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2021-09-30	Jim Procter	JAL-2909 pass a dummy sequence object to receive features...	commit \| commitdiff \| tree
2021-09-30	Jim Procter	JAL-2909 mininal merge of bam import demo to Jalview...	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-3821 data file for failing test	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 'patch/JAL-3874_newJmolAndGradleDedup...	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 'features/r2_11_2/JAL-3829_3dbeacons'...	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 '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
2021-09-14	Jim Procter	JAL-3829 move mock query and responses to files	commit \| commitdiff \| tree
2021-09-14	Jim Procter	Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons	commit \| commitdiff \| tree
2021-09-14	Jim Procter	Merge branch 'feature/JAL-2422ChimeraX' into develop	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3829 3d-beacons doesn’t work as a sequence source...	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3829 avoid sending rubbish to PDBe search api	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3829 some providers don’t provide model quality...	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3829 allow multiple URL mocks and include P01308...	commit \| commitdiff \| tree
2021-09-13	Jim Procter	Merge branch 'releases/Release_2_11_2_Branch' into...	commit \| commitdiff \| tree
2021-09-13	Jim Procter	Merge branch 'features/r2_11_2/JAL-3829_3dbeacons'...	commit \| commitdiff \| tree
2021-09-13	Jim Procter	Merge branch 'features/r2_11_2/JAL-3829_3dbeacons'...	commit \| commitdiff \| tree
2021-09-13	Jim Procter	JAL-3829 ensure unmock the FTS PDB and TDB clients...	commit \| commitdiff \| tree
2021-09-13	Jim Procter	JAL-3829 minimal test of additional TDB filters - not...	commit \| commitdiff \| tree
2021-09-13	Jim Procter	JAL-3829 select single best TDB structure and select...	commit \| commitdiff \| tree
2021-09-12	Jim Procter	JAL-3829 JalviewJS workarounds/patches	commit \| commitdiff \| tree
2021-09-12	Jim Procter	JAL-3829 upgrade Jmol to 14.31.53, SwingJS-JSMol to...	commit \| commitdiff \| tree
2021-09-11	Jim Procter	JAL-3829 ensure tests use mocked service - proper exception...	commit \| commitdiff \| tree
2021-09-11	Jim Procter	JAL-3829 patch failing tests and todo for future	commit \| commitdiff \| tree
2021-09-10	Jim Procter	JAL-3829 provide both PDBe queries and 3D-Beacons queries...	commit \| commitdiff \| tree
2021-09-10	Jim Procter	JAL-3829 insert title for structures from PDBe	commit \| commitdiff \| tree
2021-09-10	Jim Procter	JAL-3829 update for v1.0 3d-beacons api spec	commit \| commitdiff \| tree
2021-09-10	Jim Procter	JAL-3829 point at production 3d-beacons url	commit \| commitdiff \| tree
2021-09-08	Jim Procter	JAL-3829 refactor and JAL-3391 JAL-2935 first stab...	commit \| commitdiff \| tree
2021-09-08	Jim Procter	JAL-3829 allow client-side selection of structures...	commit \| commitdiff \| tree
2021-09-08	Jim Procter	JAL-3829 JAL-3868 TODO	commit \| commitdiff \| tree
2021-09-08	Jim Procter	JAL-3829 formatting	commit \| commitdiff \| tree
2021-09-08	Jim Procter	JAL-3829 integration test verifying mock response is...	commit \| commitdiff \| tree
2021-09-06	Jim Procter	JAL-3829 work in progress - look up additional metadata...	commit \| commitdiff \| tree
2021-09-06	Jim Procter	JAL-3829 look up column in FTS data	commit \| commitdiff \| tree
2021-09-06	Jim Procter	JAL-3829 mocking for PDBFTS for related query to UniprotFTS...	commit \| commitdiff \| tree
2021-09-06	Jim Procter	JAL-3829 pull out structure chooser query source tests...	commit \| commitdiff \| tree
2021-09-03	Jim Procter	JAL-3829 JAL-3865 test structure chooser queries to...	commit \| commitdiff \| tree
2021-09-03	Jim Procter	JAL-3829 use sequence dependent constructor for structure...	commit \| commitdiff \| tree
2021-09-03	Jim Procter	JAL-3829 mocking for testing 3D-Beacons FTS endpoint	commit \| commitdiff \| tree
2021-09-03	Jim Procter	JAL-3863 promote non-canonical version of dbref to...	commit \| commitdiff \| tree
2021-09-03	Jim Procter	JAL-3829 comments on the 3D structure chooser’s initialisati...	commit \| commitdiff \| tree
2021-09-03	Jim Procter	JAL-3865 isolate PDB and TDB clients and last query...	commit \| commitdiff \| tree
2021-09-03	Jim Procter	JAL-3863 passing test to verify a uniprot accession...	commit \| commitdiff \| tree
2021-09-03	Jim Procter	JAL-3829 JAL-3865 StructureChooserQuerySource implementation...	commit \| commitdiff \| tree
2021-09-03	Jim Procter	JAL-3855 don’t need to query Alphafold2 repository...	commit \| commitdiff \| tree
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