double GRN::aminoASAlignment(std::string s, int s_size, std::string t, int t_size){
double G_ = gap;
double _G = gap;
double normalization_s = 0;
double normalization_t = 0;
double similarity = 0;
std::vector< std::vector<double> > alignMatrix (t_size, std::vector<double>(s_size));
//initialize alignMatrix;
alignMatrix[0][0] = 0;
for (int i = 1; i != t_size; ++i) {
alignMatrix[i][0] = alignMatrix[i - 1][0] + G_;
}
for (int j = 1; j != s_size; ++j) {
alignMatrix[0][j] = alignMatrix[0][j - 1] + _G;
}
for (int i = 1; i != t_size; ++i) {
for (int j = 1; j != s_size; ++j) {
//alignMatrix[i][j] = maxValue(alignMatrix[i-1][j-1] + alignScore(s[j],t[i]), alignMatrix[i-1][j] + alignScore(s[j], ' '), alignMatrix[i][j-1] + alignScore(' ', t[i]));
double st = 0;
double s_ = 0;
double _t = 0;
st = alignMatrix[i - 1][j - 1] + alignScore(s[j], t[i]);
s_ = alignMatrix[i - 1][j] + alignScore(s[j], ' ');
_t = alignMatrix[i][j - 1] + alignScore(' ', t[i]);
alignMatrix[i][j] = maxValue(st, s_, _t);
}
}
//normalize alignment score;
for (int i = 1; i != s_size; ++i) {
normalization_s += alignScore(s[i], s[i]);
}
for (int i = 0; i != t_size; ++i) {
normalization_t += alignScore(t[i], t[i]);
}
similarity = fabs(2 * alignMatrix[t_size - 1][s_size - 1]) / (normalization_s + normalization_t);
return similarity;
}
int Transcript::variationAdjust(const Genome &mapGen, char *R)
{
Variation &Var=*mapGen.Var;
if (!Var.yes)
{//no variation
return 0;
};
int dScore=0;//change in the score
uint nMM1=0;
//for each block, check whether it overlaps one or more SNPs
for (uint ie=0; ie<nExons; ie++)
{
//binary search to find nearest SNP
int32 isnp=binarySearch1b <uint> (exons[ie][EX_G], Var.snp.loci, Var.snp.N);
if (isnp>=0)
{
while ((uint)isnp<Var.snp.N && exons[ie][EX_G]+exons[ie][EX_L]>Var.snp.loci[isnp])
{//these SNPs overlap the block
varInd.push_back(isnp); //record snp index
varGenCoord.push_back(Var.snp.loci[isnp]-mapGen.chrStart[Chr]);
varReadCoord.push_back(exons[ie][EX_R]+Var.snp.loci[isnp]-exons[ie][EX_G]);
char ntR=R[varReadCoord.back()];//nt of the read in the SNP position, already trnasformed to + genome strand
uint8 igt;
if (ntR>3) {
igt=4;
} else {
for (igt=1; igt<3; igt++) {//1st or 2nd allele, =3 of none
if (Var.snp.nt[isnp][igt]==ntR) {
break;
};
};
};
//if (ntR == Var.snp.nt[isnp][0])
//{//mark snp that agrees with the reference
// igt*=10;
//};
varAllele.push_back(igt);
if (igt<3 && ntR != Var.snp.nt[isnp][0])
{//non-reference allele, correct nMM and score
++nMM1;
};
++isnp;
};
};
};
#define VAR_noScoreCorrection
#ifndef VAR_noScoreCorrection
if (nMM1>0)
{//one or more mismtaches need to be corrected
uint nMMold=nMM;
alignScore(Read1, G, P);
nMM-=nMM1;
nMatch+=nMM1;
dScore=2*(nMMold-nMM);//score only changes if the number of mismatches is reduced after SNP adjustment
};
#else
//#warning VAR_noScoreCorrection set: no variation score correction
#endif
return dScore;
};