jalview

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Commits this week: 10
Total Committers: 73
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Commits this week: 10

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Monday 06 Sep 2021
2:47 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
    • -0
    • +28
    /src/jalview/fts/core/FTSRestClient.java
    • -9
    • +370
    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
    • -16
    • +1
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -1
    • +1
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
10:52 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 pull out structure chooser query source tests to new class

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    • -102
    • +18
    /test/jalview/gui/StructureChooserTest.java
    • -0
    • +280
    /test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
Friday 03 Sep 2021
6:47 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 JAL-3865 test structure chooser queries to mocked 3D Beacons FTS

Options
    • -1
    • +95
    /test/jalview/gui/StructureChooserTest.java
6:42 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 use sequence dependent constructor for structure chooser query engine testing

Options
    • -1
    • +4
    /test/jalview/gui/StructureChooserTest.java
6:41 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 mocking for testing 3D-Beacons FTS endpoint

Options
    • -5
    • +39
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -0
    • +74
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
6:39 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
    • -2
    • +19
    /src/jalview/datamodel/DBRefEntry.java
    • -0
    • +15
    /test/jalview/datamodel/DBRefEntryTest.java
    • -1
    • +11
    /test/jalview/datamodel/SequenceTest.java
6:17 pm

Ben Soares

JAL-3785 renaming, adding to interface, tidying

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    • +11
    /src/jalview/httpserver/HttpServer.java
    • -2
    • +9
    /src/jalview/rest/API.java
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    • +128
    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/AbstractEndpointAsync.java
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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
    • -0
    • +64
    /src/jalview/rest/FetchSequencesEndpoint.java
    • -8
    • +11
    /src/jalview/rest/HighlightSequenceEndpoint.java
    • -0
    • +183
    /src/jalview/rest/InputAlignmentEndpoint.java
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    • +0
    /src/jalview/rest/OpenAlignmentEndpoint.java
    • -3
    • +21
    /src/jalview/rest/RestHandler.java
5:01 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 comments on the 3D structure chooser’s initialisation process

Options
    • -0
    • +8
    /src/jalview/gui/StructureChooser.java
5:01 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3865 isolate PDB and TDB clients and last query records in their query objects

Options
    • -0
    • +11
    /src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
    • -4
    • +3
    /src/jalview/gui/structurechooser/StructureChooserQuerySource.java
    • -7
    • +19
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
4:45 pm

Jim Procter <j.procter@dundee.ac.uk>

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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    • -0
    • +2
    /src/jalview/api/DBRefEntryI.java
    • -1
    • +1
    /src/jalview/datamodel/DBRefEntry.java
    • -0
    • +11
    /test/jalview/datamodel/SequenceTest.java
    • -0
    • +22
    /test/jalview/ws/seqfetcher/DbRefFetcherTest.java
4:27 pm

Mateusz Warowny

JAL-3878 Create Slivka Web Service adapter.

Options
    • -0
    • +175
    /src/jalview/ws2/slivka/SlivkaWS.java
3:37 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
    • -1
    • +1
    /src/jalview/gui/StructureChooser.java
    • -0
    • +32
    /src/jalview/gui/structurechooser/StructureChooserQuerySource.java
3:36 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3855 don’t need to query Alphafold2 repository directly from PDBe FTS client since 3db client will do that

Options
    • -2
    • +6
    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
3:33 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
    • -16
    • +6
    /src/jalview/gui/StructureChooser.java
    • -1
    • +24
    /src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
    • -7
    • +9
    /src/jalview/gui/structurechooser/StructureChooserQuerySource.java
    • -7
    • +25
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
    • -0
    • +86
    /src/jalview/jbgui/FilterOption.java
    • -85
    • +0
    /src/jalview/jbgui/GStructureChooser.java
    • -1
    • +1
    /test/jalview/gui/StructureChooserTest.java
Thursday 02 Sep 2021
8:25 pm

Ben Soares

JAL-3851 remove old interface

Options
    • -6
    • +0
    /src/jalview/rest/RestHandler.java
8:24 pm

Ben Soares

JAL-3851 tidy up REMOVEME logging

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    • -8
    • +0
    /src/jalview/rest/API.java
    • -38
    • +0
    /src/jalview/rest/EndpointAsync.java
    • -2
    • +0
    /src/jalview/rest/FetchSequenceEndpoint.java
    • -4
    • +0
    /src/jalview/rest/OpenAlignmentEndpoint.java
    • -6
    • +0
    /src/jalview/rest/RestHandler.java
8:21 pm

Ben Soares

JAL-3851 start highlight

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    • -0
    • +55
    /src/jalview/rest/HighlightSequenceEndpoint.java
8:18 pm

Ben Soares

JAL-3851 fix caching and tidy up old methods

Options
    • -3
    • +3
    /src/jalview/bin/Jalview.java
    • -1
    • +1
    /src/jalview/gui/SequenceFetcher.java
    • -0
    • +3
    /src/jalview/httpserver/AbstractRequestHandler.java
    • -328
    • +9
    /src/jalview/rest/API.java
    • -7
    • +8
    /src/jalview/rest/Endpoint.java
    • -34
    • +108
    /src/jalview/rest/EndpointAsync.java
    • -5
    • +21
    /src/jalview/rest/FetchSequenceEndpoint.java
    • -0
    • +183
    /src/jalview/rest/OpenAlignmentEndpoint.java
    • -164
    • +0
    /src/jalview/rest/OpenSequenceEndpoint.java
    • -11
    • +22
    /src/jalview/rest/RestHandler.java
4:11 pm

Mateusz Warowny

Add RNAalifold service instance to slivka web services.

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    • +23
    /src/jalview/ws/slivkaws/RNAalifoldServiceInstance.java
    • -0
    • +4
    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
3:53 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

Options
    • -4
    • +1
    /src/jalview/gui/SequenceFetcher.java
    • -5
    • +2
    /src/jalview/structures/models/AAStructureBindingModel.java
3:34 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
2:26 pm

Ben Soares

JAL-3851 re-engineering endpoints as separate classes

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    • +86
    /src/jalview/rest/Endpoint.java
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    /src/jalview/rest/EndpointAsync.java
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    • +48
    /src/jalview/rest/FetchSequenceEndpoint.java
    • -0
    • +164
    /src/jalview/rest/OpenSequenceEndpoint.java
2:25 pm

Ben Soares

JAL-3851 run the eclipse compiled jalview

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    • +3
    /utils/eclipse/eclipse_run.sh
2:25 pm

Ben Soares

JAL-3851 API handling of rest calls

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    • +33
    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/Desktop.java
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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
2:22 pm

Ben Soares

JAL-3851 convenience methods for logging exceptions

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    • +25
    /src/jalview/bin/Cache.java
Monday 30 Aug 2021
11:51 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3863 fix test and note about fragility

Options
    • -0
    • +7
    /test/jalview/ws/dbsources/UniprotTest.java
11:51 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3863 fix test and note about fragility

Options
    • -0
    • +7
    /test/jalview/ws/dbsources/UniprotTest.java
11:14 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3863 add canonical DBRefEntry flag to Jalview project

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    • +7
    /schemas/vamsas.xsd
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    /src/jalview/project/Jalview2XML.java
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    /src/jalview/xml/binding/jalview/AlcodonFrame.java
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    /src/jalview/xml/binding/jalview/Annotation.java
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    /src/jalview/xml/binding/jalview/AnnotationColourScheme.java
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    /src/jalview/xml/binding/jalview/AnnotationElement.java
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    /src/jalview/xml/binding/jalview/DoubleMatrix.java
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    /src/jalview/xml/binding/jalview/DoubleVector.java
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    /src/jalview/xml/binding/jalview/Feature.java
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    /src/jalview/xml/binding/jalview/FeatureMatcher.java
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    /src/jalview/xml/binding/jalview/FeatureMatcherSet.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/JalviewUserColours.java
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    /src/jalview/xml/binding/jalview/MapListType.java
  16. … 12 more files in changeset.
11:14 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3863 add canonical DBRefEntry flag to Jalview project

Options
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    • +7
    /schemas/vamsas.xsd
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    /src/jalview/project/Jalview2XML.java
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    /src/jalview/xml/binding/jalview/AlcodonFrame.java
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    /src/jalview/xml/binding/jalview/Annotation.java
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    /src/jalview/xml/binding/jalview/AnnotationColourScheme.java
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    /src/jalview/xml/binding/jalview/AnnotationElement.java
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    /src/jalview/xml/binding/jalview/DoubleMatrix.java
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    /src/jalview/xml/binding/jalview/DoubleVector.java
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    /src/jalview/xml/binding/jalview/Feature.java
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    /src/jalview/xml/binding/jalview/FeatureMatcher.java
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    /src/jalview/xml/binding/jalview/FeatureMatcherSet.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/JalviewUserColours.java
    • -73
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    /src/jalview/xml/binding/jalview/MapListType.java
  16. … 12 more files in changeset.
10:09 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 generalised Alphafold retrieval mechanism to be reused for PDBEntrys with retrieval URIs discovered via 3d beacons

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    /src/jalview/datamodel/PDBEntry.java
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    • +19
    /src/jalview/gui/AppJmol.java
    • -71
    • +101
    /src/jalview/ws/dbsources/EBIAlfaFold.java