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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
2021-11-19	Jim Procter	JAL-3926 disable autosearch by default	commit \| commitdiff \| tree
2021-11-08	Jim Procter	JAL-3855 verify pdb suffix is preserved when locally...	commit \| commitdiff \| tree
2021-11-08	Jim Procter	JAL-3855 JAL-1731 reuse the StructureViewer.fetchPdbFile...	commit \| commitdiff \| tree
2021-11-08	Jim Procter	JAL-3855 try harder to ignore DNA/RNA only structures...	commit \| commitdiff \| tree
2021-11-08	Jim Procter	JAL-3921 wait around until session file has been written	commit \| commitdiff \| tree
2021-11-05	Jim Procter	JAL-3829 remove duplicate IDs in 3DBeacons generated...	commit \| commitdiff \| tree
2021-11-05	Jim Procter	JAL-3829 format and tidy up unused code	commit \| commitdiff \| tree
2021-11-05	Jim Procter	JAL-3919 use model format field to ensure we get the...	commit \| commitdiff \| tree
2021-11-05	Jim Procter	JAL-3875 fully reset filter combo-box when fetch 3d...	commit \| commitdiff \| tree
2021-11-03	Jim Procter	JAL-3915 JAL-3746 documentation for removed rnaview...	commit \| commitdiff \| tree
2021-11-03	Jim Procter	JAL-3916 TODO for improved selection of covering structures	commit \| commitdiff \| tree
2021-11-03	Jim Procter	JAL-3916 TODO for improved selection of covering structures	commit \| commitdiff \| tree
2021-11-03	Jim Procter	JAL-3915 remove RNAview opts from preferences. Still...	commit \| commitdiff \| tree
2021-11-02	Jim Procter	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2021-11-02	Jim Procter	JAL-3875 test case and patch to verify the query 3d...	commit \| commitdiff \| tree
2021-10-18	Jim Procter	Merge branch 'bug/r2_11_2/JAL-3904_structureviewermenu...	commit \| commitdiff \| tree
2021-10-18	Jim Procter	JAL-3905 Fix: wait for response when sending mouseovers...	commit \| commitdiff \| tree
2021-10-18	Jim Procter	JAL-3904 override buildActionMenu to add in additional...	commit \| commitdiff \| tree
2021-10-18	Jim Procter	JAL-3904 failing test	commit \| commitdiff \| tree
2021-10-01	Jim Procter	JAL-3616 show name of structure viewer in ‘new view...	commit \| commitdiff \| tree
2021-10-01	Jim Procter	JAL-3616 explicit configure external viewer config	commit \| commitdiff \| tree
2021-10-01	Jim Procter	Merge branch 'develop' into releases/Release_2_11_2_Branch	commit \| commitdiff \| tree
2021-10-01	Jim Procter	Merge branch 'features/r2_11_2/JAL-3829_3dbeacons'...	commit \| commitdiff \| tree
2021-10-01	Jim Procter	JAL-3829 3d beacons logo - misi varadi gave permission...	commit \| commitdiff \| tree
2021-10-01	Jim Procter	Merge branch 'develop' into releases/Release_2_11_2_Branch	commit \| commitdiff \| tree
2021-10-01	Jim Procter	Merge branch 'features/r2_11_2/JAL-3829_3dbeacons'...	commit \| commitdiff \| tree
2021-10-01	Jim Procter	JAL-3829 fetch 3D beacons now started by clicking button...	commit \| commitdiff \| tree
2021-10-01	Jim Procter	Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons	commit \| commitdiff \| tree
2021-09-30	Jim Procter	Merge branch 'bug/JAL-3885_sequence_fetched_not_displaying_P...	commit \| commitdiff \| tree
2021-09-29	Jim Procter	JAL-3884 squish alarming but harmless errors when uniprot...	commit \| commitdiff \| tree
2021-09-29	Jim Procter	JAL-3881 split on any nonalphanumeric symbol (plus...	commit \| commitdiff \| tree
2021-09-29	Jim Procter	JAL-3829 report when 3d-beacons doesn’t provide any...	commit \| commitdiff \| tree
2021-09-27	Jim Procter	JAL-3746 update the example corefile for jalviewjs	commit \| commitdiff \| tree
2021-09-24	Jim Procter	JAL-3829 open web page for 3d beacons structure by...	commit \| commitdiff \| tree
2021-09-24	Jim Procter	Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons	commit \| commitdiff \| tree
2021-09-24	Jim Procter	Merge branch 'develop' into releases/Release_2_11_2_Branch	commit \| commitdiff \| tree
2021-09-24	Jim Procter	JAL-3821 data file for failing test	commit \| commitdiff \| tree
2021-09-24	Jim Procter	JAL-3829 right click to view popup menu to show link...	commit \| commitdiff \| tree
2021-09-24	Jim Procter	JAL-3829 abstract essential TDB metadata from the user...	commit \| commitdiff \| tree
2021-09-23	Jim Procter	Merge branch 'develop' into releases/Release_2_11_2_Branch	commit \| commitdiff \| tree
2021-09-23	Jim Procter	Merge branch 'features/r2_11_2/JAL-3821_reinstate_patch...	commit \| commitdiff \| tree
2021-09-23	Jim Procter	JAL-3821 less ambiguous base class name for EMBL and...	commit \| commitdiff \| tree
2021-09-23	Jim Procter	JAL-3821 ported to refactored FlatFile parser	commit \| commitdiff \| tree
2021-09-23	Jim Procter	JAL-3821 failing test	commit \| commitdiff \| tree
2021-09-23	Jim Procter	JAL-3692 JAL-3861 remove extra call to .parse() so...	commit \| commitdiff \| tree
2021-09-23	Jim Procter	Merge branch 'develop' into releases/Release_2_11_2_Branch	commit \| commitdiff \| tree
2021-09-23	Jim Procter	Merge branch 'patch/JAL-3874_newJmolAndGradleDedup...	commit \| commitdiff \| tree
2021-09-23	Jim Procter	Merge branch 'develop' into releases/Release_2_11_2_Branch	commit \| commitdiff \| tree
2021-09-21	Jim Procter	JAL-3746 release notes and what’s new for 2.11.2 -...	commit \| commitdiff \| tree
2021-09-21	Jim Procter	Merge branch 'doc/JAL-3746_Release_2_11_2' into develop	commit \| commitdiff \| tree
2021-09-21	Jim Procter	Merge branch 'features/r2_11_2/JAL-3829_3dbeacons'...	commit \| commitdiff \| tree
2021-09-21	Jim Procter	JAL-3829 - callback finessing - leave DBRefFetcher...	commit \| commitdiff \| tree
2021-09-21	Jim Procter	JAL-3829 prefix PDBe filters with PDBe to make clear...	commit \| commitdiff \| tree
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