From 02816cb583d01a3a0cdd612d5d0a1f24c0d0b99d Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 14 Oct 2022 17:05:06 +0100
Subject: [PATCH] JAL-3855 refactor the pAE retrieval code so it can be called
 via structureselectionmanager

---
 src/jalview/ws/dbsources/EBIAlfaFold.java |   88 +++++++++++++++++++----------
 1 file changed, 58 insertions(+), 30 deletions(-)

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index e0ab54d..fa867cd 100644
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -23,6 +23,7 @@ package jalview.ws.dbsources;
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
@@ -196,33 +197,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
                 "exception.no_pdb_records_for_chain", new String[]
                 { id, ((chain == null) ? "' '" : chain) }));
       }
-
-      // import PAE as contact matrix - assume this will work if there was a
-      // model
-      File pae = File.createTempFile(id, "pae_json");
-      String paeURL = getAlphaFoldPaeDownloadUrl(id, AF_VERSION);
-
-      if (retrievalUrl != null)
-      {
-        // manufacture the PAE url from a url like ...-model-vN.cif
-        paeURL = retrievalUrl.replace("model", "predicted_aligned_error")
-                .replace(".cif", ".json");
-      }
-      Console.debug("Downloading pae from " + paeURL + " to "
-              + pae.toString() + "");
-
-      try
-      {
-        UrlDownloadClient.download(paeURL, pae);
-        if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
-        {
-          Console.warn("Couln't import contact matrix from " + paeURL
-                  + " (stored in " + pae.toString() + ")");
-        }
-      } catch (Exception pae_ex)
-      {
-        Console.debug("Couldn't download PAE", pae_ex);
-      }
+      retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl);
 
     } catch (Exception ex) // Problem parsing PDB file
     {
@@ -232,10 +207,63 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     return pdbAlignment;
   }
 
-  private boolean importPaeJSONAsContactMatrix(AlignmentI pdbAlignment,
-          File pae) throws Exception
+  /**
+   * get an alphafold pAE for the given id, and add it to sequence 0 in
+   * pdbAlignment (assuming it came from structurefile parser).
+   * 
+   * @param id
+   * @param pdbAlignment
+   * @param retrievalUrl
+   *          - URL of .mmcif from EBI-AlphaFold - will be used to generate the
+   *          pAE URL automatically
+   * @throws Exception
+   */
+  public static void retrieve_AlphaFold_pAE(String id,
+          AlignmentI pdbAlignment, String retrievalUrl) throws Exception
+  {
+    // import PAE as contact matrix - assume this will work if there was a
+    // model
+    File pae = File.createTempFile(id, "pae_json");
+    String paeURL = getAlphaFoldPaeDownloadUrl(id, AF_VERSION);
+
+    if (retrievalUrl != null)
+    {
+      // manufacture the PAE url from a url like ...-model-vN.cif
+      paeURL = retrievalUrl.replace("model", "predicted_aligned_error")
+              .replace(".cif", ".json");
+    }
+    Console.debug("Downloading pae from " + paeURL + " to " + pae.toString()
+            + "");
+
+    try
+    {
+      UrlDownloadClient.download(paeURL, pae);
+      FileInputStream pae_input = new FileInputStream(pae);
+
+      if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input))
+      {
+        Console.warn("Couln't import contact matrix from " + paeURL
+                + " (stored in " + pae.toString() + ")");
+      }
+    } catch (Exception pae_ex)
+    {
+      Console.debug("Couldn't download PAE", pae_ex);
+    }
+
+  }
+
+  /**
+   * parses the given pAE matrix and adds it to sequence 0 in the given
+   * alignment
+   * 
+   * @param pdbAlignment
+   * @param pae_input
+   * @return true if there was a pAE matrix added
+   * @throws Exception
+   */
+  public static boolean importPaeJSONAsContactMatrix(
+          AlignmentI pdbAlignment, InputStream pae_input) throws Exception
   {
-    FileInputStream pae_input = new FileInputStream(pae);
 
     List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
     if (pae_obj == null)
-- 
1.7.10.2