//*****************************************************************************
//
// File:    Test02.java
// Package: edu.rit.compbio.phyl.test
// Unit:    Class edu.rit.compbio.phyl.test.Test02
//
// This Java source file is copyright (C) 2008 by Alan Kaminsky. All rights
// reserved. For further information, contact the author, Alan Kaminsky, at
// ark@cs.rit.edu.
//
// This Java source file is part of the Parallel Java Library ("PJ"). PJ 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.
//
// PJ 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 PURPOSE. See the GNU General Public License for more details.
//
// Linking this library statically or dynamically with other modules is making a
// combined work based on this library. Thus, the terms and conditions of the
// GNU General Public License cover the whole combination.
//
// As a special exception, the copyright holders of this library give you
// permission to link this library with independent modules to produce an
// executable, regardless of the license terms of these independent modules, and
// to copy and distribute the resulting executable under terms of your choice,
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// library, you may extend this exception to your version of the library, but
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// exception statement from your version.
//
// A copy of the GNU General Public License is provided in the file gpl.txt. You
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//******************************************************************************

package edu.rit.compbio.phyl.test;

import edu.rit.compbio.phyl.DnaSequenceList;

import java.io.File;

/**
 * Class Test02 is a unit test program for class {@linkplain
 * edu.rit.compbio.phyl.DnaSequenceList}. It reads DNA sequences from a
 * PHYLIP-formatted input file, excises the uninformative sites, and prints the
 * resulting DNA sequences to a PHYLIP-formatted output file. It also prints the
 * number of state changes from the uninformative sites.
 * <P>
 * Usage: java edu.rit.compbio.phyl.test.Test02 <I>infile</I> <I>outfile</I>
 *
 * @author  Alan Kaminsky
 * @version 14-Jul-2008
 */
public class Test02
	{

// Prevent construction.

	private Test02()
		{
		}

// Main program.

	/**
	 * Unit test main program.
	 */
	public static void main
		(String[] args)
		throws Exception
		{
		if (args.length != 2) usage();
		File infile = new File (args[0]);
		File outfile = new File (args[1]);
		System.out.println ("Reading input file ...");
		DnaSequenceList list = DnaSequenceList.read (infile);
		int sites = list.seq(0).length();
		System.out.println ("Excising uninformative sites ...");
		int nChanges = list.exciseUninformativeSites();
		System.out.println ("Writing output file ...");
		list.write (outfile, 70, true, false);
		System.out.println (sites + " sites");
		System.out.println (list.seq(0).length() + " informative sites");
		System.out.println (nChanges + " state changes from uninformative sites");
		}

// Hidden operations.

	private static void usage()
		{
		System.err.println ("Usage: java edu.rit.compbio.phyl.test.Test02 <infile> <outfile>");
		System.exit (1);
		}

	}