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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
2014-02-03	Jim Procter	Merge branch 'try_r20b1_merge' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-02-03	Jim Procter	Merge branch 'Release_2_8_1_Branch_i18n' into try_r20b1_merge	commit \| commitdiff \| tree
2014-02-03	Jim Procter	JAL-1358 JWS-69 add Daniel to the list of Jalview Authors	commit \| commitdiff \| tree
2014-02-03	Jim Procter	Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge	commit \| commitdiff \| tree
2014-02-03	Jim Procter	Merge branch 'JAL-957_jbake' into r281_JAL-957	commit \| commitdiff \| tree
2014-01-30	Jim Procter	JAL-1432 'whats new' and release history	commit \| commitdiff \| tree
2014-01-29	Jim Procter	JAL-957 reinstate jnetfile parameter	commit \| commitdiff \| tree
2014-01-29	Jim Procter	JAL-1432 patch broken comments in css	commit \| commitdiff \| tree
2014-01-29	Jim Procter	JAL-1432 natasha's name on applet author list	commit \| commitdiff \| tree
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	commit \| commitdiff \| tree
2014-01-29	Jim Procter	JAL-1432 AUTHORS file and updated authors properties...	commit \| commitdiff \| tree
2014-01-29	Jim Procter	JAL-1432 update dependency and licensing info	commit \| commitdiff \| tree
2014-01-29	Jim Procter	JAL-1432 bump version	commit \| commitdiff \| tree
2014-01-29	Jim Procter	Merge branch 'JAL-957_jbake' into Release_2_8_Branch	commit \| commitdiff \| tree
2014-01-29	Jim Procter	JAL-1400 added explanation about signed/unsigned applet...	commit \| commitdiff \| tree
2014-01-29	Jim Procter	JAL-970 JAL-1400 fixed layout	commit \| commitdiff \| tree
2014-01-28	Jim Procter	Merge branch 'JAL-957_jbake' into Release_2_8_Branch	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 reinstate the PDBfile parameter	commit \| commitdiff \| tree
2014-01-28	Jim Procter	Merge branch 'JAL-957_jbake' into Release_2_8_Branch	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-1400 sign the jnlp for arbitrary memory	commit \| commitdiff \| tree
2014-01-28	Jim Procter	Merge branch 'JAL-957_jbake' into Release_2_8_Branch	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 JAL-1400 only sign specific jar artefacts for...	commit \| commitdiff \| tree
2014-01-28	Jim Procter	Merge branch 'JAL-957_jbake' into Release_2_8_Branch	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 neater boilerplate link to signed/unsigned...	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 shorten title for linked applets example	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 removed cruft on appletParameters page	commit \| commitdiff \| tree
2014-01-28	Jim Procter	Merge branch 'JAL-957_jbake' into Release_2_8_Branch	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 make a copy of the applet/Jmol applet jars...	commit \| commitdiff \| tree
2014-01-28	Jim Procter	Merge branch 'JAL-1400_sandboxapp' into JAL-957_jbake	commit \| commitdiff \| tree
2014-01-28	Jim Procter	Merge branch 'JAL-957_jbake' into Release_2_8_Branch	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 permissions property for example pages (jbake...	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 unsigned applet demo pages created with jbake	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 tidier source and ensure permissions is explicitly...	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 new jbake-generated example pages	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 instructions on runnning Jbake to regenerate...	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 standardise formatting for example preamble	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 standard link to signed/unsigned demo pages...	commit \| commitdiff \| tree
2014-01-28	Jim Procter	JAL-957 tidy jbake directory	commit \| commitdiff \| tree
2014-01-27	Jim Procter	Merge branch 'JAL-1430_mfa_ext' into Release_2_8_Branch	commit \| commitdiff \| tree
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