/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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
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.*;
/**
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
+ * @throws Exception
*/
- public JPredFile(String inFile, String type) throws IOException
+ public JPredFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
- public JPredFile(FileParse source) throws IOException
+ public JPredFile(FileParse source) throws Exception
{
super(source);
}
for (int j = 0; j < i; j++)
{
- scores.setElementAt((Object) ((Float) scores.elementAt(j))
- .toString(), j);
+ scores.setElementAt(
+ (Object) ((Float) scores.elementAt(j)).toString(), j);
}
scores.addElement((Object) ascore);
}
if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
- .startsWith("align;"))
- && (QuerySeqPosition == -1))
+ .startsWith("align;")) && (QuerySeqPosition == -1))
{
QuerySeqPosition = seqs.size();
}
*
* @param args
* DOCUMENT ME!
+ * @throws Exception
*/
- public static void main(String[] args)
+ public static void main(String[] args) throws Exception
{
try
{