Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / gui / AssociatePdbFileWithSeq.java

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index e2637a9..ddf38c6 100644 (file)
--- 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;
@@ -44,7 +45,7 @@ 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)
   {
@@ -52,7 +53,7 @@ public class AssociatePdbFileWithSeq
     StructureFile pdbfile = null;
     pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
             .setMapping(false, new SequenceI[] { sequence }, null, choice,
-                    protocol);
+                    file);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
@@ -64,11 +65,11 @@ public class AssociatePdbFileWithSeq
 
       if (prompt)
       {
-        reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
                 MessageManager
                         .getString("label.couldnt_find_pdb_id_in_file"),
                 MessageManager.getString("label.no_pdb_id_in_file"),
-                JOptionPane.QUESTION_MESSAGE);
+                JvOptionPane.QUESTION_MESSAGE);
       }
       if (reply == null)
       {