jalview

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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
JAL-3829 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
JAL-3863 mark first accession retrieved from Uniprot as the canonical accession

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    /src/jalview/datamodel/DBRefEntry.java
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    /src/jalview/ws/dbsources/Uniprot.java
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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-3863 mark first accession retrieved from Uniprot as the canonical accession

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    /src/jalview/datamodel/DBRefEntry.java
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    /src/jalview/ws/dbsources/Uniprot.java
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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-3929 Structure chooser specific FTS interface and query source logic for PDBe and 3D-Beacons

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    /src/jalview/fts/api/StructureFTSRestClientI.java
JAL-3829 Structure chooser specific FTS interface and query source logic for PDBe and 3D-Beacons

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    /src/jalview/fts/api/StructureFTSRestClientI.java
Merge branch 'feature/JAL-3855_ebi_alphafold_import' (commit '7856e91f60adc5c2d4943bad84a5a83e1412f00c') into features/r2_11_2_JAL-3929_3dbeacons

Merge branch 'feature/JAL-3855_ebi_alphafold_import' (commit '7856e91f60adc5c2d4943bad84a5a83e1412f00c') into features/r2_11_2_JAL-3929_3dbeacons

JAL-3929 3d-beacons structure chooser logic (not yet finished)

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    /src/jalview/datamodel/PDBEntry.java
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    /src/jalview/fts/api/FTSRestClientI.java
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    /src/jalview/fts/core/FTSRestClient.java
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    /src/jalview/gui/StructureChooser.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 3d-beacons structure chooser logic (not yet finished)

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    /src/jalview/datamodel/PDBEntry.java
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    /src/jalview/fts/api/FTSRestClientI.java
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    /src/jalview/fts/core/FTSRestClient.java
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    /src/jalview/gui/StructureChooser.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 pulled out more of the FTS dependent parts of structurechooser

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-3929 pulled out more of the FTS dependent parts of structurechooser

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-3929 updated tests for 3db fetcher’s working FTS metadata

JAL-3829 updated tests for 3db fetcher’s working FTS metadata

JAL-3829 proof in principle 3d-beacons sequence fetcher - still some TODOs !

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    /resources/fts/tdbeacons_data_columns.txt
JAL-3929 proof in principle 3d-beacons sequence fetcher - still some TODOs !

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    /resources/fts/tdbeacons_data_columns.txt
JAL-3829 3d-beacons has a custom alignment retrieval model but re-uses the parseAlignment method from sequence fetcher

JAL-3929 3d-beacons has a custom alignment retrieval model but re-uses the parseAlignment method from sequence fetcher

JAL-3829 fixed up the 3d-beacons data columns definitions, tests and client.

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    /resources/fts/tdbeacons_data_columns.txt