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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "ProfileStandard.h"
namespace clustalw
{
/**
*
* @param prfLen
* @param firstS
* @param lastS
* @return
*/
ProfileStandard::ProfileStandard(int prfLen, int firstS, int lastS)
: ProfileBase(prfLen, firstS, lastS)
{
}
/**
*
*/
void ProfileStandard::resetPrf2()
{
profile.clear();
}
/**
*
* @param seqArray
* @param seqWeight
*/
void ProfileStandard::calcStandardProfile(SeqArray* seqArray, vector<int>* seqWeight)
{
/** DONT FORGET TO CHECK THE SIZES ARE CORRECT */
int sum1, sum2;
int i, d;
int r;
int _maxAA = userParameters->getMaxAA();
profile.resize(prfLength + 2, vector<int>(LENCOL + 2));
int _gapPos1 = userParameters->getGapPos1();
int _gapPos2 = userParameters->getGapPos2();
for (r = 0; r < prfLength; r++)
{
/*
* calculate sum2 = number of residues found in this column
*/
sum2 = 0;
for (i = firstSeq; i < lastSeq; i++)
{
sum2 += (*seqWeight)[i];
}
/*
* only include matrix comparison scores for those residue types found in this
* column
*/
if (sum2 == 0)
{
for (d = 0; d <= _maxAA; d++)
{
profile[r + 1][d] = 0;
}
profile[r + 1][_gapPos1] = 0;
profile[r + 1][_gapPos2] = 0;
}
else
{
for (d = 0; d <= _maxAA; d++)
{
sum1 = 0;
for (i = firstSeq; i < lastSeq; i++)
{
if (d == (*seqArray)[i][r])
{
sum1 += (*seqWeight)[i];
}
}
profile[r + 1][d] = (int)(10 *(float)sum1 / (float)sum2);
}
sum1 = 0;
for (i = firstSeq; i < lastSeq; i++)
{
if (_gapPos1 == (*seqArray)[i][r])
{
sum1 += (*seqWeight)[i];
}
}
profile[r + 1][_gapPos1] = (int)(10 *(float)sum1 / (float)sum2);
sum1 = 0;
for (i = firstSeq; i < lastSeq; i++)
{
if (_gapPos2 == (*seqArray)[i][r])
{
sum1 += (*seqWeight)[i];
}
}
profile[r + 1][_gapPos2] = (int)(10 *(float)sum1 / (float)sum2);
}
}
}
}
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