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Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
[jalview.git]
/
src
/
2014-06-04
Jim Procter
JAL-1355 key typo
tree
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commitdiff
2014-06-03
Jim Procter
JAL-690 jvp rather than jar for save/restore state...
tree
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commitdiff
2014-06-03
Jim Procter
JAL-690 JAL-1503 update file types/extensions in Jalvie...
tree
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commitdiff
2014-06-03
Jim Procter
JAL-1473 exclude score models not compatible with PCA...
tree
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commitdiff
2014-06-03
Jim Procter
JAL-690 add .jvp as default jalview project filetype
tree
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commitdiff
2014-06-03
Jim Procter
JAL-1512 comment out for 2.8.1 release
tree
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commitdiff
2014-06-03
Jim Procter
JAL-1512 fix calculation once again and include score...
tree
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commitdiff
2014-06-03
Jim Procter
JAL-1473 make it easier to generate HTML documentation...
tree
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commitdiff
2014-06-02
Jim Procter
JAL-1512 rejig buggy conservation-basesd score matrix...
tree
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commitdiff
2014-05-28
Jim Procter
JAL-1507 bugfix
tree
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commitdiff
2014-05-27
Jim Procter
JAL-1507 added loop to throw dummy javascript calls...
tree
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commitdiff
2014-05-27
Jim Procter
JAL-1402 conditional logic to ensure annotation & label...
tree
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commitdiff
2014-05-27
Jim Procter
JAL-1508 make default font size 11pt for embedded menus...
tree
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commitdiff
2014-05-23
Jim Procter
JAL-1445 extend functionality to select or toggle selec...
tree
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commitdiff
2014-05-22
Jim Procter
JAL-1503 update version in GPL header
tree
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commitdiff
2014-05-13
Jim Procter
JAL-1239 cancelled flag should be checked and counted
tree
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commitdiff
2014-05-13
Jim Procter
JAL-1239 make doubly sure sub job status is set to...
tree
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commitdiff
2014-05-12
Jim Procter
JAL-1397 catch other random version strings
tree
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commitdiff
2014-05-12
Jim Procter
patch for regression introduced JAL-1397
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commitdiff
2014-05-02
Jim Procter
JAL-1397 JAL-1066 JAL-1233 refactored annotation colour...
tree
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commitdiff
2014-05-02
Jim Procter
JAL-1369 JAL-1397 version check to support correct...
tree
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commitdiff
2014-05-02
Jim Procter
formatting
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commitdiff
2014-05-02
Jim Procter
JAL-1233 JAL-1066 fix for JAL-1397 test: allow per...
tree
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commitdiff
2014-05-01
Jim Procter
remove todo
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commitdiff
2014-05-01
Jim Procter
JAL-1492 formatting and squash NPEs
tree
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commitdiff
2014-05-01
Jim Procter
JAL-1092 TODO - allow Jalview/JalviewLite to generate...
tree
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commitdiff
2014-05-01
Jim Procter
JAL-1492 JAL-1397 make AnnotatedCollectionI context...
tree
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commitdiff
2014-05-01
Jim Procter
JAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and...
tree
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commitdiff
2014-05-01
Jim Procter
JAL-1492 JAL-1397 JAL-643 JAL-969 factory method to...
tree
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commitdiff
2014-05-01
Jim Procter
JAL-1492 JAL-1397 JAL-643 JAL-969 modifiable flag on...
tree
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commitdiff
2014-05-01
Jim Procter
javadoc
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commitdiff
2014-05-01
Jim Procter
JAL-1497 check to see if tree structure is ready for...
tree
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commitdiff
2014-05-01
Jim Procter
fix for JAL-1495 - initialise menu entry from current...
tree
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commitdiff
2014-05-01
Jim Procter
fix for JAL-1494 tweaked logic to fix NPEs and modify...
tree
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commitdiff
2014-05-01
Jim Procter
JAL-969 remove unnecessary overrides
tree
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commitdiff
2014-05-01
Jim Procter
JAL-961 configure conservation worker from alignment...
tree
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commitdiff
2014-05-01
Jim Procter
JAL-961 store result of conservation analysis worker...
tree
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commitdiff
2014-05-01
Jim Procter
make sure valid value for non-gapped calculation with...
tree
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commitdiff
2014-04-29
Jim Procter
JAL-643 - abstracted colourscheme components to allow...
tree
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commitdiff
2014-04-28
Jim Procter
JAL-1340 mark redundant sequences as soon as redundancy...
tree
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commitdiff
2014-04-28
Jim Procter
JAL-1340 simpler and more efficient interactive highlig...
tree
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commitdiff
2014-04-28
Jim Procter
JAL-1340 ensure slider value wide enough to see three...
tree
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commitdiff
2014-04-27
Jim Procter
JAL-1322 avoid rounding error causing non functional...
tree
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commitdiff
2014-04-27
Jim Procter
JAL-1322 allow slider to reach maximum value for parameter
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commitdiff
2014-04-27
Jim Procter
JAL-1322 only update slider when return is pressed
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commitdiff
2014-04-27
Jim Procter
Merge branch 'JAL-952_rnahelix' into Release_2_8_1_Branch
tree
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commitdiff
2014-04-27
Jim Procter
workaround for JAL-1319 - catch unexpected NPE thrown...
tree
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commitdiff
2014-04-27
Jim Procter
JAL-1164 (regression) reinstate 'apply disorder predict...
tree
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commitdiff
2014-04-27
Jim Procter
JAL-952 JAL-1268 add RNA Helices and T-Coffee to list...
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commitdiff
2014-04-27
Jim Procter
JAL-952 resolve colour scheme as 'RNA Helices'
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commitdiff
2014-04-27
Jim Procter
JAL-952 refactor code to select annotation for colourin...
tree
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commitdiff
2014-04-25
Jim Procter
fix for JAL-1268
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commitdiff
2014-04-25
Jim Procter
JAL-1177 additional saveState calls to write a dataset...
tree
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commitdiff
2014-04-25
Jim Procter
JAL-1177 patches to loader to cope with dataset only...
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commitdiff
2014-04-25
Jim Procter
JAL-1177 new flag to write a dataset only jalview XML...
tree
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commitdiff
2014-04-25
Jim Procter
JAL-1177 allow jalview alignments to be saved that...
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commitdiff
2014-04-25
Jim Procter
JAL-1177 propagate sequence associated annotation to...
tree
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commitdiff
2014-04-24
Jim Procter
JAL-1232 fix - ensure display all columns flag is set...
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commitdiff
2014-04-23
Jim Procter
Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8...
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commitdiff
2014-04-23
Jim Procter
Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8...
tree
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commitdiff
2014-04-23
Jim Procter
JAL-1486 todo for 2.8.2 release
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1383 scrubbed envision GUI and documentation
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1355 keys for colours
tree
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commitdiff
2014-04-21
Jim Procter
fix for JAL-1438
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1473 define defaults for DNA/Protein PCA calculation
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1485 JAL-1483 show i18n key for different available...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1473 JAL-1355 i18n for score model submenu
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1485 JAL-1473 use compound i18n messages to constru...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1485
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commitdiff
2014-04-21
Jim Procter
JAL-1484 always update the dataset sequence if 'trimDat...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1466 don't include empty columns if no upstream...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1355 JAL-1466 i18n for flanking sequence menu entry...
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...
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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
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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
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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...
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commitdiff
2014-04-21
Jim Procter
JAL-1473 show available score matrices for use in PCA...
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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
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commitdiff
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