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//*****************************************************************************
//
// File: PhylogenyParsExhSeq.java
// Package: edu.rit.compbio.phyl
// Unit: Class edu.rit.compbio.phyl.PhylogenyParsExhSeq
//
// 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;
import edu.rit.pj.Comm;
import java.io.File;
/**
* Class PhylogenyParsExhSeq is a sequential program for maximum parsimony
* phylogenetic tree construction using exhaustive search. The program reads a
* {@linkplain DnaSequenceList} from a file in interleaved PHYLIP format,
* constructs a list of one or more maximum parsimony phylogenetic trees using
* exhaustive search, and stores the results in an output directory. If the
* third command line argument <I>N</I> is specified, only the first <I>N</I>
* DNA sequences in the file are used; if <I>N</I> is not specified, all DNA
* sequences in the file are used. If the fourth command line argument <I>T</I>
* is specified, the program will only report the first <I>T</I> maximum
* parsimony phylogenetic trees it finds; if <I>T</I> is not specified, the
* default is <I>T</I> = 100.
* <P>
* To examine the results, use a web browser to look at the
* <TT>"index.html"</TT> file in the output directory. For further information,
* see class {@linkplain Results}.
* <P>
* Usage: java edu.rit.compbio.phyl.PhylogenyParsExhSeq <I>infile</I>
* <I>outdir</I> [ <I>N</I> [ <I>T</I> ] ]
* <BR><I>infile</I> = Input DNA sequence list file name
* <BR><I>outdir</I> = Output directory name
* <BR><I>N</I> = Number of DNA sequences to use (default: all)
* <BR><I>T</I> = Number of trees to report (default: 100)
*
* @author Alan Kaminsky
* @version 21-Nov-2008
*/
public class PhylogenyParsExhSeq
{
// Prevent construction.
private PhylogenyParsExhSeq()
{
}
// Main program.
/**
* Main program.
*/
public static void main
(String[] args)
throws Exception
{
// Start timing.
long t1 = System.currentTimeMillis();
Comm.init (args);
// Parse command line arguments.
if (args.length < 2 || args.length > 4) usage();
File infile = new File (args[0]);
File outdir = new File (args[1]);
int T = 100;
if (args.length >= 4) T = Integer.parseInt (args[3]);
// Read DNA sequence list from file and truncate to N sequences if
// necessary.
DnaSequenceList seqList = DnaSequenceList.read (infile);
int N = seqList.length();
if (args.length >= 3) N = Integer.parseInt (args[2]);
seqList.truncate (N);
// Excise uninformative sites.
DnaSequenceList excisedList = new DnaSequenceList (seqList);
int uninformativeScore = excisedList.exciseUninformativeSites();
long t2 = System.currentTimeMillis();
// Run the exhaustive search.
MaximumParsimonyResults results = new MaximumParsimonyResults (T);
MaximumParsimonyExhSeq searcher =
new MaximumParsimonyExhSeq (excisedList, results);
searcher.findTrees();
results.score (results.score() + uninformativeScore);
long t3 = System.currentTimeMillis();
// Report results.
Results.report
(/*directory */ outdir,
/*programName */ "edu.rit.compbio.phyl.PhylogenyParsExhSeq",
/*hostName */ Comm.world().host(),
/*K */ 1,
/*infile */ infile,
/*originalSeqList*/ seqList,
/*sortedSeqList */ seqList,
/*initialBound */ -1,
/*treeStoreLimit */ T,
/*results */ results,
/*t1 */ t1,
/*t2 */ t2,
/*t3 */ t3);
// Stop timing.
long t4 = System.currentTimeMillis();
System.out.println ((t2-t1)+" msec pre");
System.out.println ((t3-t2)+" msec calc");
System.out.println ((t4-t3)+" msec post");
System.out.println ((t4-t1)+" msec total");
}
// Hidden operations.
/**
* Print a usage message and exit.
*/
private static void usage()
{
System.err.println ("Usage: java edu.rit.compbio.phyl.PhylogenyParsExhSeq <infile> <outdir> [<N> [<T>]]");
System.err.println ("<infile> = Input DNA sequence list file name");
System.err.println ("<outdir> = Output directory name");
System.err.println ("<N> = Number of DNA sequences to use (default: all)");
System.err.println ("<T> = Number of trees to report (default: 100)");
System.exit (1);
}
}
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