X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=979a2e2b1f00b70b2894962bc9813774d7adae64;hb=1e5dc0e8a71d9eb0be4748f994072b11f25b04e0;hp=3bd21b57b8a747c10309e0dbe6f390276c3d7850;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 3bd21b5..979a2e2 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,20 +1,20 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+/*
+ * 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;
@@ -28,53 +28,44 @@ import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.IdentifyFile;
 
 /**
  * GUI related routines for associating PDB files with sequences
+ * 
  * @author JimP
- *
+ * 
  */
 public class AssociatePdbFileWithSeq
 {
 
-/**
- * assocate the given PDB file with 
- * @param choice
- * @param sequence
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
- */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  /**
+   * 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
     {
- 
-    		System.out.println("This is a annotation PDB");
-    	
-    	
-      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;
@@ -86,7 +77,7 @@ public class AssociatePdbFileWithSeq
       {
         entry.setId(pdbfile.id);
       }
-    	
+
     } catch (java.io.IOException ex)
     {
       ex.printStackTrace();
@@ -95,7 +86,5 @@ public class AssociatePdbFileWithSeq
     entry.setFile(choice);
     sequence.getDatasetSequence().addPDBId(entry);
     return entry;
-    
   }
-
 }