parameter order with LinkedHashMap
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commitdiff
2013-06-18
Jim Procter
JAL-1320 sort options and parameters according to their...
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commitdiff
2013-06-18
Jim Procter
typo
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commitdiff
2013-06-18
Jim Procter
JAL-1321 don't show a tooltip for empty strings
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commitdiff
2013-06-17
Jim Procter
JAL-1319 (blacklist fix) check for presence of a score...
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commitdiff
2013-06-17
Jim Procter
JAL-1027 fix errors in alternative codon table
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commitdiff
2013-06-17
Jim Procter
JAL-1027 use alternative codon table in ResidueProperti...
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commitdiff
2013-06-17
Jim Procter
JAL-1035 option to allow 'STOP' codon to translate...
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commitdiff
2013-06-17
Jim Procter
JAL-1312 patch for regression noticed after patch to...
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commitdiff
2013-06-17
Jim Procter
JAL-1312 rewrite of code for first reported exception...
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commitdiff
2013-06-17
Jim Procter
JAL-1312 more helpful error message when translation...
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commitdiff
2013-06-17
Jim Procter
JAL-529 - IUBMB nucleotide ambiguity codes and programm...
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commitdiff
2013-06-17
Jim Procter
JAL-1318 - route warnings to stderr (need to find a...
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commitdiff
2013-06-17
Jim Procter
JAL-1318 avoid failure if SequenceI objects don't have...
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commitdiff
2013-06-17
Jim Procter
JAL-966 avoid using java.util.Vector
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commitdiff
2013-06-14
Jim Procter
JAL-1316 compact '' to '
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commitdiff
2013-06-14
Jim Procter
JAL-1316 recognise and extract quoted region as nodename
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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
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commitdiff
2013-06-09
Jim Procter
fix for JAL-1298
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commitdiff
2013-06-09
Jim Procter
JAL-715 - TODO
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commitdiff
2013-06-07
Jim Procter
JAL-1309 fix broken partition computation for adding...
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commitdiff
2013-06-07
Jim Procter
JAL-945 uniquify prior to submission
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commitdiff
2013-06-07
Jim Procter
formatting
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commitdiff
2013-06-07
Jim Procter
JAL-715 allow headless construction for testing
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commitdiff
2013-06-07
Jim Procter
JAL-724 JAL-715 refactor and create new test for RSBS...
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commitdiff
2013-06-07
Jim Procter
fix for JAL-1246
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commitdiff
2013-06-07
Jim Procter
JAL-1307 patch to squash number format exceptions when...
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commitdiff
2013-05-31
Jim Procter
JAL-1259 patch to avoid NPE
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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...
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commitdiff
2013-05-24
Jim Procter
JAL-1291 - don't touch the graphics object until after...
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commitdiff
2013-05-24
Jim Procter
JAL-1291 conditional output of rendering debugging...
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commitdiff
2013-05-24
Jim Procter
patch for JAL-1300 fixes JAL-1294: read and write COMBI...
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commitdiff
2013-05-24
Jim Procter
JAL-1295 relaxed test for Annotation element equivalenc...
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commitdiff
2013-05-24
Jim Procter
JAL-381 Desktop.addInternalFrame cannot be called in...
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commitdiff
2013-05-24
Jim Procter
JAL-1299 fix: ensure a new graphGroup is created if...
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commitdiff
2013-05-24
Jim Procter
fix for JAL-1297: COMBINE output now follows specificat...
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commitdiff
2013-05-24
Jim Procter
javadoc and formatting
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commitdiff
2013-05-24
Jim Procter
JAL-1297 JAL-1295 JAL-1294 sensible toString for benefi...
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commitdiff
2013-05-24
Jim Procter
JAL-1070 - [ not a real patch ] - include offending...
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commitdiff
2013-05-24
Jim Procter
JAL-966 paintrefresher should be abstract [ Merge branc...
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commitdiff
2013-05-24
Jim Procter
JAL-1161 conditional parameters for controlling clipping
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commitdiff
2013-05-24
Jim Procter
JAL-1292 avoid exception by using bitset of arbitrary...
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commitdiff
2013-05-24
Jim Procter
JAL-1161 changed signature to allow clipping bounds...
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commitdiff
2013-05-24
Jim Procter
formatting
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commitdiff
2013-05-24
Jim Procter
JAL-1161 only trigger an annotation repaint in unwrappe...
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commitdiff
2013-05-24
Jim Procter
JAL-1161 enable fastPaint for nudges from scroll bars...
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commitdiff
2013-05-24
Jim Procter
JAL-1161 stick to api
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commitdiff
2013-05-24
Jim Procter
typo
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commitdiff
2013-05-13
Jim Procter
Merge branch 'JAL-1289_initCallBack' into Release_2_8_B...
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commitdiff
2013-05-13
Jim Procter
JAL-1289 call oninit callback even if no alignment...
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commitdiff
2013-04-12
Jim Procter
JAL-1286 URL stream reader tries to use a GZIPInputStre...
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commitdiff
2013-02-06
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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commitdiff
2013-02-06
jprocter
JAL-1265 basic support for parsing database accessions...
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commitdiff
2013-02-06
jprocter
JAL-1199 refactored stockholm test code from main class...
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commitdiff
2013-02-05
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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commitdiff
2013-02-05
jprocter
formatting
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commitdiff
next