From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 13 Dec 2021 17:49:19 +0000 (+0000)
Subject: JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve... 
X-Git-Tag: Release_2_11_2_0~20^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bb9efbe53b2e92a1e3fcc78d7a6b6f5563e43e97;p=jalview.git

JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve been given it
---

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 30ecc80..ae2128b 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -1156,7 +1156,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     {
       if (afclient.isValidReference(pdbid))
       {
-        pdbseq = afclient.getSequenceRecords(pdbid);
+        pdbseq = afclient.getSequenceRecords(pdbid,processingEntry.getRetrievalUrl());
       } else {
           if (processingEntry.hasRetrievalUrl())
           {
diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index b77fc47..4449b0b 100644
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -124,6 +124,10 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
+    return getSequenceRecords(queries, null);
+  }
+  public AlignmentI getSequenceRecords(String queries, String retrievalUrl) throws Exception
+  {
     AlignmentI pdbAlignment = null;
     String chain = null;
     String id = null;
@@ -145,6 +149,10 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       return null;
     }
     String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+    if (retrievalUrl != null)
+    {
+      alphaFoldCif = retrievalUrl;
+    }
 
     try
     {
@@ -327,4 +335,5 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   {
     return new PDBFeatureSettings();
   }
+
 }