X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=689686341994b6c181070a9cebd3851c0275b76a;hb=0f8e8fef1abe7837642706ee5b5f97d3e1eda9db;hp=cbfbbc46d093ef649f92adc13795d9117e358c37;hpb=28c13a67af0d57c53de532d0d50add7ab83f7d42;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index cbfbbc4..6896863 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,42 +1,63 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.gui;
 
 import javax.swing.JOptionPane;
 
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
 /**
  * GUI related routines for associating PDB files with sequences
+ * 
  * @author JimP
- *
+ * 
  */
 public class AssociatePdbFileWithSeq
 {
 
-/**
- * assocate the given PDB file with 
- * @param choice
- * @param sequence
- */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt)
+  /**
+   * assocate the given PDB file with
+   * 
+   * @param choice
+   * @param sequence
+   */
+  public PDBEntry associatePdbWithSeq(String choice, String protocol,
+          SequenceI sequence, boolean prompt)
   {
     PDBEntry entry = new PDBEntry();
     try
     {
-      MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
-              protocol);
+      MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol);
 
       if (pdbfile.id == null)
       {
         String reply = null;
-      
-        if (prompt) { reply = JOptionPane
-                .showInternalInputDialog(
-                        Desktop.desktop,
-                        "Couldn't find a PDB id in the file supplied."
-                                + "Please enter an Id to identify this structure.",
-                        "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);}
+
+        if (prompt)
+        {
+          reply = JOptionPane
+                  .showInternalInputDialog(
+                          Desktop.desktop,
+                          "Couldn't find a PDB id in the file supplied."
+                                  + "Please enter an Id to identify this structure.",
+                          "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+        }
         if (reply == null)
         {
           return null;