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//******************************************************************************
//
// File: ExtractProtein.java
// Package: edu.rit.compbio.seq.test
// Unit: Class edu.rit.compbio.seq.test.ExtractProtein
//
// 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.seq.test;
import edu.rit.compbio.seq.ProteinDatabase;
import edu.rit.compbio.seq.ProteinSequence;
import java.io.File;
/**
* Class ExtractProtein is a unit test main program for classes {@linkplain
* edu.rit.compbio.seq.ProteinDatabase} and {@linkplain
* edu.rit.compbio.seq.ProteinSequence}. The program extracts the protein
* sequence at a given index from the protein sequence database and prints it on
* the standard output in FASTA format.
* <P>
* Usage: java edu.rit.compbio.seq.test.ExtractProtein <I>databasefile</I>
* <I>indexfile</I> <I>index</I>
* <BR><I>databasefile</I> = Protein sequence database file
* <BR><I>indexfile</I> = Protein sequence index file
* <BR><I>index</I> = Protein sequence index
*
* @author Alan Kaminsky
* @version 01-Jul-2008
*/
public class ExtractProtein
{
// Prevent construction.
private ExtractProtein()
{
}
// Main program.
/**
* Main program.
*/
public static void main
(String[] args)
throws Exception
{
// Parse command line arguments.
if (args.length != 3) usage();
File databasefile = new File (args[0]);
File indexfile = new File (args[1]);
long index = Long.parseLong (args[2]);
// Set up protein sequence database.
ProteinDatabase db = new ProteinDatabase (databasefile, indexfile);
// Get and print protein sequence.
ProteinSequence seq = db.getProteinSequence (index);
System.out.print (seq.description());
String s = seq.elementsToString();
int n = s.length();
int i = 0;
while (i < n)
{
if (i % 60 == 0) System.out.println();
System.out.print (s.charAt(i));
++ i;
}
System.out.println();
// All done.
db.close();
}
// Hidden operations.
/**
* Print a usage message and exit.
*/
private static void usage()
{
System.err.println ("Usage: java edu.rit.compbio.seq.test.ExtractProtein <databasefile> <indexfile> <index>");
System.err.println ("<databasefile> = Protein sequence database file");
System.err.println ("<indexfile> = Protein sequence index file");
System.err.println ("<index> = Protein sequence index");
System.exit (1);
}
}
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