public static double BLAST_SpougeStoE(int y_, Blast_KarlinBlk kbp, Blast_GumbelBlk gbp, int m_, int n_)
{
// the score and lambda may have been rescaled. We will compute the scaling factor
// and use it to scale a, alpha, and Sigma similarly.
double scale_factor = kbp.Lambda / gbp.Lambda;
// the pair-wise e-value must be scaled back to db-wise e-value
double db_scale_factor = (gbp.db_length.HasValue) ?
(double)gbp.db_length.Value / (double)n_ : 1.0;
double lambda_ = kbp.Lambda;
double k_ = kbp.K;
double ai_hat_ = gbp.a * scale_factor;
double bi_hat_ = gbp.b;
double alphai_hat_ = gbp.Alpha * scale_factor;
double betai_hat_ = gbp.Beta;
double sigma_hat_ = gbp.Sigma * scale_factor;
double tau_hat_ = gbp.Tau;
/* here we consider symmetric matrix only */
double aj_hat_ = ai_hat_;
double bj_hat_ = bi_hat_;
double alphaj_hat_ = alphai_hat_;
double betaj_hat_ = betai_hat_;
/* this is 1/sqrt(2.0*PI) */
double const_val = 0.39894228040143267793994605993438;
double m_li_y, vi_y, sqrt_vi_y, m_F, P_m_F;
double n_lj_y, vj_y, sqrt_vj_y, n_F, P_n_F;
double c_y, p1, p2, area;
double e_value;
m_li_y = m_ - (ai_hat_ * y_ + bi_hat_);
vi_y = Math.Max(2.0 * alphai_hat_ / lambda_, alphai_hat_ * y_ + betai_hat_);
sqrt_vi_y = Math.Sqrt(vi_y);
m_F = m_li_y / sqrt_vi_y;
P_m_F = AdvancedMath.Erfc(-m_F / Math.Sqrt(2.0)) / 2.0;
p1 = m_li_y * P_m_F + sqrt_vi_y * const_val * Math.Exp(-0.5 * m_F * m_F);
n_lj_y = n_ - (aj_hat_ * y_ + bj_hat_);
vj_y = Math.Max(2.0 * alphaj_hat_ / lambda_, alphaj_hat_ * y_ + betaj_hat_);
sqrt_vj_y = Math.Sqrt(vj_y);
n_F = n_lj_y / sqrt_vj_y;
P_n_F = AdvancedMath.Erfc(-n_F / Math.Sqrt(2.0)) / 2.0;
p2 = n_lj_y * P_n_F + sqrt_vj_y * const_val * Math.Exp(-0.5 * n_F * n_F);
c_y = Math.Max(2.0 * sigma_hat_ / lambda_, sigma_hat_ * y_ + tau_hat_);
area = p1 * p2 + c_y * P_m_F * P_n_F;
e_value = area * k_ * Math.Exp(-lambda_ * y_) * db_scale_factor;
//ASSERT(e_value >= 0.0);
return(e_value);
}
public static double BLAST_KarlinStoE_simple(int score, Blast_KarlinBlk kbp, int searchsp)
{
var lambda = kbp.Lambda;
var k = kbp.K;
var h = kbp.H;
if (lambda < 0.0 || k < 0.0 || h < 0.0)
{
return(-1);
}
return(searchsp * Math.Exp(-lambda * score + kbp.logK));
}
