v2

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

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index cbfbbc4..ade341d 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,10 +1,36 @@
+/*******************************************************************************
+ * 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
+ *
+ * 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 javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 
 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
@@ -18,12 +44,22 @@ 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 
  */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt)
+  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
   {
     PDBEntry entry = new PDBEntry();
     try
     {
+ 
+               System.out.println("This is a annotation PDB");
+       
+       
       MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
               protocol);
 
@@ -48,6 +84,7 @@ public class AssociatePdbFileWithSeq
       {
         entry.setId(pdbfile.id);
       }
+       
     } catch (java.io.IOException ex)
     {
       ex.printStackTrace();
@@ -56,6 +93,7 @@ public class AssociatePdbFileWithSeq
     entry.setFile(choice);
     sequence.getDatasetSequence().addPDBId(entry);
     return entry;
+    
   }
 
 }