X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=a854bdfc87f360e3c181e12241cbf58eb3046613;hb=e143144f435c147df014d545ef6760b531462850;hp=ce75821a3535dea439bf1dcef203e730aea0e8f1;hpb=e248608bb20e000c17ddc79390d9c1f1f0470e4f;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index ce75821..a854bdf 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -20,11 +20,14 @@
  */
 package jalview.gui;
 
-import javax.swing.JOptionPane;
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
+import javax.swing.JOptionPane;
+
 /**
  * GUI related routines for associating PDB files with sequences
  * 
@@ -41,46 +44,50 @@ public class AssociatePdbFileWithSeq
    * @param sequence
    */
   public PDBEntry associatePdbWithSeq(String choice, String protocol,
-          SequenceI sequence, boolean prompt)
+          SequenceI sequence, boolean prompt,
+          StructureSelectionManagerProvider ssmp)
   {
     PDBEntry entry = new PDBEntry();
     MCview.PDBfile pdbfile = null;
-    try
+    pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+            .setMapping(false, new SequenceI[]
+            { sequence }, null, choice, protocol);
+    if (pdbfile == null)
     {
-      // TODO JAL-674 extract secondary structure and transfer it to associated
-      // sequence
-      pdbfile = new MCview.PDBfile(false, false, choice, protocol);
-      if (pdbfile.id == null)
-      {
-        String reply = null;
-
-        if (prompt)
-        {
-          reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
-                  MessageManager
-                          .getString("label.couldnt_find_pdb_id_in_file"),
-                  MessageManager.getString("label.no_pdb_id_in_file"),
-                  JOptionPane.QUESTION_MESSAGE);
-        }
-        if (reply == null)
-        {
-          return null;
-        }
+      // stacktrace already thrown so just return
+      return null;
+    }
+    if (pdbfile.id == null)
+    {
+      String reply = null;
 
-        entry.setId(reply);
+      if (prompt)
+      {
+        reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+                MessageManager
+                        .getString("label.couldnt_find_pdb_id_in_file"),
+                MessageManager.getString("label.no_pdb_id_in_file"),
+                JOptionPane.QUESTION_MESSAGE);
       }
-      else
+      if (reply == null)
       {
-        entry.setId(pdbfile.id);
+        return null;
       }
 
-    } catch (java.io.IOException ex)
+      entry.setId(reply);
+    }
+    else
     {
-      ex.printStackTrace();
+      entry.setId(pdbfile.id);
     }
 
-    entry.setFile(choice);
-    sequence.getDatasetSequence().addPDBId(entry);
+    if (pdbfile != null)
+    {
+      entry.setFile(choice);
+      sequence.getDatasetSequence().addPDBId(entry);
+      StructureSelectionManager.getStructureSelectionManager(ssmp)
+              .registerPDBEntry(entry);
+    }
     return entry;
   }
 }