X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=154582f5dbfb3bca840b6542e35b2bdc6cfee0c1;hb=87256ba36fb105a1115067ffe2563412e9281d2d;hp=f0cee7c39e287e42dcf6c8d366124a65101fc0ce;hpb=fee1b781ca14aadea5d112fc554fe14879c787c5;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index f0cee7c..154582f 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -23,6 +23,7 @@ package jalview.gui;
 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;
@@ -44,15 +45,15 @@ public class AssociatePdbFileWithSeq
    * @param choice
    * @param sequence
    */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol,
+  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
           SequenceI sequence, boolean prompt,
           StructureSelectionManagerProvider ssmp)
   {
     PDBEntry entry = new PDBEntry();
     StructureFile pdbfile = null;
     pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
-            .setMapping(false, new SequenceI[] { sequence }, null, choice,
-                    protocol);
+            .setMapping(false, new SequenceI[]
+            { sequence }, null, choice, file);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
@@ -64,7 +65,7 @@ public class AssociatePdbFileWithSeq
 
       if (prompt)
       {
-        reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
+        reply = JvOptionPane.showInternalInputDialog(Desktop.getDesktopPane(),
                 MessageManager
                         .getString("label.couldnt_find_pdb_id_in_file"),
                 MessageManager.getString("label.no_pdb_id_in_file"),