X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAlignFile.java;h=c0f85313ee804aa666ff9395e0e0ecbe0121205e;hb=1a8f953dd71a9e319e910261927f269d69b4692c;hp=36dbdb6193df2e8055eca82770ca0e88a4167e7b;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 36dbdb6..c0f8531 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * 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 
@@ -27,6 +27,15 @@ 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!
  * 
@@ -65,6 +74,8 @@ public abstract class AlignFile extends FileParse
    */
   public AlignFile()
   {
+	  // Shouldn't we init data structures (JBPNote: not sure - initData is for initialising the structures used for reading from a datasource, and the bare constructor hasn't got any datasource)
+	  initData();
   }
 
   /**
@@ -74,8 +85,9 @@ 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 IOException
+  public AlignFile(String inFile, String type) throws Exception
   {
     super(inFile, type);
     initData();
@@ -92,9 +104,9 @@ public abstract class AlignFile extends FileParse
    * off.
    * 
    * @param source
-   * @throws IOException
+ * @throws Exception 
    */
-  public AlignFile(FileParse source) throws IOException
+  public AlignFile(FileParse source) throws Exception
   {
     super(source);
     initData();
@@ -239,8 +251,9 @@ public abstract class AlignFile extends FileParse
 
   /**
    * This method must be implemented to parse the contents of the file.
+
    */
-  public abstract void parse() throws IOException;
+  public abstract void parse() throws Exception;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.