structurechooser

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JAL-3829 remove duplicate IDs in 3DBeacons generated PDBFTS query and update mocks

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 format and tidy up unused code

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    ./ThreeDBStructureChooserQuerySource.java
JAL-3919 use model format field to ensure we get the file extension correct when creating temp files for structure viewers

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3916 TODO for improved selection of covering structures

JAL-3829 open web page for 3d beacons structure by right-clicking and selecting pop up menu item

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 abstract essential TDB metadata from the user configurable data array displayed in the JTable

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 prefix PDBe filters with PDBe to make clear what they search

JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need to be fetched

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    ./StructureChooserQuerySource.java
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JAL-3829 TDBeacons fetcher needs a sequence with at least one canonical uniprot accession

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JAL-3829 do better at detecting structure type, prompt to retrieve Uniprot ids for proteins without canonical Ids and show provider in the Structure Chooser’s cache view

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 belt and braces check to make sure there is a pdbe response available to join records from

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    ./ThreeDBStructureChooserQuerySource.java
JAL-3855 JAL-3829 better checks on PDB or mmCIF file based on URL path (though should really determine when processing via jmolData now we have mechanism) - ChimeraX in particular cares about file endings

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 avoid sending rubbish to PDBe search api

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    ./ThreeDBStructureChooserQuerySource.java
JAL-3829 some providers don’t provide model quality, some experimental methods don’t provide a resolution - try to leave these in their natural order

JAL-3829 select single best TDB structure and select structures from particular provider (this code is horrific !)

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 provide both PDBe queries and 3D-Beacons queries in the filter combo box

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    ./PDBStructureChooserQuerySource.java
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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 insert title for structures from PDBe

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 update for v1.0 3d-beacons api spec

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JAL-3829 refactor and JAL-3391 JAL-2935 first stab at coverage based selection of models for a sequence

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    ./TDBResultAnalyser.java
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    ./ThreeDBStructureChooserQuerySource.java
JAL-3829 allow client-side selection of structures for a sequence by passing in discovered structures

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 work in progress - look up additional metadata from PDBe for structures discovered via TDBFTS

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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3865 isolate PDB and TDB clients and last query records in their query objects

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    ./PDBStructureChooserQuerySource.java
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    ./ThreeDBStructureChooserQuerySource.java
JAL-3829 JAL-3865 StructureChooserQuerySource implementation now dependent on the type of sequences and whether they have uniprot sequence IDs

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JAL-3829 refactored FilterOption provider to the StructureChooserQuerySource implementation - implementation now is completely independent of GUI code.

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    ./PDBStructureChooserQuerySource.java
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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3929 Structure chooser specific FTS interface and query source logic for PDBe and 3D-Beacons

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    ./PDBStructureChooserQuerySource.java
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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3829 Structure chooser specific FTS interface and query source logic for PDBe and 3D-Beacons

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    ./PDBStructureChooserQuerySource.java
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    ./ThreeDBStructureChooserQuerySource.java
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JAL-3929 3d-beacons structure chooser logic (not yet finished)

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    ./StructureChooserQuerySource.java
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JAL-3829 3d-beacons structure chooser logic (not yet finished)

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    ./StructureChooserQuerySource.java
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