/*
- * 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
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!
*
*/
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();
}
/**
* 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();
* off.
*
* @param source
- * @throws IOException
+ * @throws Exception
*/
- public AlignFile(FileParse source) throws IOException
+ public AlignFile(FileParse source) throws Exception
{
super(source);
initData();
/**
* 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.