From e0edbbd56a07a9ef4f8b50e3c616062aa013544c Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Tue, 27 Jul 2021 13:35:40 +0100
Subject: [PATCH] JAL-3855 check if an alpha fold ID and retrieve using that
 source

---
 src/jalview/gui/AppJmol.java             |   10 +++++++++-
 src/jalview/gui/StructureViewerBase.java |    9 ++++++++-
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 7cf10e7..d085117 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -51,6 +51,7 @@ import jalview.util.BrowserLauncher;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.dbsources.Pdb;
 
 public class AppJmol extends StructureViewerBase
@@ -437,6 +438,8 @@ public class AppJmol extends StructureViewerBase
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
       Pdb pdbclient = new Pdb();
+      EBIAlfaFold afclient = new EBIAlfaFold();
+      
       for (int pi = 0; pi < jmb.getPdbCount(); pi++)
       {
         String file = jmb.getPdbEntry(pi).getFile();
@@ -452,7 +455,12 @@ public class AppJmol extends StructureViewerBase
                   { pdbid }), hdl);
           try
           {
-            pdbseq = pdbclient.getSequenceRecords(pdbid);
+            if (afclient.isValidReference(pdbid))
+            {
+              pdbseq = afclient.getSequenceRecords(pdbid);
+            } else {
+              pdbseq = pdbclient.getSequenceRecords(pdbid);
+            }
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index a0b199b..b349559 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -63,6 +63,7 @@ import jalview.structure.StructureMapping;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
+import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.dbsources.Pdb;
 
 /**
@@ -1121,6 +1122,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     String filePath = null;
     Pdb pdbclient = new Pdb();
+    EBIAlfaFold afclient =  new EBIAlfaFold();
     AlignmentI pdbseq = null;
     String pdbid = processingEntry.getId();
     long handle = System.currentTimeMillis()
@@ -1138,7 +1140,12 @@ public abstract class StructureViewerBase extends GStructureViewer
     // { pdbid }));
     try
     {
-      pdbseq = pdbclient.getSequenceRecords(pdbid);
+      if (afclient.isValidReference(pdbid))
+      {
+        pdbseq = afclient.getSequenceRecords(pdbid);
+      } else {
+        pdbseq = pdbclient.getSequenceRecords(pdbid);
+      }
     } catch (Exception e)
     {
       System.err.println(
-- 
1.7.10.2