void pvalues::calculate_P_values(
Int4 Score1,
Int4 Score2,
Int4 Seq1Len,
Int4 Seq2Len,
set_of_parameters &ParametersSet,
vector<double> &P_values,
vector<double> &P_values_errors)
{
if(Score2<Score1)
{
throw error("Error - Score2<Score1\n",2);
};
if(Seq1Len<=0||Seq2Len<=0)
{
throw error("Error - Seq1Len<=0||Seq2Len<=0\n",2);
};
Int4 ymin_=Score1;//calculation of P-values in the range [ymin_,ymax_]
Int4 ymax_=Score2;
Int4 m_=Seq1Len;//length of the first sequence
Int4 n_=Seq2Len;//length of the second sequence
set_of_parameters &par_=ParametersSet;
P_values.resize(ymax_-ymin_+1);
P_values_errors.resize(ymax_-ymin_+1);
Int4 y;
for(y=ymin_;y<=ymax_;y++)
{
double P;
double P_error;
double area;
bool area_is_1_flag=false;
if(read_Sbs_par_flag)
{
get_appr_tail_prob_with_cov_without_errors(
par_,
blast,
(double)y,
m_,
n_,
P,
P_error,
area,
a_normal,
b_normal,
h_normal,
N_normal,
p_normal,
area_is_1_flag);
double P_tmp,area_tmp;
if(par_.m_LambdaSbs.size()>0)
{
get_P_error_using_splitting_method(
par_,
blast,
(double)y,
m_,
n_,
P_tmp,
P_error,
area_tmp,
a_normal,
b_normal,
h_normal,
N_normal,
p_normal,
area_is_1_flag);
if(P_tmp>0)
{
P_error=P_error/P_tmp*P;
};
P_values_errors[y-ymin_]=P_error;
}
else
{
P_values_errors[y-ymin_]=-DBL_MAX;
};
}
else
{
get_appr_tail_prob_with_cov(
par_,
blast,
(double)y,
m_,
n_,
P,
P_error,
area,
a_normal,
b_normal,
h_normal,
N_normal,
p_normal,
area_is_1_flag);
P_values_errors[y-ymin_]=P_error;
};
P_values[y-ymin_]=P;
};
};
void pvalues::get_P_error_using_splitting_method(
set_of_parameters &par_,
bool blast_,
double y_,
double m_,
double n_,
double &P_,
double &P_error_,
double &area_,
double a_normal_,
double b_normal_,
double h_normal_,
Int4 N_normal_,
double *p_normal_,
bool &area_is_1_flag_)
{
Int4 dim=par_.m_LambdaSbs.size();
if(dim==0)
{
throw error("Unexpected error in get_P_error_using_splitting_method\n",1);
};
P_=0;
P_error_=0;
vector<double> P_values(dim);
Int4 i;
for(i=0;i<dim;i++)
{
set_of_parameters par_tmp;
par_tmp.a_I=par_.m_AISbs[i];
par_tmp.a_I_error=0;
par_tmp.a_J=par_.m_AJSbs[i];
par_tmp.a_J_error=0;
par_tmp.gapless_a=par_.gapless_a;
par_tmp.gapless_a_error=par_.gapless_a_error;
par_tmp.a=0.5*(par_tmp.a_I+par_tmp.a_J);
par_tmp.a_error=0;
par_tmp.sigma=par_.m_SigmaSbs[i];
par_tmp.sigma_error=0;
par_tmp.gapless_alpha=par_.gapless_alpha;
par_tmp.gapless_alpha_error=par_.gapless_alpha_error;
par_tmp.C=par_.m_CSbs[i];
par_tmp.C_error=0;
par_tmp.K=par_.m_KSbs[i];
par_tmp.K_error=0;
par_tmp.lambda=par_.m_LambdaSbs[i];
par_tmp.lambda_error=0;
par_tmp.alpha_I=par_.m_AlphaISbs[i];
par_tmp.alpha_I_error=0;
par_tmp.alpha_J=par_.m_AlphaJSbs[i];
par_tmp.alpha_J_error=0;
par_tmp.alpha=0.5*(par_tmp.alpha_I+par_tmp.alpha_J);
par_tmp.alpha_error=0;
par_tmp.G=par_.G;
double P_tmp,P_tmp_error,area_tmp;
get_appr_tail_prob_with_cov_without_errors(
par_tmp,
blast_,
y_,
m_,
n_,
P_tmp,
P_tmp_error,
area_tmp,
a_normal_,
b_normal_,
h_normal_,
N_normal_,
p_normal_,
area_is_1_flag_);
P_values[i]=P_tmp;
P_+=P_tmp;
};
if(dim<=1)
{
return;
};
if(P_<=0)
{
return;
};
P_/=(double)dim;
for(i=0;i<dim;i++)
{
double tmp=P_values[i]/P_;
P_error_+=tmp*tmp;
};
P_error_/=(double)dim;
P_error_-=1;
P_error_=P_*alp_reg::sqrt_for_errors(P_error_/(double)dim);
}
