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NCBI C++ ToolKit: src/algo/blast/gumbel_params/sls_pvalues.cpp Source File

56 if

(v1_error_>=1e100||v2_error_>=1e100)

61 return

sqrt(v1_error_*v1_error_+v2_error_*v2_error_);

70 if

(v1_error_>=1e100||v2_error_>=1e100)

75 double

a1=(v1_+v1_error_)*(v2_+v2_error_);

76 double

a2=(v1_-v1_error_)*(v2_+v2_error_);

77 double

a3=(v1_+v1_error_)*(v2_-v2_error_);

78 double

a4=(v1_-v1_error_)*(v2_-v2_error_);

91 if

(v1_error_>=1e100||v1_<0)

109 if

(v1_error_>=1e100||v2_error_>=1e100)

120 if

(v1_==0&&v1_error_==0)

128 if

(((v2_+v2_error_)*v2_<=0))

130 double

a3=(v1_+v1_error_)/(v2_-v2_error_);

131 double

a4=(v1_-v1_error_)/(v2_-v2_error_);

135 if

(((v2_-v2_error_)*v2_<=0))

137 double

a1=(v1_+v1_error_)/(v2_+v2_error_);

138 double

a2=(v1_-v1_error_)/(v2_+v2_error_);

143 double

a1=(v1_+v1_error_)/(v2_+v2_error_);

144 double

a2=(v1_-v1_error_)/(v2_+v2_error_);

145 double

a3=(v1_+v1_error_)/(v2_-v2_error_);

146 double

a4=(v1_-v1_error_)/(v2_-v2_error_);

163 return

-(y_+y_*y_/2.0+y_*y_*y_/6.0+y_*y_*y_*y_/24.0);

172 double pi

=3.1415926535897932384626433832795;

186 double

x=x_/sqrt(2.0);

187 return

1-0.5*exp(-x*x)/(x*sqrt(

))*(1-1.0/(2*x*2*x));

192 double

x=x_/sqrt(2.0);

193 return

0.5*exp(-x*x)/(-x*sqrt(

))*(1-1.0/(2*x*2*x));

197 double

const_val=1/sqrt(2.0*

);

203 double

h=x_/(double)

N

;

209 for

(

i

=0;

i

<=

N

;

i

++)

212 double tmp

=exp(-0.5*y*y);

213 if

(

i

==0||

i

==

N

)

225 return

0.5+const_val*(res);

244 return

p_[x_n]+(p_[x_n+1]-p_[x_n])*(x_-(h_*x_n+a_))/h_;

255 return

-val_-val_*val_/2.0-val_*val_*val_/3.0;

278 bool

&area_is_1_flag_)

282 double

lambda_=par_.

;

285 double

k_error_=par_.

;

287 double

ai_hat_=par_.

;

291 double

alphai_hat_=par_.

;

296 double

aj_hat_=par_.

;

300 double

alphaj_hat_=par_.

;

305 double

sigma_hat_=par_.

;

311 bool

where_it_is_works_flag=

false

;

312 bool

negative_flag=

false

;

333 double

const_val=1/sqrt(2.0*3.1415926535897932384626433832795);

334 double eps

=0.000001;

338 double

m_li_y_error = 0.0;

346 if

(where_it_is_works_flag)

348 if

(ai_hat_*y_+bi_hat_<0)

350

negative_flag=

true

;

357 double

vi_y_error = 0.0;

360 bool

flag_Mii=

true

;

362 if

(flag_Mii||blast_)

364

vi_y_error=

error_of_the_sum

(y_*alphai_hat_,

(y_)*alphai_hat_error_,betai_hat_,betai_hat_error_);

366 if

(where_it_is_works_flag)

368 if

(alphai_hat_*y_+betai_hat_<0)

370

negative_flag=

true

;

376 double

sqrt_vi_y=sqrt(vi_y);

381 if

(sqrt_vi_y==0.0||blast_)

389

m_F=m_li_y/sqrt_vi_y;

394 double

P_m_F_error=const_val*exp(-0.5*m_F*m_F)*m_F_error;

396 double

E_m_F=-const_val*exp(-0.5*m_F*m_F);

397 double

E_m_F_error=

(-E_m_F*m_F)*m_F_error;

400 double

m_li_y_P_m_F=m_li_y*P_m_F;

402 double

sqrt_vi_y_E_m_F_error=

error_of_the_product

(sqrt_vi_y,sqrt_vi_y_error,E_m_F,E_m_F_error);

403 double

sqrt_vi_y_E_m_F=sqrt_vi_y*E_m_F;

405 double

p1_error=

error_of_the_sum

(m_li_y_P_m_F,m_li_y_P_m_F_error,sqrt_vi_y_E_m_F,sqrt_vi_y_E_m_F_error);

406 double

p1=m_li_y_P_m_F-sqrt_vi_y_E_m_F;

409 double

n_lj_y_error = 0.0;

420 if

(where_it_is_works_flag)

422 if

(aj_hat_*y_+bj_hat_<0)

424

negative_flag=

true

;

430 double

vj_y_error = 0.0;

433 bool

flag_Mjj=

true

;

435 if

(flag_Mjj||blast_)

437

vj_y_error=

error_of_the_sum

(y_*alphaj_hat_,

(y_)*alphaj_hat_error_,betaj_hat_,betaj_hat_error_);

440 if

(where_it_is_works_flag)

442 if

(alphaj_hat_*y_+betaj_hat_<0)

444

negative_flag=

true

;

453 double

sqrt_vj_y=sqrt(vj_y);

458 if

(sqrt_vj_y==0.0||blast_)

466

n_F=n_lj_y/sqrt_vj_y;

470 double

P_n_F_error=const_val*exp(-0.5*n_F*n_F)*n_F_error;

472 double

E_n_F=-const_val*exp(-0.5*n_F*n_F);

473 double

E_n_F_error=

(-E_n_F*n_F)*n_F_error;

476 double

n_lj_y_P_n_F=n_lj_y*P_n_F;

478 double

sqrt_vj_y_E_n_F_error=

error_of_the_product

(sqrt_vj_y,sqrt_vj_y_error,E_n_F,E_n_F_error);

479 double

sqrt_vj_y_E_n_F=sqrt_vj_y*E_n_F;

481 double

p2_error=

error_of_the_sum

(n_lj_y_P_n_F,n_lj_y_P_n_F_error,sqrt_vj_y_E_n_F,sqrt_vj_y_E_n_F_error);

482 double

p2=n_lj_y_P_n_F-sqrt_vj_y_E_n_F;

487 double

c_y_error = 0.0;

490 bool

flag_Mij=

true

;

492 if

(flag_Mij||blast_)

494

c_y_error=

error_of_the_sum

(sigma_hat_*y_,sigma_hat_error_*y_,tau_hat_,tau_hat_error_);

497 if

(where_it_is_works_flag)

499 if

(sigma_hat_*y_+tau_hat_<0)

501

negative_flag=

true

;

508 double

P_m_F_P_n_F=P_m_F*P_n_F;

510 double

c_y_P_m_F_P_n_F_error=

error_of_the_product

(c_y,c_y_error,P_m_F_P_n_F,P_m_F_P_n_F_error);

511 double

c_y_P_m_F_P_n_F=c_y*P_m_F_P_n_F;

519 double

area_error=

error_of_the_sum

(p1_p2,p1_p2_error,c_y_P_m_F_P_n_F,c_y_P_m_F_P_n_F_error);

520 double

area=p1_p2+c_y_P_m_F_P_n_F;

533

area_is_1_flag_=

true

;

542 if

(negative_flag&&where_it_is_works_flag)

549 double

exp_lambda_y_error=

(lambda_error_*y_*exp(-lambda_*y_));

550 double

exp_lambda_y=exp(-lambda_*y_);

553 double

area_k=area*k_;

555 double

area_k_exp_lambda_y_error=

error_of_the_product

(area_k,area_k_error,exp_lambda_y,exp_lambda_y_error);

556 double

area_k_exp_lambda_y=-area_k*exp_lambda_y;

558

P_error_=exp(area_k_exp_lambda_y)*area_k_exp_lambda_y_error;

590 bool

&area_is_1_flag_)

595 double

lambda_=par_.

;

598 double

ai_hat_=par_.

;

600 double

alphai_hat_=par_.

;

603 double

aj_hat_=par_.

;

605 double

alphaj_hat_=par_.

;

608 double

sigma_hat_=par_.

;

612 bool

where_it_is_works_flag=

false

;

613 bool

negative_flag=

false

;

628 double

const_val=1/sqrt(2.0*3.1415926535897932384626433832795);

629 double eps

=0.000001;

639 if

(where_it_is_works_flag)

641 if

(ai_hat_*y_+bi_hat_<0)

643

negative_flag=

true

;

651 bool

flag_Mii=

true

;

653 if

(flag_Mii||blast_)

656 if

(where_it_is_works_flag)

658 if

(alphai_hat_*y_+betai_hat_<0)

660

negative_flag=

true

;

665 double

sqrt_vi_y=sqrt(vi_y);

669 if

(sqrt_vi_y==0.0||blast_)

675

m_F=m_li_y/sqrt_vi_y;

681 double

E_m_F=-const_val*exp(-0.5*m_F*m_F);

683 double

m_li_y_P_m_F=m_li_y*P_m_F;

685 double

sqrt_vi_y_E_m_F=sqrt_vi_y*E_m_F;

687 double

p1=m_li_y_P_m_F-sqrt_vi_y_E_m_F;

699 if

(where_it_is_works_flag)

701 if

(aj_hat_*y_+bj_hat_<0)

703

negative_flag=

true

;

711 bool

flag_Mjj=

true

;

713 if

(flag_Mjj||blast_)

717 if

(where_it_is_works_flag)

719 if

(alphaj_hat_*y_+betaj_hat_<0)

721

negative_flag=

true

;

729 double

sqrt_vj_y=sqrt(vj_y);

733 if

(sqrt_vj_y==0.0||blast_)

739

n_F=n_lj_y/sqrt_vj_y;

744 double

E_n_F=-const_val*exp(-0.5*n_F*n_F);

746 double

n_lj_y_P_n_F=n_lj_y*P_n_F;

748 double

sqrt_vj_y_E_n_F=sqrt_vj_y*E_n_F;

750 double

p2=n_lj_y_P_n_F-sqrt_vj_y_E_n_F;

757 bool

flag_Mij=

true

;

759 if

(flag_Mij||blast_)

763 if

(where_it_is_works_flag)

765 if

(sigma_hat_*y_+tau_hat_<0)

767

negative_flag=

true

;

773 double

P_m_F_P_n_F=P_m_F*P_n_F;

775 double

c_y_P_m_F_P_n_F=c_y*P_m_F_P_n_F;

782 double

area=p1_p2+c_y_P_m_F_P_n_F;

795

area_is_1_flag_=

true

;

804 if

(negative_flag&&where_it_is_works_flag)

811 double

exp_lambda_y=exp(-lambda_*y_);

813 double

area_k=area*k_;

815 double

area_k_exp_lambda_y=-area_k*exp_lambda_y;

842 bool

&area_is_1_flag_)

847 throw error

(

"Unexpected error in get_P_error_using_splitting_method\n"

,1);

854

vector<double> P_values(dim);

857 for

(

i

=0;

i

<dim;

i

++)

872

par_tmp.

a

=0.5*(par_tmp.

+par_tmp.

);

902

par_tmp.

G

=par_.

G

;

904 double

P_tmp,P_tmp_error,area_tmp;

945 for

(

i

=0;

i

<dim;

i

++)

947 double tmp

=P_values[

i

]/P_;

951

P_error_/=(double)dim;

963 bool

ee_error_flag=

false

;

964 error

ee_error(

""

,0);

984

ee_error_flag=

true

;

990

ee_error_flag=

true

;

991

ee_error=

(

"Internal error in the program\n"

,1);

1017

vector<double> &P_values,

1018

vector<double> &P_values_errors)

1022 throw error

(

"Error - Score2<Score1\n"

,2);

1025 if

(Seq1Len<=0||Seq2Len<=0)

1027 throw error

(

"Error - Seq1Len<=0||Seq2Len<=0\n"

,2);

1036

P_values.resize(ymax_-ymin_+1);

1037

P_values_errors.resize(ymax_-ymin_+1);

1042 for

(y=ymin_;y<=ymax_;y++)

1048 bool

area_is_1_flag=

false

;

1075 double

P_tmp,area_tmp;

1100

P_error=P_error/P_tmp*

P

;

1103

P_values_errors[y-ymin_]=P_error;

1107

P_values_errors[y-ymin_]=-DBL_MAX;

1133

P_values_errors[y-ymin_]=P_error;

1138

P_values[y-ymin_]=

P

;

static double round(const double &x_)

static T Tmax(T i_, T j_)

static T Tmin(T i_, T j_)

static double sqrt_for_errors(double x_)

static double ln_one_minus_val(double val_)

static double one_minus_exp_function(double y_)

static void get_appr_tail_prob_with_cov(set_of_parameters &par_, bool blast_, double y_, Int4 m_, Int4 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_)

static double error_of_the_ratio(double v1_, double v1_error_, double v2_, double v2_error_)

static double normal_probability(double x_, double eps_)

static double error_of_the_product(double v1_, double v1_error_, double v2_, double v2_error_)

static void get_P_error_using_splitting_method(set_of_parameters &par_, bool blast_, double y_, Int4 m_, Int4 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_)

static double error_of_the_sum(double v1_, double v1_error_, double v2_, double v2_error_)

static double error_of_the_sqrt(double v1_, double v1_error_)

static void get_appr_tail_prob_with_cov_without_errors(set_of_parameters &par_, bool blast_, double y_, Int4 m_, Int4 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_)

void calculate_P_values(Int4 Score1, Int4 Score2, Int4 Seq1Len, Int4 Seq2Len, set_of_parameters &ParametersSet, std::vector< double > &P_values, std::vector< double > &P_values_errors)

int32_t Int4

4-byte (32-bit) signed integer

#define NORMAL_DISTR_ARRAY_DIM

double * GetNormalDistrArrayForPvaluesCalculation(void)

const bool read_Sbs_par_flag

std::vector< double > m_KSbs

std::vector< double > m_SigmaSbs

std::vector< double > m_AlphaJSbs

std::vector< double > m_CSbs

std::vector< double > m_AlphaISbs

std::vector< double > m_AJSbs

std::vector< double > m_LambdaSbs

std::vector< double > m_AISbs

double gapless_alpha_error

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