revised RNA stem/loop processing code that copes with pseudoknots

[jalview.git] / src / jalview / io / MSFfile.java

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 7c70a09..dcbe37d 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -20,6 +20,15 @@ package jalview.io;
 import java.io.*;
 import java.util.*;
 
+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.*;
 import jalview.util.*;
 
@@ -46,16 +55,14 @@ public class MSFfile extends AlignFile
    *          DOCUMENT ME!
    * @param type
    *          DOCUMENT ME!
-   * 
-   * @throws IOException
-   *           DOCUMENT ME!
+ * @throws Exception 
    */
-  public MSFfile(String inFile, String type) throws IOException
+  public MSFfile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public MSFfile(FileParse source) throws IOException
+  public MSFfile(FileParse source) throws Exception
   {
     super(source);
   }