X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=20e8dfef7077f9b340a115dd82de6bfa2c28f27c;hb=3609d4b908fa64cab35f2348401baab3347188fc;hp=01f1cb0f960c4ebbba0249e96c5704d743ac8e4e;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 01f1cb0..20e8dfe 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.
  * 
@@ -20,9 +20,12 @@
  */
 package jalview.gui;
 
-import javax.swing.JOptionPane;
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
 /**
@@ -40,45 +43,52 @@ public class AssociatePdbFileWithSeq
    * @param choice
    * @param sequence
    */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol,
-          SequenceI sequence, boolean prompt)
+  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+          SequenceI sequence, boolean prompt,
+          StructureSelectionManagerProvider ssmp)
   {
     PDBEntry entry = new PDBEntry();
-    try
+    StructureFile pdbfile = null;
+    pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+            .setMapping(false, new SequenceI[]
+            { sequence }, null, choice, file);
+    if (pdbfile == null)
     {
-      MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol);
+      // stacktrace already thrown so just return
+      return null;
+    }
+    if (pdbfile.getId() == null)
+    {
+      String reply = null;
 
-      if (pdbfile.id == null)
+      if (prompt)
       {
-        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;
-        }
-
-        entry.setId(reply);
+        reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
+                MessageManager
+                        .getString("label.couldnt_find_pdb_id_in_file"),
+                MessageManager.getString("label.no_pdb_id_in_file"),
+                JvOptionPane.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.getId());
     }
+    entry.setType(PDBEntry.Type.FILE);
 
-    entry.setFile(choice);
-    sequence.getDatasetSequence().addPDBId(entry);
+    if (pdbfile != null)
+    {
+      entry.setFile(choice);
+      sequence.getDatasetSequence().addPDBId(entry);
+      StructureSelectionManager.getStructureSelectionManager(ssmp)
+              .registerPDBEntry(entry);
+    }
     return entry;
   }
 }