From f39645b94f7fc0540fd449dffd8a8d9fdce1d3b8 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 8 Nov 2021 18:22:35 +0000
Subject: [PATCH] JAL-3855 JAL-1731 reuse the
 StructureViewer.fetchPdbFile(PDBEntry) method in
 JmolBinding - avoid code duplication for retrieval and
 import of 3d data

---
 src/jalview/gui/AppJmolBinding.java |   50 +++++------------------------------
 1 file changed, 7 insertions(+), 43 deletions(-)

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 037b97e..6b06e56 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -222,45 +222,17 @@ public class AppJmolBinding extends JalviewJmolBinding
       String[] filesInViewer = getStructureFiles();
       // 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 < getPdbCount(); pi++)
       {
-        String file = getPdbEntry(pi).getFile();
+        PDBEntry strucEntry = getPdbEntry(pi);
+
+        String file = strucEntry.getFile();
         if (file == null)
         {
-          // todo: extract block as method and pull up (also ChimeraViewFrame)
-          // retrieve the pdb and store it locally
-          AlignmentI pdbseq = null;
-          PDBEntry strucEntry = getPdbEntry(pi);
           pdbid = strucEntry.getId();
-          long hdl = pdbid.hashCode() - System.currentTimeMillis();
-          structureViewer.setProgressMessage(MessageManager
-                  .formatMessage("status.fetching_pdb", new String[]
-                  { pdbid }), hdl);
-          try
-          {
-            if (afclient.isValidReference(pdbid))
-            {
-              pdbseq = afclient.getSequenceRecords(pdbid);
-            } else {
-              if (strucEntry.hasRetrievalUrl())
-              {
-                File tmpFile = File.createTempFile(pdbid, ".cif");
-                String fromUrl = strucEntry.getRetrievalUrl();
-                UrlDownloadClient.download(fromUrl, tmpFile);
-                
-                // may not need this check ?
-                file = tmpFile.getAbsolutePath();
-                if (file != null)
-                {
-                  pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,tmpFile,pdbid,null,null,null);
-                }
-              } else {
-                pdbseq = pdbclient.getSequenceRecords(pdbid);
-              }
-            }
+          try{ 
+            file = structureViewer.fetchPdbFile(strucEntry);
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
@@ -268,18 +240,10 @@ public class AppJmolBinding extends JalviewJmolBinding
           {
             ex.printStackTrace();
             errormsgs.append("'").append(pdbid).append("'");
-          } finally
-          {
-            structureViewer.setProgressMessage(
-                    MessageManager.getString("label.state_completed"), hdl);
           }
-          if (pdbseq != null)
+          if (file!=null)
           {
-            // just transfer the file name from the first sequence's first
-            // PDBEntry
-            file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
-                    .elementAt(0).getFile()).getAbsolutePath();
-            getPdbEntry(pi).setFile(file);
+            // success
             files.add(file);
           }
           else
-- 
1.7.10.2