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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 "ProfileWithSub.h"
namespace clustalw
{
/**
*
* @param prfLen
* @param firstS
* @param lastS
* @return
*/
ProfileWithSub::ProfileWithSub(int prfLen, int firstS, int lastS)
: ProfileBase(prfLen, firstS, lastS)
{
}
/**
*
*/
void ProfileWithSub::resetPrf1()
{
profile.clear();
}
/**
*
* @param seqArray
* @param gaps
* @param matrix[][]
* @param seqWeight
*/
void ProfileWithSub::calcProfileWithSub(SeqArray* seqArray, vector<int>* gaps,
int matrix[NUMRES][NUMRES], vector<int>* seqWeight)
{
vector<vector<int> > weighting;
int sum2, aa, seq, res;
int _numSeq;
int col, pos;
int f;
float scale;
int _maxAA = userParameters->getMaxAA();
int _gapPos1 = userParameters->getGapPos1();
int _gapPos2 = userParameters->getGapPos2();
weighting.resize(NUMRES + 2, vector<int>(prfLength + 2));
_numSeq = lastSeq - firstSeq;
sum2 = 0;
for (seq = firstSeq; seq < lastSeq; seq++)
{
sum2 += (*seqWeight)[seq];
}
for (col = 0; col < prfLength; col++)
{
for (aa = 0; aa <= _maxAA; aa++)
{
weighting[aa][col] = 0;
for (seq = firstSeq; seq < lastSeq; seq++)
if (aa == (*seqArray)[seq][col])
{
weighting[aa][col] += (*seqWeight)[seq];
}
}
weighting[_gapPos1][col] = 0;
for (seq = firstSeq; seq < lastSeq; seq++)
{
if (_gapPos1 == (*seqArray)[seq][col])
{
weighting[_gapPos1][col] += (*seqWeight)[seq];
}
}
weighting[_gapPos2][col] = 0;
for (seq = firstSeq; seq < lastSeq; seq++)
{
if (_gapPos2 == (*seqArray)[seq][col])
{
weighting[_gapPos2][col] += (*seqWeight)[seq];
}
}
}
for (pos = 0; pos < prfLength; pos++)
{
if ((*gaps)[pos] == _numSeq) // If all gaps
{
for (res = 0; res <= _maxAA; res++)
{
profile[pos + 1][res] = matrix[res][_gapPos1];
}
profile[pos + 1][_gapPos1] = matrix[_gapPos1][_gapPos1];
profile[pos + 1][_gapPos2] = matrix[_gapPos2][_gapPos1];
}
else
{
scale = (float)(_numSeq - (*gaps)[pos]) / (float)_numSeq;
for (res = 0; res <= _maxAA; res++)
{
f = 0;
for (aa = 0; aa <= _maxAA; aa++)
{
f += (weighting[aa][pos] * matrix[aa][res]);
}
f += (weighting[_gapPos1][pos] * matrix[_gapPos1][res]);
f += (weighting[_gapPos2][pos] * matrix[_gapPos2][res]);
profile[pos + 1][res] = (int)(((float)f / (float)sum2) * scale);
}
f = 0;
for (aa = 0; aa <= _maxAA; aa++)
{
f += (weighting[aa][pos] * matrix[aa][_gapPos1]);
}
f += (weighting[_gapPos1][pos] * matrix[_gapPos1][_gapPos1]);
f += (weighting[_gapPos2][pos] * matrix[_gapPos2][_gapPos1]);
profile[pos + 1][_gapPos1] = (int)(((float)f / (float)sum2) * scale);
f = 0;
for (aa = 0; aa <= _maxAA; aa++)
{
f += (weighting[aa][pos] * matrix[aa][_gapPos2]);
}
f += (weighting[_gapPos1][pos] * matrix[_gapPos1][_gapPos2]);
f += (weighting[_gapPos2][pos] * matrix[_gapPos2][_gapPos2]);
profile[pos + 1][_gapPos2] = (int)(((float)f / (float)sum2) * scale);
}
}
}
}
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