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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-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	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	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
2021-09-03	Jim Procter	JAL-3829 refactored FilterOption provider to the StructureCh...	commit \| commitdiff \| tree
2021-09-02	Jim Procter	Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons	commit \| commitdiff \| tree
2021-09-02	Jim Procter	Merge branch 'cherry-pick/r2_11_2_JAL-3509' into develop	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3863 fix test and note about fragility	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3863 add canonical DBRefEntry flag to Jalview project	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 generalised Alphafold retrieval mechanism...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3863 mark first accession retrieved from Uniprot...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 Structure chooser specific FTS interface and...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	Merge branch 'feature/JAL-3855_ebi_alphafold_import...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 3d-beacons structure chooser logic (not yet...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 pulled out more of the FTS dependent parts...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 updated tests for 3db fetcher’s working FTS...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 proof in principle 3d-beacons sequence fetcher...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 3d-beacons has a custom alignment retrieval...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3674 Jmol seems to sometimes return a null for...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 fixed up the 3d-beacons data columns definitions...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 JAL-2176 - TODO re unused argument in FTSRestClientI	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 tidying up PDBFTSRestClient test responses...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 Javadoc for FTSColumnPreferences	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 pushed the PDBFTSClient specific code to new...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 removed unneeded attribute in FTS core	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 forgot to add in the dummy 3d-beacons db proxy	commit \| commitdiff \| tree
2021-07-27	Jim Procter	JAL-3674 Jmol seems to sometimes return a null for...	commit \| commitdiff \| tree
2021-07-27	Jim Procter	JAL-3855 suppress NPE when trying to retrieve SIFTS...	commit \| commitdiff \| tree
2021-07-27	Jim Procter	JAL-3855 ALPHAFOLD database source based on the PDB...	commit \| commitdiff \| tree
2021-07-27	Jim Procter	JAL-3855 check if an alpha fold ID and retrieve using...	commit \| commitdiff \| tree
2021-07-27	Jim Procter	JAL-3855 check for existence of an alpha fold model...	commit \| commitdiff \| tree
2021-07-27	Jim Procter	JAL-3855 convenience method to check a URL will return...	commit \| commitdiff \| tree
2021-06-09	Jim Procter	JAL-3840 don’t update the modal residue count for gaps	commit \| commitdiff \| tree
2021-06-09	Jim Procter	fixes JAL-3840	commit \| commitdiff \| tree
2021-06-09	Jim Procter	JAL-3840 failing test - show that addGaps overflows	commit \| commitdiff \| tree
2021-04-06	Jim Procter	JAL-3832 dummy 3d-beacons database client and code...	commit \| commitdiff \| tree
2021-02-17	Jim Procter	JAL-3821 patch for 2.11.2 to retrieve RNA ENA records...	commit \| commitdiff \| tree
2021-02-17	Jim Procter	Merge branch 'feature/JAL-3692enaEndpoint' into patch...	commit \| commitdiff \| tree
2020-11-13	Jim Procter	JAL-3757 JAL-3689 use AppletFormat.checkProtocol to...	commit \| commitdiff \| tree
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