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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 "LowScoreSegProfile.h"
namespace clustalw
{
LowScoreSegProfile::LowScoreSegProfile(int prfLen, int firstS, int lastS)
: prfLength(prfLen),
firstSeq(firstS),
lastSeq(lastS)
{
profile.resize(prfLength + 2, vector<int>(LENCOL + 2));
}
void LowScoreSegProfile::calcLowScoreSegProfile(const SeqArray* seqArray,
int matrix[NUMRES][NUMRES], vector<int>* seqWeight)
{
vector<vector<int> > weighting;
int d, i, res;
int r, pos;
int f;
int _gapPos1 = userParameters->getGapPos1();
int _gapPos2 = userParameters->getGapPos2();
int _maxAA = userParameters->getMaxAA();
weighting.resize(NUMRES + 2, vector<int>(prfLength + 2));
for (r = 0; r < prfLength; r++)
{
for (d = 0; d <= _maxAA; d++)
{
weighting[d][r] = 0;
for (i = firstSeq; i < lastSeq; i++)
{
if (r + 1 < (int)(*seqArray)[i + 1].size() - 1)
{
if (d == (*seqArray)[i + 1][r + 1])
{
weighting[d][r] += (*seqWeight)[i];
}
}
}
}
weighting[_gapPos1][r] = 0;
for (i = firstSeq; i < lastSeq; i++)
{
if (r + 1 < (int)(*seqArray)[i + 1].size() - 1)
{
if (_gapPos1 == (*seqArray)[i + 1][r + 1])
{
weighting[_gapPos1][r] += (*seqWeight)[i];
}
}
}
weighting[_gapPos2][r] = 0;
for (i = firstSeq; i < lastSeq; i++)
{
if (r + 1 < (int)(*seqArray)[i + 1].size() - 1)
{
if (_gapPos2 == (*seqArray)[i + 1][r + 1])
{
weighting[_gapPos2][r] += (*seqWeight)[i];
}
}
}
}
for (pos = 0; pos < prfLength; pos++)
{
for (res = 0; res <= _maxAA; res++)
{
f = 0;
for (d = 0; d <= _maxAA; d++)
{
f += (weighting[d][pos] * matrix[d][res]);
}
f += (weighting[_gapPos1][pos] * matrix[_gapPos1][res]);
f += (weighting[_gapPos2][pos] * matrix[_gapPos2][res]);
profile[pos + 1][res] = f;
}
f = 0;
for (d = 0; d <= _maxAA; d++)
{
f += (weighting[d][pos] * matrix[d][_gapPos1]);
}
f += (weighting[_gapPos1][pos] * matrix[_gapPos1][_gapPos1]);
f += (weighting[_gapPos2][pos] * matrix[_gapPos2][_gapPos1]);
profile[pos + 1][_gapPos1] = f;
f = 0;
for (d = 0; d <= _maxAA; d++)
{
f += (weighting[d][pos] * matrix[d][_gapPos2]);
}
f += (weighting[_gapPos1][pos] * matrix[_gapPos1][_gapPos2]);
f += (weighting[_gapPos2][pos] * matrix[_gapPos2][_gapPos2]);
profile[pos + 1][_gapPos2] = f;
}
}
}
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