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JAL-1375 initial import of EntrezClient code from Cytoscape3
[jalview.git] / src /
2013-09-18 Jim ProcterJAL-1375 initial import of EntrezClient code from Cytos... JAL-1375_ncbiclient tree | commitdiff
2013-09-03 Jim ProcterJAL-1373 tweak precision calculation so alignments... tree | commitdiff
2013-09-03 Jim ProcterJAL-920 compute a consensus for single sequence tree | commitdiff
2013-09-02 Jim ProcterJAL-1373 JAL-520 wrap tooltips for columns in annotatio... tree | commitdiff
2013-09-02 Jim ProcterJAL-1373 generate percentages with appropriate precision tree | commitdiff
2013-09-02 Jim ProcterJAL-1373 pass size of sequence set to consensus renderi... tree | commitdiff
2013-08-27 Jim ProcterJAL-1359 simpler logic for deciding if all threads... tree | commitdiff
2013-08-27 Jim ProcterJAL-1332 regression from 7ce72ca7fadf35a249427ecb836b22... tree | commitdiff
2013-08-27 Jim ProcterJAL-1332 - defer SSM provision to root provider for... tree | commitdiff
2013-07-12 Jim ProcterJAL-1347 RNA Structure consensus follows the alignment... tree | commitdiff
2013-07-12 Jim ProcterJAL-1347 flow control for display of profile data is... tree | commitdiff
2013-07-11 Jim ProcterJAL-1347 identify and set rendering settings for consen... tree | commitdiff
2013-07-11 Jim ProcterJAL-1347 refactor logic for setting display flags for... tree | commitdiff
2013-07-11 Jim ProcterJAL-1347 make it efficient to call getConsensus to... tree | commitdiff
2013-07-07 Jim ProcterJAL-1345 - set nSeconds arg for chemapps.stolaf.edu... tree | commitdiff
2013-07-07 Jim ProcterJAL-1016 Instruct user to report situations where the... tree | commitdiff
2013-07-07 Jim ProcterJAL-1332 make SSM context discovery safer (particularly... tree | commitdiff
2013-07-07 Jim ProcterJAL-583 refactor todo about separating code to construc... tree | commitdiff
2013-07-07 Jim Procterfix for JAL-1016 - wait around until we have a complete... tree | commitdiff
2013-07-07 Jim ProcterJAL-1016 - do our assertions immediatly tree | commitdiff
2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch tree | commitdiff
2013-06-23 Jim ProcterJAL-1230 update alignment state for annotation edits... tree | commitdiff
2013-06-23 Jim ProcterJAL-1230 proxy method for synchronising internal Alignm... tree | commitdiff
2013-06-23 Jim ProcterJAL-1230 simplify initialisation of consensus, conserva... tree | commitdiff
2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch tree | commitdiff
2013-06-23 Jim ProcterMerge commit '72c628b' into Release_2_8_Branch tree | commitdiff
2013-06-22 Jim ProcterJAL-1330 pick primary seqeunce data source for authorit... tree | commitdiff
2013-06-21 Jim ProcterJAL-1230 comment unused code to avoid NPE tree | commitdiff
2013-06-21 Jim ProcterJAL-1327 TODO tree | commitdiff
2013-06-21 Jim ProcterJAL-1326 JAL-1327 update all graphline thresholds with... tree | commitdiff
2013-06-21 Jim ProcterJAL-1241 - generate colour for all annotation values... tree | commitdiff
2013-06-21 Jim ProcterJAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF... tree | commitdiff
2013-06-21 Jim ProcterJAL-1294 JAL-1325 store graphline for individual annota... tree | commitdiff
2013-06-21 Jim ProcterJAL-1294 JAL-1325 bugfix equals tree | commitdiff
2013-06-21 Jim ProcterJAL-1294 JAL-1325 test annotation threshold line equiva... tree | commitdiff
2013-06-21 Jim ProcterJAL-1127 set option widgets to service defaults only... tree | commitdiff
2013-06-19 Jim ProcterJAL-1240 avoid NPE when source has no proxy available 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
2013-06-17 Jim ProcterJAL-1319 (blacklist fix) check for presence of a score... 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 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 ProcterJAL-1314 allow 'nogui' and 'headless' as synonyms for... tree | commitdiff
2013-06-13 Jim Procterfix for JAL-1315 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 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
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE 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
2013-05-13 Jim ProcterMerge branch 'JAL-1289_initCallBack' into Release_2_8_B... 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
2013-02-06 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
2013-02-06 jprocterJAL-1199 refactored stockholm test code from main class... tree | commitdiff
2013-02-05 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch tree | commitdiff
2013-02-05 jprocterformatting tree | commitdiff
2013-02-05 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch tree | commitdiff
2013-01-18 jprocterJAL-1238 order to place primary sources before lower... tree | commitdiff
2013-01-18 jprocterJAL-1238 method to test if DAS source is a primary... tree | commitdiff
2013-01-18 jprocterJAL-1238 tier index indicating distance of a source... tree | commitdiff
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