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/* $Id: $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's offical duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================*/
/*****************************************************************************
File name: njn_localmaxstatmatrix.cpp
Author: John Spouge
Contents:
******************************************************************************/
#include "njn_localmaxstatmatrix.hpp"
#include "njn_localmaxstatutil.hpp"
#include "njn_memutil.hpp"
using namespace Njn;
void LocalMaxStatMatrix::init (size_t dimMatrix_, size_t dimMatrix2_)
{
if (dimMatrix2_ == 0) dimMatrix2_ = dimMatrix_;
if (dimMatrix_ > 0 && dimMatrix2_ > 0)
{
d_scoreMatrix_p = MemUtil::newMatrix <long int> (dimMatrix_, dimMatrix2_);
d_p_p = new double [dimMatrix_];
d_p2_p = new double [dimMatrix2_];
}
d_dimMatrix = dimMatrix_;
d_dimMatrix2 = dimMatrix2_;
}
void LocalMaxStatMatrix::free2 ()
{
if (getDimMatrix () > 0 && getDimMatrix2 () > 0)
{
MemUtil::deleteMatrix <long int> (d_scoreMatrix_p, getDimMatrix (), getDimMatrix2 ());
d_scoreMatrix_p = 0;
delete [] d_p_p; d_p_p = 0;
delete [] d_p2_p; d_p2_p = 0;
}
d_dimMatrix = 0;
d_dimMatrix2 = 0;
}
void LocalMaxStatMatrix::copy (
size_t dimMatrix_, // #(distinct values) of scores & probabilities (which are paired)
const long int *const *scoreMatrix_, // score matrix [0...dimMatrix_)[0...dimMatrix_)
const double *p_, // probability of "letters" p_ [0...dimMatrix_)
const double *p2_, // probability of "letters" p2_ [0...dimMatrix_), the second (j) set of letter-probabilities
size_t dimMatrix2_) // #(distinct letters) in the second alphabet
{
if (! p2_) p2_ = p_;
if (dimMatrix2_ == 0) dimMatrix2_ = dimMatrix_;
free2 ();
init (dimMatrix_, dimMatrix2_);
if (getDimMatrix () == 0)
{
LocalMaxStat::copy (0, 0, 0, 0.0, 0.0, 0.0, 0.0, 0.0, 0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0);
return;
}
size_t i = 0;
size_t j = 0;
d_dimMatrix = dimMatrix_;
d_dimMatrix2 = dimMatrix2_;
for (i = 0; i < getDimMatrix (); i++)
{
memcpy (d_scoreMatrix_p [i], scoreMatrix_ [i], sizeof (long int) * getDimMatrix2 ());
}
memcpy (d_p_p, p_, sizeof (double) * getDimMatrix ());
memcpy (d_p2_p, p2_, sizeof (double) * getDimMatrix2 ());
size_t dim = 0;
long int *score = 0;
double *p = 0;
double **probMatrix = MemUtil::newMatrix <double> (getDimMatrix (), getDimMatrix2 ());
for (i = 0; i != getDimMatrix (); i++)
{
for (j = 0; j != getDimMatrix2 (); j++)
{
probMatrix [i][j] = p_ [i] * p2_ [j];
}
}
LocalMaxStatUtil::flatten (getDimMatrix (), getScoreMatrix (), probMatrix, &dim, &score, &p, getDimMatrix2 ());
LocalMaxStat::copy (dim, score, p);
delete [] p; p = 0;
delete [] score; score = 0;
MemUtil::deleteMatrix <double> (probMatrix, getDimMatrix (), getDimMatrix2 ());
}
void LocalMaxStatMatrix::copy (
LocalMaxStat localMaxStat_, // base object
size_t dimMatrix_, // #(distinct values) of scores & probabilities (which are paired)
const long int *const *scoreMatrix_, // score matrix [0...dimMatrix_)[0...dimMatrix_)
const double *p_, // probability of "letters" p_ [0...dimMatrix_)
const double *p2_, // probability of "letters" p2_ [0...dimMatrix_), the second (j) set of letter-probabilities
size_t dimMatrix2_) // #(distinct letters) in the second alphabet
{
if (! p2_) p2_ = p_;
if (dimMatrix2_ == 0) dimMatrix2_ = dimMatrix_;
free2 ();
init (dimMatrix_);
size_t i = 0;
/*sls deleted size_t j = 0;*/
d_dimMatrix = dimMatrix_;
d_dimMatrix2 = dimMatrix2_;
for (i = 0; i < getDimMatrix (); i++)
{
memcpy (d_scoreMatrix_p [i], scoreMatrix_ [i], sizeof (long int) * getDimMatrix2 ());
}
memcpy (d_p_p, p_, sizeof (double) * getDimMatrix ());
memcpy (d_p2_p, p2_, sizeof (double) * getDimMatrix2 ());
LocalMaxStat::copy (localMaxStat_);
}
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