fix merge conflicts for finess on JAL-1140 (introduced by 1a8f953dd71a9e319e910261927...

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

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index ef7dad0..4c31ce4 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -18,15 +18,6 @@
 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 fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
@@ -39,23 +30,19 @@ import jalview.datamodel.SequenceI;
 public class AssociatePdbFileWithSeq
 {
 
-/**
- * assocate the given PDB file with 
- * @param choice
- * @param sequence
- * @throws IOException 
- */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws Exception
+  /**
+   * 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)
       {
@@ -81,7 +68,7 @@ public class AssociatePdbFileWithSeq
       {
         entry.setId(pdbfile.id);
       }
-       
+
     } catch (java.io.IOException ex)
     {
       ex.printStackTrace();
@@ -90,7 +77,5 @@ public class AssociatePdbFileWithSeq
     entry.setFile(choice);
     sequence.getDatasetSequence().addPDBId(entry);
     return entry;
-    
   }
-
 }