jalview

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

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    /resources/fts/tdbeacons_data_columns.txt
JAL-3829 JAL-2176 - TODO re unused argument in FTSRestClientI

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    /src/jalview/fts/api/FTSRestClientI.java
JAL-3929 JAL-2176 - TODO re unused argument in FTSRestClientI

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    /src/jalview/fts/api/FTSRestClientI.java
JAL-3929 tidying up PDBFTSRestClient test responses - still one failing external test which expects to raise a server exception

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

JAL-3829 Javadoc for FTSColumnPreferences

JAL-3929 Javadoc for FTSColumnPreferences

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

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/StructureChooserQuerySource.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-3929 pushed the PDBFTSClient specific code to new ‘StructureChooserQuerySource’ class in preparation for adapting it to query 3d-beacons

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/StructureChooserQuerySource.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 removed unneeded attribute in FTS core

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    /src/jalview/fts/core/FTSRestResponse.java
JAL-3929 removed unneeded attribute in FTS core

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    /src/jalview/fts/core/FTSRestResponse.java
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

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

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    /src/jalview/gbtest/TestListener.java
JAL-3851 eclipse_run.sh

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

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    /src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
JAL-3851 throwaway code

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    /src/jalview/gbtest/TestListener.java
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    /src/jalview/gui/SequenceFetcher.java
JAL-3855 EBI Alphafold database fetcher

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

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    /src/jalview/ws/dbsources/EBIAlfaFold.java
JAL-2349 - deobfuscate the renderer and fix it .. work in progress

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

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    /src/jalview/datamodel/ContactMatrix.java
Merge branch 'feature/JAL-3855_ebi_alphafold_import' into features/JAL-2349_matrixvis_2112

JAL-2349 patch NPE exception during gradle test..

JAL-2349 remove test code

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    /src/jalview/io/AppletFormatAdapter.java
Merge branch 'features/JAL-2349_matrixvis' into features/JAL-2349_matrixvis_2112

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

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    /src/jalview/gbtest/TestListener.java
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    /src/jalview/httpserver/HttpServer.java