jalview

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JAL-3829 mocking for PDBFTS for related query to UniprotFTS mock.

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    /src/jalview/fts/core/FTSRestClient.java
JAL-3829 pull out structure chooser query source tests to new class

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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 JAL-3865 test structure chooser queries to mocked 3D Beacons FTS

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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 use sequence dependent constructor for structure chooser query engine testing

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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 mocking for testing 3D-Beacons FTS endpoint

JAL-3863 promote non-canonical version of dbref to a canonical one

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    /src/jalview/datamodel/DBRefEntry.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-3785 renaming, adding to interface, tidying

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    /src/jalview/httpserver/HttpServer.java
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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/AbstractEndpointAsync.java
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    /src/jalview/rest/EndpointAsync.java
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    /src/jalview/rest/FetchSequenceEndpoint.java
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    /src/jalview/rest/FetchSequencesEndpoint.java
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    /src/jalview/rest/InputAlignmentEndpoint.java
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    /src/jalview/rest/OpenAlignmentEndpoint.java
JAL-3829 comments on the 3D structure chooser’s initialisation process

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    /src/jalview/gui/StructureChooser.java
JAL-3865 isolate PDB and TDB clients and last query records in their query objects

JAL-3863 passing test to verify a uniprot accession with canonical flag set is transferred via the DBRefFetcher (and the SequenceI.transferAnnotation method it calls)

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    /src/jalview/datamodel/DBRefEntry.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-3878 Create Slivka Web Service adapter.

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    /src/jalview/ws2/slivka/SlivkaWS.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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    /src/jalview/gui/StructureChooser.java
JAL-3855 don’t need to query Alphafold2 repository directly from PDBe FTS client since 3db client will do that

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

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/FilterOption.java
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    /src/jalview/jbgui/GStructureChooser.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-3851 remove old interface

JAL-3851 tidy up REMOVEME logging

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    /src/jalview/rest/EndpointAsync.java
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    /src/jalview/rest/FetchSequenceEndpoint.java
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    /src/jalview/rest/OpenAlignmentEndpoint.java
JAL-3851 start highlight

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    /src/jalview/rest/HighlightSequenceEndpoint.java
JAL-3851 fix caching and tidy up old methods

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    /src/jalview/rest/EndpointAsync.java
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    /src/jalview/rest/FetchSequenceEndpoint.java
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    /src/jalview/rest/OpenAlignmentEndpoint.java
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    /src/jalview/rest/OpenSequenceEndpoint.java
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    /src/jalview/rest/RestHandler.java
Add RNAalifold service instance to slivka web services.

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    /src/jalview/ws/slivkaws/RNAalifoldServiceInstance.java
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

Merge branch 'cherry-pick/r2_11_2_JAL-3509' into develop

JAL-3851 re-engineering endpoints as separate classes

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    /src/jalview/rest/Endpoint.java
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    /src/jalview/rest/EndpointAsync.java
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    /src/jalview/rest/FetchSequenceEndpoint.java
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    /src/jalview/rest/OpenSequenceEndpoint.java
JAL-3851 run the eclipse compiled jalview

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    /utils/eclipse/eclipse_run.sh
JAL-3851 API handling of rest calls

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    /src/jalview/gui/SequenceFetcher.java
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    /src/jalview/httpserver/HttpServer.java
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    /src/jalview/rest/API.java
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    /src/jalview/rest/RestHandler.java
JAL-3851 convenience methods for logging exceptions

JAL-3863 fix test and note about fragility

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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-3863 fix test and note about fragility

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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-3863 add canonical DBRefEntry flag to Jalview project

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    /src/jalview/xml/binding/jalview/Annotation.java
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    /src/jalview/xml/binding/jalview/Feature.java
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    /src/jalview/xml/binding/jalview/FilterBy.java
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    /src/jalview/xml/binding/jalview/JalviewModel.java
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    /src/jalview/xml/binding/jalview/MapListType.java
  1. … 12 more files in changeset.
JAL-3863 add canonical DBRefEntry flag to Jalview project

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    /src/jalview/xml/binding/jalview/Annotation.java
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    /src/jalview/xml/binding/jalview/Feature.java
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    /src/jalview/xml/binding/jalview/FilterBy.java
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    /src/jalview/xml/binding/jalview/JalviewModel.java
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    /src/jalview/xml/binding/jalview/MapListType.java
  1. … 12 more files in changeset.
JAL-3929 generalised Alphafold retrieval mechanism to be reused for PDBEntrys with retrieval URIs discovered via 3d beacons

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    /src/jalview/ws/dbsources/EBIAlfaFold.java