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2021-12-15	Jim Procter	JAL-3933 configure root logger console appender to...	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
2021-09-21	Jim Procter	JAL-3829 alternative UX: need to select 3d-beacons...	commit \| commitdiff \| tree
2021-09-21	Jim Procter	JAL-3829 ignore the fake ID generated when a PDB format...	commit \| commitdiff \| tree
2021-09-20	Jim Procter	JAL-3829 updated response for P01308	commit \| commitdiff \| tree
2021-09-20	Jim Procter	JAL-3829 tests need to wait for dialog to be closed...	commit \| commitdiff \| tree
2021-09-20	Jim Procter	JAL-3829 TDBeacons fetcher needs a sequence with at...	commit \| commitdiff \| tree
2021-09-20	Jim Procter	JAL-3829 throw the exception even if it has no message	commit \| commitdiff \| tree
2021-09-20	Jim Procter	JAL-3829 ensure nulls are not wildcards when retrieving...	commit \| commitdiff \| tree
2021-09-20	Jim Procter	JAL-3829 do better at detecting structure type, prompt...	commit \| commitdiff \| tree
2021-09-20	Jim Procter	JAL-3829 make sure structure data type reflects actual...	commit \| commitdiff \| tree
2021-09-20	Jim Procter	JAL-3829 store 3db metadata on PDBEntry so it can be...	commit \| commitdiff \| tree
2021-09-20	Jim Procter	JAL-3829 allow PDBEntry with file and ID with mismatching...	commit \| commitdiff \| tree
2021-09-17	Jim Procter	Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons	commit \| commitdiff \| tree
2021-09-17	Jim Procter	JAL-3079 JAL-3055 remember to reset font transform...	commit \| commitdiff \| tree
2021-09-17	Jim Procter	JAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create...	commit \| commitdiff \| tree
2021-09-17	Jim Procter	JAL-3874 - replace Jmol with custom build of 14.31...	commit \| commitdiff \| tree
2021-09-17	Jim Procter	JAL-2226 transfer chain annotation when calcId, label...	commit \| commitdiff \| tree
2021-09-17	Jim Procter	JAL-2226 new method to search for annotation matching...	commit \| commitdiff \| tree
2021-09-17	Jim Procter	JAL-3829 belt and braces check to make sure there is...	commit \| commitdiff \| tree
2021-09-16	Jim Procter	Merge branch 'develop' into doc/JAL-3746_Release_2_11_2	commit \| commitdiff \| tree
2021-09-16	Jim Procter	JAL-3794 X and N are counted as DNA characters, but...	commit \| commitdiff \| tree
2021-09-16	Jim Procter	JAL-3794 new test for recognition of protein or DNA...	commit \| commitdiff \| tree
2021-09-15	Jim Procter	Merge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoA...	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3746 fix bad merge from 2.11.1.4/5 branch cherrypick	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3842 fix automatic what's new link for custom version...	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3842 2.11.1.5 what’s new, release notes, and version...	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3816 bump version number and cut release notes	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3766 cut new patch release	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3758 2.11.1.2 patch release notes and version bump	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3741 http to https (and jar to jvp for exampleFile...	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3477 added help documentation for executable jar...	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3675 version update and documentation for JAL-3493...	commit \| commitdiff \| tree
2021-09-15	Jim Procter	JAL-3638 JAL-3680 fix docs for Alt + Arrow LRUD in...	commit \| commitdiff \| tree
2021-09-15	Jim Procter	Merge branch 'develop' into releases/Release_2_11_2_Branch	commit \| commitdiff \| tree
2021-09-15	Jim Procter	Merge branch 'features/r2_11_2/JAL-3829_3dbeacons'...	commit \| commitdiff \| tree
2021-09-15	Jim Procter	Merge branch 'develop' into releases/Release_2_11_2_Branch	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3815 default /etc/jalview_properties under utils...	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3829 parallel not welcome here	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3829 test flakiness and human flakiness	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3829 more info on test fail - seems to be flaky	commit \| commitdiff \| tree
2021-09-14	Jim Procter	Merge branch 'develop' into releases/Release_2_11_2_Branch	commit \| commitdiff \| tree
2021-09-14	Jim Procter	Merge branch 'features/r2_11_2/JAL-3829_3dbeacons'...	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3551 - doc tweak	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3855 JAL-3829 better checks on PDB or mmCIF file...	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3829 JAL-3855 moved routing for retrieving structures...	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3829 JAL-3855 ignore case when detecting alphafold ID	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3855 detect an alphafold model and import its temperatur...	commit \| commitdiff \| tree
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