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2014-05-12	Jim Procter	Merge branch 'JAL-1397' into JAL-1372_referenceseq	commit \| commitdiff \| tree
2014-05-12	Jim Procter	JAL-1397 catch other random version strings	commit \| commitdiff \| tree
2014-05-12	Jim Procter	patch for regression introduced JAL-1397	commit \| commitdiff \| tree
2014-05-02	Jim Procter	Merge branch 'Release_2_8_1_Branch' into JAL-1372_referenceseq	commit \| commitdiff \| tree
2014-05-02	Jim Procter	Merge branch 'JAL-1397' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-05-02	Jim Procter	JAL-1397 JAL-1066 JAL-1233 refactored annotation colours...	commit \| commitdiff \| tree
2014-05-02	Jim Procter	JAL-1369 JAL-1397 version check to support correct...	commit \| commitdiff \| tree
2014-05-02	Jim Procter	formatting	commit \| commitdiff \| tree
2014-05-02	Jim Procter	JAL-1233 JAL-1066 fix for JAL-1397 test: allow per...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-1397 (probably buggy) test for recovery of background...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	remove todo	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-1492 formatting and squash NPEs	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-1092 TODO - allow Jalview/JalviewLite to generate...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-1492 JAL-1397 make AnnotatedCollectionI context...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-1492 JAL-1397 JAL-643 JAL-969 factory method to...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-1492 JAL-1397 JAL-643 JAL-969 modifiable flag on...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	javadoc	commit \| commitdiff \| tree
2014-05-01	Jim Procter	properly quit so JUnit marks tests as successful	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-1497 check to see if tree structure is ready for...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	fix for JAL-1495 - initialise menu entry from current...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	fix for JAL-1494 tweaked logic to fix NPEs and modify...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-969 remove unnecessary overrides	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-961 configure conservation worker from alignment...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	JAL-961 store result of conservation analysis worker...	commit \| commitdiff \| tree
2014-05-01	Jim Procter	make sure valid value for non-gapped calculation with...	commit \| commitdiff \| tree
2014-04-29	Jim Procter	Merge branch 'JAL-1340_redundancy' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-28	Jim Procter	JAL-1340 mark redundant sequences as soon as redundancy...	commit \| commitdiff \| tree
2014-04-28	Jim Procter	JAL-1340 simpler and more efficient interactive highlighting...	commit \| commitdiff \| tree
2014-04-28	Jim Procter	JAL-1340 ensure slider value wide enough to see three...	commit \| commitdiff \| tree
2014-04-27	Jim Procter	Merge branch 'JAL-1322' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-27	Jim Procter	JAL-1322 avoid rounding error causing non functional...	commit \| commitdiff \| tree
2014-04-27	Jim Procter	JAL-1322 allow slider to reach maximum value for parameter	commit \| commitdiff \| tree
2014-04-27	Jim Procter	JAL-1322 only update slider when return is pressed	commit \| commitdiff \| tree
2014-04-27	Jim Procter	Merge branch 'JAL-952_rnahelix' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-27	Jim Procter	Merge branch 'JAL-1164_regression' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-27	Jim Procter	workaround for JAL-1319 - catch unexpected NPE thrown...	commit \| commitdiff \| tree
2014-04-27	Jim Procter	JAL-1164 (regression) reinstate 'apply disorder prediction...	commit \| commitdiff \| tree
2014-04-27	Jim Procter	JAL-952 JAL-1268 document TCoffee and RNA helices coloursche...	commit \| commitdiff \| tree
2014-04-27	Jim Procter	JAL-952 JAL-1268 document RNA Helices and T-Coffee...	commit \| commitdiff \| tree
2014-04-27	Jim Procter	JAL-952 JAL-1268 add RNA Helices and T-Coffee to list...	commit \| commitdiff \| tree
2014-04-27	Jim Procter	JAL-952 resolve colour scheme as 'RNA Helices'	commit \| commitdiff \| tree
2014-04-27	Jim Procter	JAL-952 refactor code to select annotation for colouring...	commit \| commitdiff \| tree
2014-04-27	Jim Procter	test for JAL-952	commit \| commitdiff \| tree
2014-04-25	Jim Procter	Merge branch 'JAL-1177_prop_rnasecstr' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-25	Jim Procter	fix for JAL-1268	commit \| commitdiff \| tree
2014-04-25	Jim Procter	test for JAL-1268	commit \| commitdiff \| tree
2014-04-25	Jim Procter	JAL-1177 additional saveState calls to write a dataset...	commit \| commitdiff \| tree
2014-04-25	Jim Procter	JAL-1177 patches to loader to cope with dataset only...	commit \| commitdiff \| tree
2014-04-25	Jim Procter	JAL-1177 new flag to write a dataset only jalview XML...	commit \| commitdiff \| tree
2014-04-25	Jim Procter	JAL-1177 allow jalview alignments to be saved that...	commit \| commitdiff \| tree
2014-04-25	Jim Procter	JAL-1177 propagate sequence associated annotation to...	commit \| commitdiff \| tree
2014-04-25	Jim Procter	JAL-1177 refactored command line test harness	commit \| commitdiff \| tree
2014-04-25	Jim Procter	test for JAL-1177 store and recover RNA secondary structure...	commit \| commitdiff \| tree
2014-04-24	Jim Procter	JAL-1232 fix - ensure display all columns flag is set...	commit \| commitdiff \| tree
2014-04-23	Jim Procter	Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-23	Jim Procter	JAL-1486 todo for 2.8.2 release	commit \| commitdiff \| tree
2014-04-23	Jim Procter	Merge branch 'jims_marckhacks' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1458 updated logo for installer	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1383 scrubbed envision GUI and documentation	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1355 keys for colours	commit \| commitdiff \| tree
2014-04-21	Jim Procter	fix for JAL-1438	commit \| commitdiff \| tree
2014-04-21	Jim Procter	Merge branch 'jims_marckhacks' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1473 define defaults for DNA/Protein PCA calculation	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1485 JAL-1483 show i18n key for different available...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1473 JAL-1355 i18n for score model submenu	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1485 JAL-1473 use compound i18n messages to construct...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1485	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1484 always update the dataset sequence if 'trimDatasetS...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1466 don't include empty columns if no upstream...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1355 JAL-1466 i18n for flanking sequence menu entry...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	Merge branch 'jims_marckhacks' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-741 (poss related JAL-971) - fix NPE raised when...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1476 JAL-1016 avoid NPE messiness if structures...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	don't unhook existing group associated annotation JAL...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	fix for JAL-1478	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1478 test to demonstrate bug	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1477 tooltip	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1476 - don't send broken commands to Jmol when...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1477 first implementation of 'View all representative...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1466 import full length sequence to dataset sequence...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1466 flag and jalview_properties setting to control...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1466 improved test and patched off by one that...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1466 new calculation menu option to recover the...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	tidy imports	commit \| commitdiff \| tree
2014-04-21	Jim Procter	patch v2 for JAL-1474 add the newly recovered dataset...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	patch v1 for JAL-1474 - make sure we actually set the...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1474 note about buggy 'merge sequence' operation...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1473 tree calcs performed with ScoreModelI instances	commit \| commitdiff \| tree
2014-04-21	Jim Procter	don't finness the alignment annotation modification...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	patch for JAL-1465 - set min/max thresholds for each...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1473 menu entries for different score models available...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1473 provide Amino acid physicochemical conservation...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1473 show available score matrices for use in PCA...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1473 refactor score matrices and tree score calculations...	commit \| commitdiff \| tree
2014-04-21	Jim Procter	JAL-1355 missing message	commit \| commitdiff \| tree
2014-04-06	Jim Procter	fix for JAL-1464 avoid NPE with per-sequence annotation...	commit \| commitdiff \| tree
2014-04-05	Jim Procter	Merge branch 'r281_JAL-1211' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-04-04	Jim Procter	JAL-1211 - set annotation panel height according to...	commit \| commitdiff \| tree
2014-04-04	Jim Procter	JAL-1211 - pick up site-defined defined window geometry...	commit \| commitdiff \| tree
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