From 2dc9a48f09149e6df2a09f7cfb07155bd4429be8 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 13 Oct 2009 15:13:03 +0000
Subject: [PATCH] use Pdb database source for fetching and warn user if PDB
 reference did not resolve to a record.

---
 src/jalview/gui/AppJmol.java |   40 +++++++++++++++++++++++++++++-----------
 1 file changed, 29 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 2137a80..3b94bf4 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -76,8 +76,10 @@ public class AppJmol extends GStructureViewer implements StructureListener,
   {
     this(file, id, seq, ap, loadStatus, bounds, null);
   }
+
   public AppJmol(String file, String id, SequenceI[] seq,
-            AlignmentPanel ap, String loadStatus, Rectangle bounds, String viewid)
+          AlignmentPanel ap, String loadStatus, Rectangle bounds,
+          String viewid)
   {
     loadingFromArchive = true;
     pdbentry = new PDBEntry();
@@ -315,11 +317,25 @@ public class AppJmol extends GStructureViewer implements StructureListener,
   {
     try
     {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String query = "pdb:" + pdbentry.getId();
-      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
-              .getAbsolutePath());
-      initJmol("load " + pdbentry.getFile());
+      // TODO: replace with reference fetching/transfer code (validate PDBentry as a DBRef?)
+      jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+      AlignmentI pdbseq;
+      if ((pdbseq=pdbclient.getSequenceRecords(pdbentry.getId())) != null)
+      {
+        // just transfer the file name from the first seuqence's first PDBEntry
+        pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId().elementAt(0)).getFile());
+        initJmol("load " + pdbentry.getFile());
+      }
+      else
+      {
+        JOptionPane
+                .showInternalMessageDialog(
+                        Desktop.desktop,
+                        pdbentry.getId()
+                                + " could not be retrieved. Please try downloading the file manually.",
+                        "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+
+      }
     } catch (OutOfMemoryError oomerror)
     {
       new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
@@ -379,7 +395,7 @@ public class AppJmol extends GStructureViewer implements StructureListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void eps_actionPerformed(ActionEvent e)
   {
@@ -390,7 +406,7 @@ public class AppJmol extends GStructureViewer implements StructureListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void png_actionPerformed(ActionEvent e)
   {
@@ -973,12 +989,14 @@ public class AppJmol extends GStructureViewer implements StructureListener,
       }
     }
   }
-  String viewId=null;
+
+  String viewId = null;
+
   public String getViewId()
   {
-    if (viewId==null)
+    if (viewId == null)
     {
-      viewId=System.currentTimeMillis()+"."+this.hashCode();
+      viewId = System.currentTimeMillis() + "." + this.hashCode();
     }
     return viewId;
   }
-- 
1.7.10.2