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JAL-1483 cut and paste from SW score model to allow scores based on sequences to...
[jalview.git]
/
src
/
2014-04-21
Jim Procter
JAL-1483 cut and paste from SW score model to allow...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1483 interface to allow score model to be parameter...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-967 abstract feature renderer
tree
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commitdiff
2014-04-21
Jim Procter
JAL-967 JAL-1482 new feature renderer api - needs more...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-736 hack to show the conserved property values...
tree
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commitdiff
2014-04-21
Jim Procter
avoid potential NPE
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1427 make sure we are working with dataset sequence...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1481 relevant todo re warning user for broken regex
tree
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commitdiff
2014-04-21
Jim Procter
JAL-741 (poss related JAL-971) - fix NPE raised when...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1476 JAL-1016 avoid NPE messiness if structures...
tree
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commitdiff
2014-04-21
Jim Procter
don't unhook existing group associated annotation JAL...
tree
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commitdiff
2014-04-21
Jim Procter
fix for JAL-1478
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1476 - don't send broken commands to Jmol when...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1477 first implementation of 'View all representati...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1466 import full length sequence to dataset sequenc...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1466 flag and jalview_properties setting to control...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1466 improved test and patched off by one that...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1466 new calculation menu option to recover the...
tree
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commitdiff
2014-04-21
Jim Procter
tidy imports
tree
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commitdiff
2014-04-21
Jim Procter
patch v2 for JAL-1474 add the newly recovered dataset...
tree
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commitdiff
2014-04-21
Jim Procter
patch v1 for JAL-1474 - make sure we actually set the...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1474 note about buggy 'merge sequence' operation...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1473 tree calcs performed with ScoreModelI instances
tree
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commitdiff
2014-04-21
Jim Procter
don't finness the alignment annotation modification...
tree
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commitdiff
2014-04-21
Jim Procter
patch for JAL-1465 - set min/max thresholds for each...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1473 menu entries for different score models availa...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1473 provide Amino acid physicochemical conservatio...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1473 show available score matrices for use in PCA...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1473 refactor score matrices and tree score calcula...
tree
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commitdiff
2014-04-06
Jim Procter
fix for JAL-1464 avoid NPE with per-sequence annotation...
tree
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commitdiff
2014-04-05
Jim Procter
Merge branch 'r281_JAL-1211' into Release_2_8_1_Branch
tree
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commitdiff
2014-04-04
Jim Procter
JAL-1211 - set annotation panel height according to...
tree
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commitdiff
2014-04-04
Jim Procter
JAL-1211 - pick up site-defined defined window geometry...
tree
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commitdiff
2014-04-04
Jim Procter
fix for JAL-1461 - check that filetype setting in brows...
tree
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commitdiff
2014-04-04
Jim Procter
Merge branch 'Release_2_8_1_Branch_i18n' into Release_2...
tree
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commitdiff
2014-04-04
Jim Procter
JAL-1335 typo and 'edit' action
tree
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commitdiff
2014-02-26
Jim Procter
fix for JAL-1226
tree
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commitdiff
2014-02-26
Jim Procter
JAL-1457 refactoring to explore why '-' appear in annot...
tree
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commitdiff
2014-02-26
Jim Procter
fix for JAL-686 - don't trim spaces before creating...
tree
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commitdiff
2014-02-25
Jim Procter
JAL-1355 typo in key
tree
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commitdiff
2014-02-25
Jim Procter
JAL-1454 catch exceptions during calculation and report...
tree
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commitdiff
2014-02-25
Jim Procter
JAL-1454 increase max for tqli iterations and throw...
tree
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commitdiff
2014-02-21
Jim Procter
patch for JAL-1449 - continuance of JAL-1364 - check...
tree
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commitdiff
2014-02-21
Jim Procter
JAL-1448 reinstate non-locale sensitive code for readin...
tree
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commitdiff
2014-02-21
Jim Procter
JAL-1354 typo
tree
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commitdiff
2014-02-21
Jim Procter
JAL-1354 use real var-args method signature to avoid...
tree
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commitdiff
2014-02-20
Jim Procter
Merge branch 'JAL-1447' into Release_2_8_1_Branch
tree
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commitdiff
2014-02-20
Jim Procter
JAL-1447 patch to correctly recognise FASTA files conta...
tree
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commitdiff
2014-02-18
Jim Procter
JAL-1445 (shift+) double click on feature type in deskt...
tree
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commitdiff
2014-02-18
Jim Procter
JAL-1446 use popup event trigger instead of right-click...
tree
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commitdiff
2014-02-17
Jim Procter
JAL-1445 added menu items to select containing/non...
tree
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commitdiff
2014-02-17
Jim Procter
JAL-1445 ported routine for selecting containing/non...
tree
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commitdiff
2014-02-17
Jim Procter
JAL-1445 expose columnSelection setter.
tree
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commitdiff
2014-02-17
Jim Procter
JAL-535 interface for GUI state update methods that...
tree
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commitdiff
2014-02-03
Jim Procter
Merge branch 'Release_2_8_1_Branch_i18n' into try_r20b1...
tree
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commitdiff
2014-02-03
Jim Procter
Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
tree
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commitdiff
2014-01-29
Jim Procter
JAL-1432 natasha's name on applet author list
tree
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commitdiff
2014-01-29
Jim Procter
JAL-1432 updated copyright notices
tree
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commitdiff
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 'Release_2_8_1_Branch' into Release_2_8_1_...
tree
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commitdiff
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
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
tree
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commitdiff
2014-01-07
Jim Procter
Merge branch 'fix_JAL-1423' into Release_2_8_1_Branch
tree
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commitdiff
2014-01-07
Jim Procter
JAL-1423 - console error reporting and graceful handlin...
tree
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commitdiff
2013-12-25
darolmar
JAL-1355 (basic i18n support)
tree
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commitdiff
2013-11-07
Jim Procter
Merge branch 'JAL-1286' into Release_2_8_1_Branch
tree
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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
2013-10-17
Jim Procter
fix for JAL-1398 - original colourscheme is enabled...
tree
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commitdiff
2013-10-17
Jim Procter
JAL-1233 TODO concerning the way we propagate annotatio...
tree
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commitdiff
2013-10-17
Jim Procter
JAL-1397 make sure annotation colourscheme is up to...
tree
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commitdiff
2013-10-17
Jim Procter
JAL-1397 store colour by sequence and originalColour...
tree
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commitdiff
2013-10-17
Jim Procter
JAL-1397 make sure ColourschemeI instances are up to...
tree
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commitdiff
2013-10-17
Jim Procter
JAL-1397 propagate any consensus/conservation coloursch...
tree
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commitdiff
2013-10-17
Jim Procter
JAL-1397 getters for originalColours flag
tree
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commitdiff
2013-10-16
Jim Procter
JAL-1395 do not calculate non-gap consensus when no...
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1164 regression on JAL-1292 use bitset to mark...
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1164 regression on JAL-1292 use bitset to mark...
tree
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commitdiff
2013-10-11
Jim Procter
Merge branch 'JAL-1164_disorderforselection' into Relea...
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1164 scope bySequence analysis methods to start...
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1114 javadoc
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1114 promote start/end attributes to gettable field...
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1114 API javadoc
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1164 only predict on currently selected sequences...
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1385 expose core view model methods in interface
tree
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commitdiff
2013-10-11
Jim Procter
JAL-1354 watch for exceptions when initialising (Securi...
tree
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commitdiff
2013-10-08
Jim Procter
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_...
tree
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commitdiff
2013-10-08
Jim Procter
JAL-1384 Create Group in selection popup menu
tree
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commitdiff
2013-10-08
Jim Procter
fix for JAL-1387
tree
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commitdiff
2013-10-08
Jim Procter
JAL-1384 documentation and consistent ordering for...
tree
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commitdiff
2013-10-08
Jim Procter
JAL-1384 group/ungroup sequences with command/ctrl...
tree
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commitdiff
2013-10-07
Jim Procter
JAL-1385 refactor logic to AlignmentViewController
tree
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commitdiff
2013-10-07
Jim Procter
JAL-1385 JAL-535 refactor sequence colour settings...
tree
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commitdiff
2013-10-07
Jim Procter
JAL-1385 expose core view model methods in interface
tree
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commitdiff
2013-10-07
Jim Procter
JAL-1385 Alignment view controller logic implementation...
tree
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commitdiff
2013-10-05
Jim Procter
JAL-1379 graceful degradation to legacy service when...
tree
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commitdiff
2013-10-05
Jim Procter
JAL-1379 JAL-1378 exclusion list property to ignore...
tree
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commitdiff
2013-10-05
Jim Procter
JAL-1378 hack to place 'Predictors' into Secondary...
tree
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commitdiff
2013-10-05
Jim Procter
JAL-1364 use gapMap to map RNAalifold annotation onto...
tree
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commitdiff
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