Anne reinstated general stockholm parser code but extended to support pseudoknot...

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

diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index b407a45..53d2790 100644 (file)
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 
@@ -20,8 +20,16 @@ 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.*;
 
 /**
  * parse a simple blast report. Attempt to cope with query anchored and pairwise
@@ -46,12 +54,12 @@ public class SimpleBlastFile extends AlignFile
   {
   }
 
-  public SimpleBlastFile(String inFile, String type) throws IOException
+  public SimpleBlastFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
   }
 
-  public SimpleBlastFile(FileParse source) throws IOException
+  public SimpleBlastFile(FileParse source) throws Exception
   {
     super(source);
   }