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//******************************************************************************
//
// File: ProteinLocalAlignmentSeq.java
// Package: edu.rit.compbio.seq
// Unit: Class edu.rit.compbio.seq.ProteinLocalAlignmentSeq
//
// 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;
/**
* Class ProteinLocalAlignmentSeq provides an object that does local alignments
* of {@linkplain ProteinSequence}s. For further information, see the base class
* {@linkplain ProteinLocalAlignment}.
* <P>
* The <TT>align()</TT> method is designed to be executed by a single thread.
* Thus, this class is suitable for use in a sequential program or one process
* of a cluster parallel program.
*
* @author Alan Kaminsky
* @version 01-Jul-2008
*/
public class ProteinLocalAlignmentSeq
extends ProteinLocalAlignment
{
// Exported constructors.
/**
* Construct a new protein sequence local alignment object.
*/
public ProteinLocalAlignmentSeq()
{
super();
}
// Exported operations.
/**
* Align the query sequence and the subject sequence.
*
* @return Alignment.
*/
public Alignment align()
{
// Verify preconditions.
if (A == null)
{
throw new IllegalStateException
("ProteinLocalAlignmentSeq.align(): Query sequence not set");
}
if (B == null)
{
throw new IllegalStateException
("ProteinLocalAlignmentSeq.align(): Subject sequence not set");
}
int M = A.length - 1;
int N = B.length - 1;
// Do the Smith-Waterman algorithm in a single thread.
int maxScore = 0;
int theQueryFinish = 0;
int theSubjectFinish = 0;
for (int i = 1; i <= M; ++ i)
{
int A_i = A[i];
int[] delta_A_i = delta[A_i];
int[] S_im1 = S[i-1];
int[] S_i = S[i];
int[] GA_im1 = GA[i-1];
int[] GA_i = GA[i];
int[] GB_i = GB[i];
int B_j, S_i_j, GA_i_j, GB_i_j;
for (int j = 1; j <= N; ++ j)
{
B_j = B[j];
GA_i_j = S_im1[j] + g;
GA_i_j = Math.max (GA_i_j, GA_im1[j] + h);
GB_i_j = S_i[j-1] + g;
GB_i_j = Math.max (GB_i_j, GB_i[j-1] + h);
S_i_j = S_im1[j-1] + delta_A_i[B_j];
S_i_j = Math.max (S_i_j, GA_i_j);
S_i_j = Math.max (S_i_j, GB_i_j);
S_i_j = Math.max (S_i_j, 0);
if (S_i_j > maxScore)
{
maxScore = S_i_j;
theQueryFinish = i;
theSubjectFinish = j;
}
S_i[j] = S_i_j;
GA_i[j] = GA_i_j;
GB_i[j] = GB_i_j;
}
}
// Do the traceback.
return computeTraceback (maxScore, theQueryFinish, theSubjectFinish);
}
}
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