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//******************************************************************************
//
// File: Test04.java
// Package: edu.rit.compbio.phyl.test
// Unit: Class edu.rit.compbio.phyl.test.Test04
//
// 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,
// provided that you also meet, for each linked independent module, the terms
// and conditions of the license of that module. An independent module is a
// module which is not derived from or based on this library. If you modify this
// library, you may extend this exception to your version of the library, but
// you are not obligated to do so. If you do not wish to do so, delete this
// exception statement from your version.
//
// A copy of the GNU General Public License is provided in the file gpl.txt. You
// may also obtain a copy of the GNU General Public License on the World Wide
// Web at http://www.gnu.org/licenses/gpl.html.
//
//******************************************************************************
package edu.rit.compbio.phyl.test;
import edu.rit.compbio.phyl.DnaSequence;
import edu.rit.compbio.phyl.DnaSequenceList;
import edu.rit.compbio.phyl.DnaSequenceTree;
import edu.rit.compbio.phyl.FitchParsimony;
import edu.rit.compbio.phyl.JukesCantorDistance;
import edu.rit.compbio.phyl.TreeDrawing;
import edu.rit.compbio.phyl.Upgma;
import edu.rit.draw.Drawing;
import java.io.File;
/**
* Class Test04 is a unit test program for classes {@linkplain
* edu.rit.compbio.phyl.DnaSequenceList}, {@linkplain
* edu.rit.compbio.phyl.DnaSequenceTree}, {@linkplain
* edu.rit.compbio.phyl.FitchParsimony}, and {@linkplain
* edu.rit.compbio.phyl.Upgma}. The program:
* <OL TYPE=1>
* <LI>
* Reads a {@linkplain DnaSequenceList} from the input file in interleaved
* PHYLIP format.
* <LI>
* Constructs a phylogenetic tree using the UPGMA algorithm.
* <LI>
* Computes and prints the tree's Fitch parsimony score.
* <LI>
* Reorders the list of DNA sequences into descending order of branch length and
* stores the list in an output file.
* <LI>
* Stores a picture of the tree in an output file as a serialized {@linkplain
* edu.rit.draw.Drawing} object.
* </OL>
* <P>
* The {@linkplain View} program can be used to view the drawing file and
* save it in an image file in several formats.
* <P>
* Usage: java edu.rit.compbio.phyl.test.Test04 <I>infile</I> <I>outfile</I>
* <I>drawfile</I> [ <I>format</I> ]
* <BR><I>infile</I> = Input DNA sequence list file name
* <BR><I>outfile</I> = Output DNA sequence list file name
* <BR><I>drawfile</I> = Output drawing file name
* <BR><I>format</I> = DecimalFormat string for branch lengths (default:
* <TT>"0.00"</TT>)
*
* @author Alan Kaminsky
* @version 25-Jul-2008
*/
public class Test04
{
// Prevent construction.
private Test04()
{
}
// Main program.
/**
* Main program.
*/
public static void main
(String[] args)
throws Exception
{
// Parse command line arguments.
if (args.length < 3 || args.length > 4) usage();
File infile = new File (args[0]);
File outfile = new File (args[1]);
File drawfile = new File (args[2]);
TreeDrawing artist = new TreeDrawing();
if (args.length >= 4) artist.setBranchLengthFormat (args[3]);
// Read DNA sequence list.
DnaSequenceList seqlist = DnaSequenceList.read (infile);
// Construct phylogenetic tree.
DnaSequenceTree tree =
Upgma.buildTree (seqlist, new JukesCantorDistance());
// Compute and print Fitch parsimony score.
System.out.println ("Score = "+FitchParsimony.computeScore (tree));
// Reorder DNA sequence list and store in output file.
tree.toList().write (outfile, 70, true, false);
// Draw the tree and store in drawing file.
artist.draw (tree);
Drawing.write (drawfile);
}
// Hidden operations.
/**
* Print a usage message and exit.
*/
private static void usage()
{
System.err.println ("Usage: java edu.rit.compbio.phyl.test.Test04 <infile> <outfile> <drawfile> [<format>]");
System.err.println ("<infile> = Input DNA sequence list file name");
System.err.println ("<outfile> = Output DNA sequence list file name");
System.err.println ("<drawfile> = Drawing file name");
System.err.println ("<format> = DecimalFormat string for branch lengths (default: \"0.00\")");
System.exit (1);
}
}
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