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2022-03-04	Jim Procter	JAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and...	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disables...	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3746 JAL-3814 don’t automatically launch the news...	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3746 JAL-3814 NONEWS property	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3608 JAL-3830 tweaked the what’s new text and updated...	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3608 JAL-3830 simplified command line docs a bit	commit \| commitdiff \| tree
2022-03-04	Jim Procter	Merge branch 'doc/JAL-3608+JAL-3830_added_to_help_docs...	commit \| commitdiff \| tree
2022-03-02	Jim Procter	Merge branch 'bug/JAL-3962_awt_dll_problem' into develop	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 release notes for JAL-3867	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 release note for JAL-3907 building Jalview...	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 release note for JAL-3618 Vaqua config so...	commit \| commitdiff \| tree
2022-03-02	Jim Procter	Merge branch 'benreview/JAL-3691_for_2_11_2_getdownrebuilds...	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3594 release notes and mention jalview develop...	commit \| commitdiff \| tree
2022-03-02	Jim Procter	Release notes for JAL—3728 - waiting for ben to sign...	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3208 release notes and docs for setprop	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 release notes and cli arg docs for JAL-3530	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 release notes JAL-3391 JAL-3829 improved 3dbeacons...	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 release notes for JAL-3929	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 more what’s new	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3619 fix up error messages and try to bail quietly...	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3619 fix up warning message and minimal patch to...	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 what’s new..	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 release notes for JAL-3202 (JalviewJS)	commit \| commitdiff \| tree
2022-03-02	Jim Procter	JAL-3746 update release date and release notes/docs...	commit \| commitdiff \| tree
2022-02-28	Jim Procter	JAL-3746 more what’s new and release notes	commit \| commitdiff \| tree
2022-02-28	Jim Procter	JAL-3503 2.11.2.0 release notes and docs	commit \| commitdiff \| tree
2022-02-28	Jim Procter	JAL-3746 JAL-3551 update pymol docs and what’s new...	commit \| commitdiff \| tree
2022-02-28	Jim Procter	JAL-3746 document -no-annotation cli arg	commit \| commitdiff \| tree
2022-02-17	Jim Procter	Merge branch 'develop' into improvement/JAL-3830_install4j9_...	commit \| commitdiff \| tree
2022-02-17	Jim Procter	JAL-3551 patch superpose test for additional undo dis...	commit \| commitdiff \| tree
2022-02-17	Jim Procter	JAL-3823 JAL-3830 update gradle plugin for install4j...	commit \| commitdiff \| tree
2022-02-17	Jim Procter	Merge branch 'develop' into improvement/JAL-3830_install4j9_...	commit \| commitdiff \| tree
2022-02-17	Jim Procter	JAL-3959 add key retrieval urls that support CORS needed...	commit \| commitdiff \| tree
2022-02-17	Jim Procter	JAL-3746 more release notes and docs: JAL-3863 JAL...	commit \| commitdiff \| tree
2022-02-17	Jim Procter	JAL-3691 rebuilt getdown jars	commit \| commitdiff \| tree
2022-02-17	Jim Procter	JAL-3691 patch toUpper/toLower to use Locale.ROOT for...	commit \| commitdiff \| tree
2022-02-17	Jim Procter	JAL-3691 patch toUpper/toLower to use Locale.ROOT for...	commit \| commitdiff \| tree
2022-02-16	Jim Procter	JAL-3746 release notes.. in progress	commit \| commitdiff \| tree
2022-02-16	Jim Procter	JAL-3551 - wrap pair_fit with undo_disable and undo_enable	commit \| commitdiff \| tree
2022-02-16	Jim Procter	JAL-3837 GPL license on splashscreen (finally !) and...	commit \| commitdiff \| tree
2022-02-16	Jim Procter	JAL-3949 report Pymol XMLRPC port via log.info	commit \| commitdiff \| tree
2022-02-15	Jim Procter	JAL-1761 backbone type parameter for configuring which...	commit \| commitdiff \| tree
2022-02-15	Jim Procter	JAL-1761 need to pass molecule type when generating...	commit \| commitdiff \| tree
2022-02-15	Jim Procter	JAL-3551 patch test for altloc handling atom spec in...	commit \| commitdiff \| tree
2022-02-15	Jim Procter	JAL-1761 need to pass molecule type when generating...	commit \| commitdiff \| tree
2022-02-15	Jim Procter	JAL-3906 use indicate to highlight current mousedOver...	commit \| commitdiff \| tree
2022-02-15	Jim Procter	JAL-3746 update release date to later in Feb 2022	commit \| commitdiff \| tree
2022-02-15	Jim Procter	JAL-3551 pymol documentation	commit \| commitdiff \| tree
2022-02-14	Jim Procter	Merge branch 'task/r_2_11_2/JAL-3956_alphaFill_authoritative...	commit \| commitdiff \| tree
2022-02-14	Jim Procter	JAL-3551	commit \| commitdiff \| tree
2022-02-14	Jim Procter	JAL-3956 - PDBEntry objects constructed from 3D-Beacons...	commit \| commitdiff \| tree
2022-02-12	Jim Procter	Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sa...	commit \| commitdiff \| tree
2022-02-11	Jim Procter	JAL-3949 increase command line ops test timeout	commit \| commitdiff \| tree
2022-02-11	Jim Procter	JAL-3949 ensure Jalview command line ops setup actually...	commit \| commitdiff \| tree
2022-02-11	Jim Procter	Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sa...	commit \| commitdiff \| tree
2022-02-11	Jim Procter	JAL-3931 fix - escape % symbols after urlencoding	commit \| commitdiff \| tree
2022-02-11	Jim Procter	JAL-3949 - refactor logging from jalview.bin.Cache...	commit \| commitdiff \| tree
2022-02-10	Jim Procter	Merge branch 'bug/JAL-3523_cwd_not_preserved' into...	commit \| commitdiff \| tree
2022-02-07	Jim Procter	JAL-3186 remove ‘Variable Colour’ from the sequence...	commit \| commitdiff \| tree
2022-02-04	Jim Procter	Merge branch 'bug/JAL-3806_mappingCoversSequence_for2112...	commit \| commitdiff \| tree
2022-02-04	Jim Procter	JAL-3806 JAL-3725 update tests since CDS mappings now...	commit \| commitdiff \| tree
2022-02-04	Jim Procter	JAL-3806 require mapping extent covers both sequence...	commit \| commitdiff \| tree
2022-02-03	Jim Procter	JAL-3806 use the covers() test for each selected sequence...	commit \| commitdiff \| tree
2022-02-03	Jim Procter	JAL-3806 use same logic as for mouse over highlighting...	commit \| commitdiff \| tree
2022-02-03	Jim Procter	JAL-3806 todo - problem seems to be Protein:Many CDS...	commit \| commitdiff \| tree
2022-02-03	Jim Procter	JAL-2305 comments re testFindXrefSequences_withFetch...	commit \| commitdiff \| tree
2022-01-28	Jim Procter	JAL-3137 tests are for linux only	commit \| commitdiff \| tree
2022-01-28	Jim Procter	Merge branch 'merge/develop_JAL-3725' into develop	commit \| commitdiff \| tree
2022-01-27	Jim Procter	Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_...	commit \| commitdiff \| tree
2022-01-26	Jim Procter	JAL-3763 (for whatever reason) need to increase timeout...	commit \| commitdiff \| tree
2022-01-26	Jim Procter	JAL-3746 note about adding JAL-3700,JAL-3751,JAL-3763...	commit \| commitdiff \| tree
2022-01-26	Jim Procter	Merge branch 'merge/develop_task/JAL-3763_newDatasetForCds...	commit \| commitdiff \| tree
2022-01-26	Jim Procter	JAL-3763 (for whatever reason) need to increase timeout...	commit \| commitdiff \| tree
2022-01-26	Jim Procter	Merge branch 'task/JAL-3763_newDatasetForCds' into...	commit \| commitdiff \| tree
2022-01-26	gmungoc	JAL-3806 (2.11.2 version) more lax allowance (3 positions...	commit \| commitdiff \| tree
2022-01-26	Jim Procter	JAL-3806 JAL-3725 propagate relaxed criteria for stop...	commit \| commitdiff \| tree
2022-01-26	gmungoc	JAL-3725 restrict mapped virtual feature location to...	commit \| commitdiff \| tree
2022-01-26	gmungoc	JAL-3725 helper methods for computing mapped feature...	commit \| commitdiff \| tree
2022-01-26	gmungoc	JAL-3725 exclude stop codon from CDS-to-protein mapping	commit \| commitdiff \| tree
2022-01-18	Jim Procter	JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch...	commit \| commitdiff \| tree
2022-01-17	Jim Procter	JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch...	commit \| commitdiff \| tree
2022-01-17	Jim Procter	JAL-3746 possible release date 1st Feb 2022	commit \| commitdiff \| tree
2022-01-17	Jim Procter	JAL-3746 Release notes for patch JAL-3702 JAL-3915	commit \| commitdiff \| tree
2022-01-17	Jim Procter	Merge branch 'bug/JAL-3703_saving_a_file_in_Windows_10_fails...	commit \| commitdiff \| tree
2022-01-06	Jim Procter	JAL-3746 update release history for 2.11.1.5 and 2...	commit \| commitdiff \| tree
2022-01-06	Jim Procter	Merge branch 'critical/JAL-3933_log4j_update_for_develop_bra...	commit \| commitdiff \| tree
2021-12-15	Jim Procter	JAL-3933 remove obsolete Castor logging configuration	commit \| commitdiff \| tree
2021-12-15	Jim Procter	JAL-3933 configure root logger console appender to...	commit \| commitdiff \| tree
2021-12-13	Jim Procter	JAL-3829 isCanonical should by default be false - ensure...	commit \| commitdiff \| tree
2021-12-13	Jim Procter	JAL-3855 JAL-3829 don’t need to make up alphafold model...	commit \| commitdiff \| tree
2021-12-13	Jim Procter	JAL-3929 preserve lowercase pdbid in group name for...	commit \| commitdiff \| tree
2021-12-08	Jim Procter	Merge branch 'to_merge/r2_11_2/JAL-3904_improved_alignpanelA...	commit \| commitdiff \| tree
2021-12-08	Jim Procter	JAL-3551 pymol docs - work in progress	commit \| commitdiff \| tree
2021-12-08	Jim Procter	JAL-3929 don’t use the url encoded pdbId in feature...	commit \| commitdiff \| tree
2021-12-08	Jim Procter	JAL-3616 update messages/tooltips/menu items to use...	commit \| commitdiff \| tree
2021-12-08	Jim Procter	JAL-3551 JAL-3931 view pymol commands/responses in...	commit \| commitdiff \| tree
2021-12-08	Jim Procter	JAL-3931 remove % and - from ids so Pymol doesn’t strip...	commit \| commitdiff \| tree
2021-12-08	Jim Procter	JAL-3929 URLencode pdbid to remove problematic characters...	commit \| commitdiff \| tree
2021-12-02	Jim Procter	JAL-3904 use new AlignPanel API method	commit \| commitdiff \| tree
2021-12-02	Jim Procter	JAL-3904 simple method to make an alignPanel the currently...	commit \| commitdiff \| tree
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