X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=e2637a95cf603d9eccf2e0377beb1bc6d36fa31e;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=a854bdfc87f360e3c181e12241cbf58eb3046613;hpb=9c37999eb4b461a5c7a94e10ac39583c1c29200a;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index a854bdf..e2637a9 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
@@ -48,16 +49,16 @@ public class AssociatePdbFileWithSeq
           StructureSelectionManagerProvider ssmp)
   {
     PDBEntry entry = new PDBEntry();
-    MCview.PDBfile pdbfile = null;
+    StructureFile pdbfile = null;
     pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
-            .setMapping(false, new SequenceI[]
-            { sequence }, null, choice, protocol);
+            .setMapping(false, new SequenceI[] { sequence }, null, choice,
+                    protocol);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
       return null;
     }
-    if (pdbfile.id == null)
+    if (pdbfile.getId() == null)
     {
       String reply = null;
 
@@ -78,8 +79,9 @@ public class AssociatePdbFileWithSeq
     }
     else
     {
-      entry.setId(pdbfile.id);
+      entry.setId(pdbfile.getId());
     }
+    entry.setType(PDBEntry.Type.FILE);
 
     if (pdbfile != null)
     {