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Merge branch 'JAL-1422_srs_r281' into Release_2_8_1_Branch
[jalview.git]
/
src
/
jalview
/
2014-01-13
Jim Procter
Merge branch 'JAL-1422_srs' into JAL-1422_srs_r281
tree
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commitdiff
2014-01-13
Jim Procter
JAL-1422 update any existing configuration to replace...
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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
Merge branch 'fix_JAL-1423' into Release_2_8_1_Branch
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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
Merge branch 'JAL-1286' into Release_2_8_1_Branch
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commitdiff
2013-11-07
Jim Procter
JAL-1286 check if local file ends with .gz and opens...
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commitdiff
2013-10-17
Jim Procter
fix for JAL-1398 - original colourscheme is enabled...
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commitdiff
2013-10-17
Jim Procter
JAL-1233 TODO concerning the way we propagate annotatio...
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commitdiff
2013-10-17
Jim Procter
JAL-1397 make sure annotation colourscheme is up to...
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commitdiff
2013-10-17
Jim Procter
JAL-1397 store colour by sequence and originalColour...
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commitdiff
2013-10-17
Jim Procter
JAL-1397 make sure ColourschemeI instances are up to...
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commitdiff
2013-10-17
Jim Procter
JAL-1397 propagate any consensus/conservation coloursch...
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commitdiff
2013-10-17
Jim Procter
JAL-1397 getters for originalColours flag
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commitdiff
2013-10-16
Jim Procter
JAL-1395 do not calculate non-gap consensus when no...
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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 regression on JAL-1292 use bitset to mark...
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commitdiff
2013-10-11
Jim Procter
Merge branch 'JAL-1164_disorderforselection' into Relea...
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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
2013-10-11
Jim Procter
JAL-1354 watch for exceptions when initialising (Securi...
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commitdiff
2013-10-08
Jim Procter
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_...
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commitdiff
2013-10-08
Jim Procter
JAL-1384 Create Group in selection popup menu
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commitdiff
2013-10-08
Jim Procter
fix for JAL-1387
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commitdiff
2013-10-08
Jim Procter
JAL-1384 documentation and consistent ordering for...
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commitdiff
2013-10-08
Jim Procter
JAL-1384 group/ungroup sequences with command/ctrl...
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commitdiff
2013-10-07
Jim Procter
JAL-1385 refactor logic to AlignmentViewController
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commitdiff
2013-10-07
Jim Procter
JAL-1385 JAL-535 refactor sequence colour settings...
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commitdiff
2013-10-07
Jim Procter
JAL-1385 expose core view model methods in interface
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commitdiff
2013-10-07
Jim Procter
JAL-1385 Alignment view controller logic implementation...
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commitdiff
2013-10-05
Jim Procter
JAL-1379 graceful degradation to legacy service when...
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commitdiff
2013-10-05
Jim Procter
JAL-1379 JAL-1378 exclusion list property to ignore...
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commitdiff
2013-10-05
Jim Procter
JAL-1378 hack to place 'Predictors' into Secondary...
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commitdiff
2013-10-05
Jim Procter
JAL-1364 use gapMap to map RNAalifold annotation onto...
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commitdiff
2013-10-05
Jim Procter
JAL-1379 JAL-1358 only enable/disable menu entries...
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commitdiff
2013-10-04
Jim Procter
JAL-1383 - disable startup of the Envision2 workflow...
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commitdiff
2013-10-04
Jim Procter
JAL-940 JAL-1378 EOL comment on JWS v1 services
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commitdiff
2013-10-04
Jim Procter
Merge branch 'RNAalifold' into Release_2_8_1_Branch
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commitdiff
2013-10-04
Jim Procter
fix for JAL-1380 and efficiency todo for JAL-1381
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commitdiff
2013-10-04
Jim Procter
JAL-1378 JWS-71 update to from-source build of JABA...
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commitdiff
2013-09-25
Jim Procter
JAL-1365 unified GUI building for AACon and RNAAliFold...
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commitdiff
2013-09-25
Jim Procter
JAL-1365 use AlignAnalysisUIText class to provide metad...
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commitdiff
2013-09-25
Jim Procter
JAL-1365 refactored core methods from RNAAliFold and...
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commitdiff
2013-09-25
Jim Procter
JAL-1365 new metadata class to describe instantaneous...
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commitdiff
2013-09-25
Jim Procter
JAL-1270 nominal jalview version string for projects...
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commitdiff
2013-09-25
Jim Procter
JAL-1270 Desktop.instance is null during headless jalvi...
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commitdiff
2013-09-20
Jim Procter
formatting
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commitdiff
2013-09-18
Jim Procter
JAL-1355 - fix compilation errors: typos and missing...
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commitdiff
2013-09-03
Jim Procter
Merge branch 'JAL-1373_precision' into RNAalifold
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commitdiff
2013-09-03
Jim Procter
JAL-1373 tweak precision calculation so alignments...
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commitdiff
2013-09-03
Jim Procter
JAL-920 compute a consensus for single sequence
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commitdiff
2013-09-02
Jim Procter
JAL-1373 JAL-520 wrap tooltips for columns in annotatio...
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commitdiff
2013-09-02
Jim Procter
JAL-1373 generate percentages with appropriate precision
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commitdiff
2013-09-02
Jim Procter
JAL-1373 pass size of sequence set to consensus renderi...
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commitdiff
2013-08-30
Daniel Barton
Colour be RNA helices bug fixed
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commitdiff
2013-08-30
Daniel Barton
JAL-1358 Cleaned up RNAalifoldClient.java. RNA helices...
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commitdiff
2013-08-30
darolmar
i18n date/time handling
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commitdiff
2013-08-29
darolmar
i18n
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commitdiff
2013-08-28
Daniel Barton
RNAalifoldClient updated to be more like AAConClient...
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commitdiff
2013-08-27
Daniel Barton
JAL-1358 jalview displays some RNA struture annotation...
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commitdiff
2013-08-27
Jim Procter
JAL-1359 simpler logic for deciding if all threads...
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commitdiff
2013-08-27
Daniel Barton
Merge remote-tracking branch 'origin/Release_2_8_1_Bran...
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commitdiff
2013-08-27
Daniel Barton
JAL-1358 RNAStructExportImport test file mirrors Disord...
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commitdiff
2013-08-27
Jim Procter
JAL-1332 regression from 7ce72ca7fadf35a249427ecb836b22...
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commitdiff
2013-08-27
Jim Procter
JAL-1332 - defer SSM provision to root provider for...
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commitdiff
2013-08-27
Daniel Barton
JAL-1358 Just the eclipse project/classpath files so...
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commitdiff
2013-08-14
Jim Procter
JAL-1354 replacement of bare strings in GUI dialogs...
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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
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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
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commitdiff
2013-06-23
Jim Procter
Merge commit '72c628b' into Release_2_8_Branch
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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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