jalview

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

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Wednesday 25 Aug 2021
6:10 pm

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

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

Options
    • -17
    • +18
    /resources/fts/tdbeacons_data_columns.txt
    • -86
    • +74
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
    • -3
    • +2
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
6:10 pm

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

JAL-3929 proof in principle 3d-beacons sequence fetcher - still some TODOs !

Options
    • -17
    • +18
    /resources/fts/tdbeacons_data_columns.txt
    • -86
    • +74
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
    • -3
    • +2
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
6:09 pm

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

JAL-3829 3d-beacons has a custom alignment retrieval model but re-uses the parseAlignment method from sequence fetcher

Options
    • -2
    • +9
    /src/jalview/gui/SequenceFetcher.java
6:09 pm

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

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

Options
    • -2
    • +9
    /src/jalview/gui/SequenceFetcher.java
4:26 pm

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

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

Options
    • -7
    • +14
    /resources/fts/tdbeacons_data_columns.txt
    • -2
    • +2
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -9
    • +15
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
4:26 pm

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

JAL-3929 fixed up the 3d-beacons data columns definitions, tests and client.

Options
    • -7
    • +14
    /resources/fts/tdbeacons_data_columns.txt
    • -2
    • +2
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -9
    • +15
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
4:25 pm

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

JAL-3829 JAL-2176 - TODO re unused argument in FTSRestClientI

Options
    • -1
    • +1
    /src/jalview/fts/api/FTSRestClientI.java
4:25 pm

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

JAL-3929 JAL-2176 - TODO re unused argument in FTSRestClientI

Options
    • -1
    • +1
    /src/jalview/fts/api/FTSRestClientI.java
4:24 pm

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

JAL-3929 tidying up PDBFTSRestClient test responses - still one failing external test which expects to raise a server exception

Options
    • -1
    • +0
    /resources/fts/pdb_data_columns.txt
    • -0
    • +1
    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
4:24 pm

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

JAL-3829 tidying up PDBFTSRestClient test responses - still one failing external test which expects to raise a server exception

Options
    • -1
    • +0
    /resources/fts/pdb_data_columns.txt
    • -0
    • +1
    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
Monday 23 Aug 2021
5:45 pm

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

JAL-3829 Javadoc for FTSColumnPreferences

Options
    • -1
    • +7
    /src/jalview/fts/core/FTSDataColumnPreferences.java
5:45 pm

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

JAL-3929 Javadoc for FTSColumnPreferences

Options
    • -1
    • +7
    /src/jalview/fts/core/FTSDataColumnPreferences.java
5:45 pm

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

JAL-3829 pushed the PDBFTSClient specific code to new ‘StructureChooserQuerySource’ class in preparation for adapting it to query 3d-beacons

Options
    • -202
    • +17
    /src/jalview/gui/StructureChooser.java
    • -0
    • +292
    /src/jalview/gui/StructureChooserQuerySource.java
    • -8
    • +9
    /test/jalview/gui/StructureChooserTest.java
5:45 pm

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

JAL-3929 pushed the PDBFTSClient specific code to new ‘StructureChooserQuerySource’ class in preparation for adapting it to query 3d-beacons

Options
    • -202
    • +17
    /src/jalview/gui/StructureChooser.java
    • -0
    • +292
    /src/jalview/gui/StructureChooserQuerySource.java
    • -8
    • +9
    /test/jalview/gui/StructureChooserTest.java
5:43 pm

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

JAL-3829 removed unneeded attribute in FTS core

Options
    • -10
    • +0
    /src/jalview/fts/core/FTSRestResponse.java
    • -9
    • +3
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
5:43 pm

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

JAL-3929 removed unneeded attribute in FTS core

Options
    • -10
    • +0
    /src/jalview/fts/core/FTSRestResponse.java
    • -9
    • +3
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
10:11 am

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

JAL-3851 use direct sequence mouse over event listener - nb JAL-3860 means ensembl ref genome seq mouseovers don't get propagated to transcript/etc

Options
    • -1
    • +1
    /src/jalview/gbtest/TestListener.java
Friday 20 Aug 2021
4:42 pm

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

JAL-3851 quick hack of highlighting position in an Ensembl ID

Options
    • -1
    • +62
    /src/jalview/gbtest/TestListener.java
3:40 pm

Ben Soares

JAL-3851 eclipse_run.sh

Options
    • -0
    • +3
    /utils/eclipse_run.sh
3:12 pm

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

JAL-3855 JAL-2349 (d0h) class for holding and accessing PAE as a contact matrix

Options
    • -0
    • +107
    /src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
3:02 pm

Ben Soares

JAL-3851 throwaway code

Options
    • -2
    • +1
    /src/jalview/bin/Jalview.java
    • -24
    • +120
    /src/jalview/gbtest/TestListener.java
    • -26
    • +74
    /src/jalview/gui/SequenceFetcher.java
Wednesday 18 Aug 2021
4:42 pm

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

JAL-3855 EBI Alphafold database fetcher

Options
    • -0
    • +2
    /src/jalview/ws/SequenceFetcher.java
4:41 pm

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

JAL-3855 JAL-2349 download PAE matrix along with alpha fold structure from EBI and view PAE as contact map

Options
    • -13
    • +63
    /src/jalview/ws/dbsources/EBIAlfaFold.java
    • -0
    • +29
    /test/jalview/ws/seqfetcher/DbRefFetcherTest.java
4:40 pm

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

JAL-2349 - deobfuscate the renderer and fix it .. work in progress

Options
    • -10
    • +14
    /src/jalview/renderer/ContactMapRenderer.java
4:39 pm

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

JAL-2349 allow contact map to be associated with a reference sequence

Options
    • -0
    • +5
    /src/jalview/datamodel/Alignment.java
    • -0
    • +14
    /src/jalview/datamodel/ContactMatrix.java
    • -0
    • +4
    /src/jalview/datamodel/ContactMatrixI.java
    • -0
    • +14
    /src/jalview/datamodel/SeqDistanceContactMatrix.java
Friday 13 Aug 2021
1:35 pm

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

Merge branch 'feature/JAL-3855_ebi_alphafold_import' into features/JAL-2349_matrixvis_2112

Options
1:32 pm

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

JAL-2349 patch NPE exception during gradle test..

Options
    • -1
    • +1
    /test/jalview/gui/SeqPanelTest.java
Wednesday 11 Aug 2021
6:30 pm

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

JAL-2349 remove test code

Options
    • -2
    • +0
    /src/jalview/io/AppletFormatAdapter.java
6:02 pm

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

Merge branch 'features/JAL-2349_matrixvis' into features/JAL-2349_matrixvis_2112

Options
    • -0
    • +3
    /src/jalview/api/AlignViewportI.java
    • -1
    • +1
    /src/jalview/appletgui/AnnotationPanel.java
    • -5
    • +38
    /src/jalview/datamodel/Alignment.java
    • -1
    • +1
    /src/jalview/gui/AnnotationPanel.java
    • -0
    • +3
    /src/jalview/io/AppletFormatAdapter.java
    • -0
    • +34
    /src/jalview/renderer/AnnotationRenderer.java
    • -0
    • +7
    /src/jalview/viewmodel/AlignmentViewport.java
Tuesday 03 Aug 2021
9:10 pm

Ben Soares

JAL-3851 start a listener with -testlistener and suggest a port with -testlistener_port. wget -S -O - http://localhost:20212/jalview/TEST/viewgene/ENSG00000139618

Options
    • -0
    • +35
    /src/jalview/bin/Jalview.java
    • -0
    • +82
    /src/jalview/gbtest/TestListener.java
    • -4
    • +50
    /src/jalview/httpserver/HttpServer.java