Merge branch 'JAL-1403' into develop

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index c0f8531..81d0ae4 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -27,15 +27,6 @@ import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Vector;
 
-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;
-
 /**
  * DOCUMENT ME!
  * 
@@ -85,9 +76,8 @@ public abstract class AlignFile extends FileParse
    *          Filename to read from.
    * @param type
    *          What type of file to read from (File, URL)
- * @throws Exception 
    */
-  public AlignFile(String inFile, String type) throws Exception
+  public AlignFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
     initData();
@@ -104,9 +94,9 @@ public abstract class AlignFile extends FileParse
    * off.
    * 
    * @param source
- * @throws Exception 
+   * @throws IOException
    */
-  public AlignFile(FileParse source) throws Exception
+  public AlignFile(FileParse source) throws IOException
   {
     super(source);
     initData();
@@ -251,9 +241,8 @@ public abstract class AlignFile extends FileParse
 
   /**
    * This method must be implemented to parse the contents of the file.
-
    */
-  public abstract void parse() throws Exception;
+  public abstract void parse() throws IOException;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.