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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
2014-04-04	Jim Procter	fix for JAL-1461 - check that filetype setting in browser...	commit \| commitdiff \| tree
2014-04-04	Jim Procter	Merge branch 'Release_2_8_1_Branch_i18n' into Release_2_8_1_...	commit \| commitdiff \| tree
2014-04-04	Jim Procter	JAL-1335 typo and 'edit' action	commit \| commitdiff \| tree
2014-02-26	Jim Procter	Merge branch 'JAL-1226' into Release_2_8_1_Branch_i18n	commit \| commitdiff \| tree
2014-02-26	Jim Procter	Merge branch 'JAL-1226' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-02-26	Jim Procter	fix for JAL-1226	commit \| commitdiff \| tree
2014-02-26	Jim Procter	Merge branch 'JAL-686' into Release_2_8_1_Branch_i18n	commit \| commitdiff \| tree
2014-02-26	Jim Procter	Merge branch 'JAL-686' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-02-26	Jim Procter	JAL-1457 refactoring to explore why '-' appear in annotation...	commit \| commitdiff \| tree
2014-02-26	Jim Procter	fix for JAL-686 - don't trim spaces before creating...	commit \| commitdiff \| tree
2014-02-25	Jim Procter	Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branc...	commit \| commitdiff \| tree
2014-02-25	Jim Procter	Merge branch 'JAL-1454_patch' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-02-25	Jim Procter	JAL-1355 typo in key	commit \| commitdiff \| tree
2014-02-25	Jim Procter	Merge branch 'JAL-1454_patch' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-02-25	Jim Procter	JAL-1454 catch exceptions during calculation and report...	commit \| commitdiff \| tree
2014-02-25	Jim Procter	JAL-1454 increase max for tqli iterations and throw...	commit \| commitdiff \| tree
2014-02-21	Jim Procter	Merge branch 'JAL-1364_patch' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-02-21	Jim Procter	patch for JAL-1449 - continuance of JAL-1364 - check...	commit \| commitdiff \| tree
2014-02-21	Jim Procter	Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branc...	commit \| commitdiff \| tree
2014-02-21	Jim Procter	Merge branch 'pathc_JAL-1354' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-02-21	Jim Procter	JAL-1448 reinstate non-locale sensitive code for reading...	commit \| commitdiff \| tree
2014-02-21	Jim Procter	JAL-1354 typo	commit \| commitdiff \| tree
2014-02-21	Jim Procter	JAL-1354 use real var-args method signature to avoid...	commit \| commitdiff \| tree
2014-02-21	Jim Procter	JAL-1354 quoted format strings are not substituted	commit \| commitdiff \| tree
2014-02-20	Jim Procter	Merge branch 'JAL-1447' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-02-20	Jim Procter	JAL-1447 patch to correctly recognise FASTA files containing '*'	commit \| commitdiff \| tree
2014-02-20	Jim Procter	test and data for JAL-1447	commit \| commitdiff \| tree
2014-02-20	Jim Procter	JAL-1447 - more flexible testing for file format Identity...	commit \| commitdiff \| tree
2014-02-18	Jim Procter	Merge branch 'JAL-1445' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-02-18	Jim Procter	clear out 2.8.0b1 what's new and add JAL-1445 to list...	commit \| commitdiff \| tree
2014-02-18	Jim Procter	JAL-1445 basic help docs for feature	commit \| commitdiff \| tree
2014-02-18	Jim Procter	JAL-1445 JAL-1354 english strings for select by feature	commit \| commitdiff \| tree
2014-02-18	Jim Procter	JAL-1445 (shift+) double click on feature type in desktop...	commit \| commitdiff \| tree
2014-02-18	Jim Procter	JAL-1446 use popup event trigger instead of right-click...	commit \| commitdiff \| tree
2014-02-17	Jim Procter	JAL-1445 added menu items to select containing/non...	commit \| commitdiff \| tree
2014-02-17	Jim Procter	JAL-1445 ported routine for selecting containing/non...	commit \| commitdiff \| tree
2014-02-17	Jim Procter	JAL-1445 expose columnSelection setter.	commit \| commitdiff \| tree
2014-02-17	Jim Procter	JAL-535 interface for GUI state update methods that...	commit \| commitdiff \| tree
2014-02-17	Jim Procter	JAL-1445 groovy script demonstrating how to select...	commit \| commitdiff \| tree
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