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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/slsalpdata_8hpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/gumbel_params/sls_alp_data.hpp Source File

36 #ifndef ALGO_BLAST_GUMBEL_PARAMS__INCLUDED_SLS_ALP_DATA 37 #define ALGO_BLAST_GUMBEL_PARAMS__INCLUDED_SLS_ALP_DATA 54 #include <sys/timeb.h> 56 #define _CRTDBG_MAP_ALLOC 135 throw error

(

"Unexpected error"

,4);

193 template

<

typename

T>

class array

{

323 string

smatr_file_name_,

324 string

RR1_file_name_,

325 string

RR2_file_name_,

330 string

out_file_name_);

346 string

smatr_file_name_,

348 Int4

&number_of_AA_smatr_);

351 string

out_file_name_);

355 static double round

(

373 string

RR_file_name_,

376 Int4

*&RR_sum_elements_,

377 Int4

&number_of_AA_RR_);

380 const

vector<double> &vector_,

383 Int4

*&RR_sum_elements_,

384 Int4

&number_of_AA_RR_);

393 template

<

typename

T>

399 bool

ee_error_flag=

false

;

400 error

ee_error(

""

,0);

408

matr_=

new T

*[dim_];

411 for

(

i

=0;

i

<dim_;

i

++)

416 for

(

i

=0;

i

<dim_;

i

++)

418

matr_[

i

]=

new T

[dim_];

426

ee_error_flag=

true

;

432

ee_error_flag=

true

;

433

ee_error=

(

"Internal error in the program\n"

,4);

444 for

(

i

=0;

i

<dim_;

i

++)

448 delete

[]matr_[

i

];matr_[

i

]=

;

452 delete

[]matr_;matr_=

;

460 template

<

typename

T>

468 for

(

i

=0;

i

<dim_;

i

++)

470 delete

[]matr_[

i

];matr_[

i

]=

;

472 delete

[]matr_;matr_=

;

483 template

<

typename

T>

490 if

(value_<0||value_>1)

492 throw error

(

"Unexpected error in q_elem importance_sampling::get_random_pair\n"

,4);

501 if

(sum_distr_[v3-1]==value_)

507 if

(sum_distr_[v3-1]>value_)

517 return

elements_[

-1];

634 #ifndef NCBI_OS_MSWIN 649 delete

[]d_elem;d_elem=

;

652

d_alp_data->d_memory_size_in_MB-=(double)

sizeof

(

T

)*(double)(d_dim+1)/

;

661 bool

ee_error_flag=

false

;

662 error

ee_error(

""

,0);

663 T

*d_elem_new=

;

672

d_elem_new=

new T

[d_dim+1];

676 for

(

i

=0;

i

<d_dim+1-d_step;

i

++)

678

d_elem_new[

i

]=d_elem[

i

];

681 for

(

i

=d_dim+1-d_step;

i

<d_dim+1;

i

++)

687 delete

[]d_elem;d_elem=

;

690

d_alp_data->d_memory_size_in_MB+=(double)

sizeof

(

T

)*(double)d_step/

;

693

d_elem=d_elem_new;d_elem_new=

;

698

ee_error_flag=

true

;

704

ee_error_flag=

true

;

705

ee_error=

(

"Internal error in the program\n"

,4);

712 delete

[]d_elem_new;d_elem_new=

;

723 delete

[]d_elem;d_elem=

;

726

d_alp_data->d_memory_size_in_MB-=(double)

sizeof

(

T

)*(double)(d_dim+1)/

;

734 bool

ee_error_flag=

false

;

735 error

ee_error(

""

,0);

736 T

*d_elem_new=

;

746

d_elem_new=

new T

[d_dim+1];

750 for

(

i

=0;

i

<d_dim+1-d_step;

i

++)

752

d_elem_new[

i

]=d_elem[

i

];

755 for

(

i

=d_dim+1-d_step;

i

<d_dim+1;

i

++)

760

d_dim_plus_d_ind0=d_dim+d_ind0;

764

d_alp_data->d_memory_size_in_MB+=(double)

sizeof

(

T

)*(double)d_step/

;

768 delete

[]d_elem;d_elem=

;

769

d_elem=d_elem_new;d_elem_new=

;

775

ee_error_flag=

true

;

781

ee_error_flag=

true

;

782

ee_error=

(

"Internal error in the program\n"

,4);

789 delete

[]d_elem_new;d_elem_new=

;

798 bool

ee_error_flag=

false

;

799 error

ee_error(

""

,0);

800 T

*d_elem_new=

;

809

d_elem_new=

new T

[d_dim+1];

814 for

(

i

=0;

i

<d_step;

i

++)

819 for

(

i

=0;

i

<d_dim+1-d_step;

i

++)

821

d_elem_new[

i

+d_step]=d_elem[

i

];

826

d_alp_data->d_memory_size_in_MB+=(double)

sizeof

(

T

)*(double)d_step/

;

829 delete

[]d_elem;d_elem=

;

830

d_elem=d_elem_new;d_elem_new=

;

836

ee_error_flag=

true

;

842

ee_error_flag=

true

;

843

ee_error=

(

"Internal error in the program\n"

,4);

850 delete

[]d_elem_new;d_elem_new=

;

static T Tmax(T x_, T y_, T z_)

bool d_smatr_symmetric_flag

importance_sampling * d_is

struct_for_randomization * d_rand_all

void get_memory_for_matrix(Int4 dim_, T **&matr_)

static double round(const double &x_)

alp_data(Int4 rand_, Int4 open_, Int4 epen_, string smatr_file_name_, string RR1_file_name_, string RR2_file_name_, double max_time_, double max_mem_, double eps_lambda_, double eps_K_, string out_file_name_)

Int4 * d_RR2_sum_elements

static T Tmax(T i_, T j_)

static T Tmin(T x_, T y_, T z_)

static T Tmin(T x_, T y_, T z_, T w_)

static void get_current_time(double &seconds_)

static T Tmax(T x_, T y_, T z_, T w_)

void read_smatr(string smatr_file_name_, Int4 **&smatr_, Int4 &number_of_AA_smatr_)

static T Tmin(T i_, T j_)

Int4 d_minimum_realizations_number

static Int4 random_long(double value_, Int4 dim_)

Int4 d_number_of_AA_smatr

double get_allocated_memory_in_MB()

void delete_memory_for_matrix(Int4 dim_, T **&matr_)

Int4 * d_RR1_sum_elements

static void assert_mem(void *pointer_)

static T random_long(double value_, Int4 dim_, double *sum_distr_, T *elements_)

static char digit_to_string(Int4 digit_)

void check_out_file(string out_file_name_)

double d_memory_size_in_MB

Int4 d_realizations_number2

void read_RR(string RR_file_name_, double *&RR_, double *&RR_sum_, Int4 *&RR_sum_elements_, Int4 &number_of_AA_RR_)

static string long_to_string(Int4 number_)

void increase_elem_by_x(Int4 ind_, T x_)

void increase_elem_by_1(Int4 ind_)

void set_elem(Int4 ind_, T elem_)

array_positive(alp_data *alp_data_)

void increment_array_on_the_rigth()

void increase_elem_by_1(Int4 ind_)

void increment_array_on_the_left()

array(alp_data *alp_data_)

void set_elem(Int4 ind_, T elem_)

importance_sampling(alp_data *alp_data_, Int4 open_, Int4 epen_, Int4 number_of_AA_, Int4 **smatr_, double *RR1_, double *RR2_)

double * d_elements_values

static double lambda_equation(double x_, void *func_number_)

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

TValue GetRand(void)

Get the next random number in the interval [0..GetMax()] (inclusive)

static TValue GetMax(void)

The max. value GetRand() returns.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

Front end for a platform-specific configuration summary.

The NCBI C++/STL use hints.

error_for_single_realization()

error(std::string st_, Int4 error_code_)

Int4 d_total_realizations_number_with_ALP

vector< Int4 > d_preliminary_realizations_numbers_ALP

Int4 d_total_realizations_number_with_killing

vector< Int4 > d_preliminary_realizations_numbers_killing

vector< Int4 > d_first_stage_preliminary_realizations_numbers_ALP

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