//******************************************************************************
//
// File: DefaultAlignmentStats.java
// Package: edu.rit.compbio.seq
// Unit: Class edu.rit.compbio.seq.DefaultAlignmentStats
//
// 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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// 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.
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//******************************************************************************
package edu.rit.compbio.seq;
import java.io.PrintStream;
/**
* Class DefaultAlignmentStats provides an object that computes
* statistics of an {@linkplain Alignment}. Methods are provided to compute the
* raw score, the bit score, and the E-value. The formulas for these
* statistics assume that the alignment:
*
* -
* is for two protein sequences,
*
-
* was calculated by the Smith-Waterman local alignment algorithm,
*
-
* using the BLOSUM-62 protein substitution matrix,
*
-
* using a gap existence penalty of −11 and a gap extension penalty of
* −1,
*
-
* matching a query sequence against a database of subject sequences, where the
* sum of the subject sequence lengths is supplied as a constructor parameter.
*
*
* The formulas for the bit score and E-value are:
*
* S' = (λ S − ln K)/(ln 2)
*
* E = K m n exp(−λ S)
*
* where S is the raw score, m is the query sequence length,
* n is the total subject sequence length, and the parameters are
* K = 0.035, λ = 0.252.
*
* These formulas were taken from:
*
*
* @author Alan Kaminsky
* @version 01-Jul-2008
*/
public class DefaultAlignmentStats
implements AlignmentStats
{
// Hidden constants.
private static final double K = 0.035;
private static final double lambda = 0.252;
private static final double LN_K = Math.log(K);
private static final double LN_2 = Math.log(2.0);
// Hidden data members.
// Total subject sequence length.
private long n;
// Exported constructors.
/**
* Construct a new default alignment statistics object.
*
* @param n Sum of the lengths of the subject sequences in the database.
*/
public DefaultAlignmentStats
(long n)
{
this.n = n;
}
// Exported operations.
/**
* Returns the raw score for the given alignment. A larger raw score
* signifies a greater degree of similarity between the query sequence and
* subject sequence that were aligned.
*
* @param alignment Alignment.
*
* @return Raw score.
*/
public double rawScore
(Alignment alignment)
{
return alignment.myScore;
}
/**
* Returns the bit score for the given alignment. A larger bit score
* signifies a greater degree of similarity between the query sequence and
* subject sequence that were aligned.
*
* The bit score is the raw score normalized to units of "bits." Bit scores
* for different alignment procedures may be compared, whereas raw
* (unnormalized) scores for different alignment procedures may not be
* compared.
*
* @param alignment Alignment.
*
* @return Bit score.
*/
public double bitScore
(Alignment alignment)
{
double S = alignment.myScore;
return (lambda*S - LN_K)/LN_2;
}
/**
* Returns the E-value (expect value) for the given alignment. A
* smaller E-value signifies a more statistically significant degree
* of similarity between the query sequence and subject sequence that were
* aligned.
*
* The E-value is the expected number of alignments with a score
* greater than or equal to the alignment's score when a
* randomly-chosen query of the same length as the query that produced the
* alignment is matched against the database.
*
* @param alignment Alignment.
*
* @return Bit score.
*/
public double eValue
(Alignment alignment)
{
int m = alignment.myQueryLength;
double S = alignment.myScore;
return K*m*n*Math.exp(-lambda*S);
}
/**
* Print information about this alignment statistics object on the given
* print stream.
*
* @param out Print stream.
*/
public void print
(PrintStream out)
{
out.println ("K: "+K);
out.println ("Lambda: "+lambda);
out.println ("Matrix: BLOSUM-62");
out.println ("Gap Penalties: Existence: -11, Extension: -1");
}
}