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Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
[jalview.git] / src /
2014-02-03 Jim ProcterMerge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge tree | commitdiff
2014-01-29 Jim ProcterJAL-1432 natasha's name on applet author list tree | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices tree | commitdiff
2014-01-27 Jim ProcterJAL-1430 mfa added as a known extension for FASTA files tree | commitdiff
2014-01-13 Jim ProcterMerge branch 'JAL-1422_srs' into JAL-1422_srs_r281 tree | commitdiff
2014-01-13 Jim ProcterMerge branch 'JAL-1422_srs' into Release_2_8_Branch tree | commitdiff
2014-01-13 Jim ProcterJAL-1422 update any existing configuration to replace... tree | commitdiff
2014-01-13 Jim ProcterJAL-1422 change default link to EMBL-EBI Search tree | commitdiff
2014-01-07 Jim ProcterMerge branch 'fix_JAL-1423' into Release_2_8_1_Branch tree | commitdiff
2014-01-07 Jim ProcterJAL-1423 - console error reporting and graceful handlin... tree | commitdiff
2013-11-07 Jim ProcterMerge branch 'JAL-1286' into Release_2_8_1_Branch tree | commitdiff
2013-11-07 Jim ProcterJAL-1286 check if local file ends with .gz and opens... tree | commitdiff
2013-10-17 Jim Procterfix for JAL-1398 - original colourscheme is enabled... tree | commitdiff
2013-10-17 Jim ProcterJAL-1233 TODO concerning the way we propagate annotatio... tree | commitdiff
2013-10-17 Jim ProcterJAL-1397 make sure annotation colourscheme is up to... tree | commitdiff
2013-10-17 Jim ProcterJAL-1397 store colour by sequence and originalColour... tree | commitdiff
2013-10-17 Jim ProcterJAL-1397 make sure ColourschemeI instances are up to... tree | commitdiff
2013-10-17 Jim ProcterJAL-1397 propagate any consensus/conservation coloursch... tree | commitdiff
2013-10-17 Jim ProcterJAL-1397 getters for originalColours flag tree | commitdiff
2013-10-16 Jim ProcterJAL-1395 do not calculate non-gap consensus when no... tree | commitdiff
2013-10-11 Jim ProcterJAL-1164 regression on JAL-1292 use bitset to mark... tree | commitdiff
2013-10-11 Jim ProcterJAL-1164 regression on JAL-1292 use bitset to mark... tree | commitdiff
2013-10-11 Jim ProcterMerge branch 'JAL-1164_disorderforselection' into Relea... tree | commitdiff
2013-10-11 Jim ProcterJAL-1164 scope bySequence analysis methods to start... tree | commitdiff
2013-10-11 Jim ProcterJAL-1114 javadoc tree | commitdiff
2013-10-11 Jim ProcterJAL-1114 promote start/end attributes to gettable field... tree | commitdiff
2013-10-11 Jim ProcterJAL-1114 API javadoc tree | commitdiff
2013-10-11 Jim ProcterJAL-1164 only predict on currently selected sequences... tree | commitdiff
2013-10-11 Jim ProcterJAL-1385 expose core view model methods in interface tree | commitdiff
2013-10-11 Jim ProcterJAL-1354 watch for exceptions when initialising (Securi... tree | commitdiff
2013-10-08 Jim ProcterMerge branch 'Release_2_8_1_Branch' into Release_2_8_1_... tree | commitdiff
2013-10-08 Jim ProcterJAL-1384 Create Group in selection popup menu tree | commitdiff
2013-10-08 Jim Procterfix for JAL-1387 tree | commitdiff
2013-10-08 Jim ProcterJAL-1384 documentation and consistent ordering for... tree | commitdiff
2013-10-08 Jim ProcterJAL-1384 group/ungroup sequences with command/ctrl... tree | commitdiff
2013-10-07 Jim ProcterJAL-1385 refactor logic to AlignmentViewController tree | commitdiff
2013-10-07 Jim ProcterJAL-1385 JAL-535 refactor sequence colour settings... tree | commitdiff
2013-10-07 Jim ProcterJAL-1385 expose core view model methods in interface tree | commitdiff
2013-10-07 Jim ProcterJAL-1385 Alignment view controller logic implementation... tree | commitdiff
2013-10-05 Jim ProcterJAL-1379 graceful degradation to legacy service when... tree | commitdiff
2013-10-05 Jim ProcterJAL-1379 JAL-1378 exclusion list property to ignore... tree | commitdiff
2013-10-05 Jim ProcterJAL-1378 hack to place 'Predictors' into Secondary... tree | commitdiff
2013-10-05 Jim ProcterJAL-1364 use gapMap to map RNAalifold annotation onto... tree | commitdiff
2013-10-05 Jim ProcterJAL-1379 JAL-1358 only enable/disable menu entries... tree | commitdiff
2013-10-04 Jim ProcterJAL-1383 - disable startup of the Envision2 workflow... tree | commitdiff
2013-10-04 Jim ProcterJAL-940 JAL-1378 EOL comment on JWS v1 services tree | commitdiff
2013-10-04 Jim ProcterMerge branch 'RNAalifold' into Release_2_8_1_Branch tree | commitdiff
2013-10-04 Jim Procterfix for JAL-1380 and efficiency todo for JAL-1381 tree | commitdiff
2013-10-04 Jim ProcterJAL-1378 JWS-71 update to from-source build of JABA... tree | commitdiff
2013-09-25 Jim ProcterJAL-1365 unified GUI building for AACon and RNAAliFold... tree | commitdiff
2013-09-25 Jim ProcterJAL-1365 use AlignAnalysisUIText class to provide metad... tree | commitdiff
2013-09-25 Jim ProcterJAL-1365 refactored core methods from RNAAliFold and... tree | commitdiff
2013-09-25 Jim ProcterJAL-1365 new metadata class to describe instantaneous... tree | commitdiff
2013-09-25 Jim ProcterJAL-1270 nominal jalview version string for projects... tree | commitdiff
2013-09-25 Jim ProcterJAL-1270 Desktop.instance is null during headless jalvi... tree | commitdiff
2013-09-20 Jim Procterformatting tree | commitdiff
2013-09-18 Jim ProcterJAL-1355 - fix compilation errors: typos and missing... tree | commitdiff
2013-09-03 Jim ProcterMerge branch 'JAL-1373_precision' into RNAalifold 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
2013-08-30 Daniel BartonColour be RNA helices bug fixed tree | commitdiff
2013-08-30 Daniel BartonJAL-1358 Cleaned up RNAalifoldClient.java. RNA helices... tree | commitdiff
2013-08-30 darolmari18n date/time handling tree | commitdiff
2013-08-29 darolmari18n tree | commitdiff
2013-08-28 Daniel BartonRNAalifoldClient updated to be more like AAConClient... tree | commitdiff
2013-08-27 Daniel BartonJAL-1358 jalview displays some RNA struture annotation... tree | commitdiff
2013-08-27 Jim ProcterJAL-1359 simpler logic for deciding if all threads... tree | commitdiff
2013-08-27 Daniel BartonMerge remote-tracking branch 'origin/Release_2_8_1_Bran... tree | commitdiff
2013-08-27 Daniel BartonJAL-1358 RNAStructExportImport test file mirrors Disord... 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
2013-08-27 Daniel BartonJAL-1358 Just the eclipse project/classpath files so... tree | commitdiff
2013-08-14 Jim ProcterJAL-1354 replacement of bare strings in GUI dialogs... 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
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