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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/sls__alp_8cpp_source.html below:

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

111  throw error

(

"Unexpected error"

,4);

119  bool

ee_error_flag=

false

;

120  error

ee_error(

""

,0);

186

ee_error_flag=

true

;

192

ee_error_flag=

true

;

193

ee_error=

error

(

"Internal error in the program\n"

,4);

304  if

(i<=d_alp_states->d_dim)

422  if

(i<=d_alp_states->d_dim)

486  if

(length1_==0&&length2_==0)

489

las_object_->

ran2

(),

498  if

(length1_==d_dim1_)

513

las_object_->

ran2

(),

517  goto

weight_calculation;

522  if

(length2_==d_dim2_)

538

las_object_->

ran2

(),

542  goto

weight_calculation;

547  if

(length1_==d_dim1_||length2_==d_dim2_)

553

las_object_->

ran2

(),

563

d_seqi_rglobal_[length1_]=pair.

d_a

;

564

d_seqj_rglobal_[length2_]=pair.

d_b

;

572

las_object_->

ran2

(),

576  goto

weight_calculation;

589  bool

ee_error_flag=

false

;

590  error

ee_error(

""

,0);

632

ee_error_flag=

true

;

638

ee_error_flag=

true

;

639

ee_error=

error

(

"Internal error in the program\n"

,4);

646  delete

[]d_seqi_new;d_seqi_new=

NULL

;

647  delete

[]d_seqj_new;d_seqj_new=

NULL

;

655  double

*d_WS_i_const_pred_new=

NULL

;

656  double

*d_WI_i_const_pred_new=

NULL

;

657  double

*d_WD_i_const_pred_new=

NULL

;

659  double

*d_WS_i_const_next_new=

NULL

;

660  double

*d_WI_i_const_next_new=

NULL

;

661  double

*d_WD_i_const_next_new=

NULL

;

663  double

*d_WS_j_const_pred_new=

NULL

;

664  double

*d_WI_j_const_pred_new=

NULL

;

665  double

*d_WD_j_const_pred_new=

NULL

;

667  double

*d_WS_j_const_next_new=

NULL

;

668  double

*d_WI_j_const_next_new=

NULL

;

669  double

*d_WD_j_const_next_new=

NULL

;

671  bool

ee_error_flag=

false

;

672  error

ee_error(

""

,0);

781

ee_error_flag=

true

;

787

ee_error_flag=

true

;

788

ee_error=

error

(

"Internal error in the program\n"

,4);

796  delete

[]d_WS_i_const_pred_new;d_WS_i_const_pred_new=

NULL

;

797  delete

[]d_WI_i_const_pred_new;d_WI_i_const_pred_new=

NULL

;

798  delete

[]d_WD_i_const_pred_new;d_WD_i_const_pred_new=

NULL

;

800  delete

[]d_WS_i_const_next_new;d_WS_i_const_next_new=

NULL

;

801  delete

[]d_WI_i_const_next_new;d_WI_i_const_next_new=

NULL

;

802  delete

[]d_WD_i_const_next_new;d_WD_i_const_next_new=

NULL

;

804  delete

[]d_WS_j_const_pred_new;d_WS_j_const_pred_new=

NULL

;

805  delete

[]d_WI_j_const_pred_new;d_WI_j_const_pred_new=

NULL

;

806  delete

[]d_WD_j_const_pred_new;d_WD_j_const_pred_new=

NULL

;

808  delete

[]d_WS_j_const_next_new;d_WS_j_const_next_new=

NULL

;

809  delete

[]d_WI_j_const_next_new;d_WI_j_const_next_new=

NULL

;

810  delete

[]d_WD_j_const_next_new;d_WD_j_const_next_new=

NULL

;

842  bool

ee_error_flag=

false

;

843  error

ee_error(

""

,0);

980

ee_error_flag=

true

;

986

ee_error_flag=

true

;

987

ee_error=

error

(

"Internal error in the program\n"

,4);

994  delete

[]d_HS_i_const_pred_new;d_HS_i_const_pred_new=

NULL

;

995  delete

[]d_HI_i_const_pred_new;d_HI_i_const_pred_new=

NULL

;

996  delete

[]d_HD_i_const_pred_new;d_HD_i_const_pred_new=

NULL

;

997  delete

[]d_H_i_const_pred_new;d_H_i_const_pred_new=

NULL

;

999  delete

[]d_HS_i_const_next_new;d_HS_i_const_next_new=

NULL

;

1000  delete

[]d_HI_i_const_next_new;d_HI_i_const_next_new=

NULL

;

1001  delete

[]d_HD_i_const_next_new;d_HD_i_const_next_new=

NULL

;

1002  delete

[]d_H_i_const_next_new;d_H_i_const_next_new=

NULL

;

1004  delete

[]d_HS_j_const_pred_new;d_HS_j_const_pred_new=

NULL

;

1005  delete

[]d_HI_j_const_pred_new;d_HI_j_const_pred_new=

NULL

;

1006  delete

[]d_HD_j_const_pred_new;d_HD_j_const_pred_new=

NULL

;

1007  delete

[]d_H_j_const_pred_new;d_H_j_const_pred_new=

NULL

;

1009  delete

[]d_HS_j_const_next_new;d_HS_j_const_next_new=

NULL

;

1010  delete

[]d_HI_j_const_next_new;d_HI_j_const_next_new=

NULL

;

1011  delete

[]d_HD_j_const_next_new;d_HD_j_const_next_new=

NULL

;

1012  delete

[]d_H_j_const_next_new;d_H_j_const_next_new=

NULL

;

1014  delete

[]d_H_edge_max_new;d_H_edge_max_new=

NULL

;

1040  throw error

(

"Unexpected error in increment_W_weights\n"

,4);

1075  double

deg_tmp=

degree

(d_is_tmp->

d_nu

,d_W_matr_len_1);

1083  for

(

i

=d_W_matr_len_2;

i

>=1;

i

--)

1122  throw error

(

"Error - unexpected parameter in alp::degree\n"

,4);

1137  return

exp(n_*

log

(x_));

1171  throw error

(

"Unexpected error\n"

,4);

1218  for

(

i

=d_H_matr_len_2;

i

>=1;

i

--)

1254  for

(

i

=0;

i

<=d_H_matr_len_1;

i

++)

1262  for

(

i

=0;

i

<=d_H_matr_len_1;

i

++)

1291  for

(

i

=0;

i

<=d_H_matr_len_1;

i

++)

1329  throw error

(

"The program cannot calculate the parameters for the given scoring system:\nthere is no logarithmic stage reached for the input calculation time\nPlease try to increase the allowed calculation time\n"

,1);

1386  throw error

(

"Unexpected error\n"

,4);

1443  for

(

i

=sentinel_i_boundary-1;

i

>=1;

i

--)

1451  for

(

i

=sentinel_j_boundary-1;

i

>=1;

i

--)

1482  for

(

i

=0;

i

<=sentinel_i_boundary-1;

i

++)

1487  for

(

i

=0;

i

<=sentinel_j_boundary-1;

i

++)

1493  for

(

i

=0;

i

<=sentinel_i_boundary-1;

i

++)

1498  for

(

i

=0;

i

<=sentinel_j_boundary-1;

i

++)

1513  for

(

i

=sentinel_i_boundary-1;

i

>=1;

i

--)

1522  for

(

i

=sentinel_j_boundary-1;

i

>=1;

i

--)

1549  for

(

i

=0;

i

<=sentinel_i_boundary-1;

i

++)

1557  for

(

i

=0;

i

<=sentinel_j_boundary-1;

i

++)

1588  throw error

(

"Unexpected error\n"

,4);

1604  for

(

i

=array_tmp->

d_ind0

;i<=array_tmp->d_dim_plus_d_ind0;

i

++)

1654  throw error

(

"Unexpected error\n"

,4);

1773  throw error

(

"Unexpected error\n"

,4);

1829  throw error

(

"Error - unexpected parameter in alp::John2_weight_calculation\n"

,4);

1850  for

(j=1;j<=length_-1;j++)

1853  double

UD_next=((d_is_tmp->

d_mu_DS

)*US+(d_is_tmp->

d_nu

)*UD);

1872  double

UD_next=((d_is_tmp->

d_mu_DS

)*US+(d_is_tmp->

d_nu

)*UD);

1895  throw error

(

"Unexpected error\n"

,4);

1912  throw error

(

"Unexpected error - ALP can be generated only in the importance sampling mode\n"

,4);

1917  while

(

d_nalp

<target_nalp)

1959  throw error

(

"Unexpected error\n"

,4);

importance_sampling * d_is

Int4 * d_RR2_sum_elements

static T Tmax(T i_, T j_)

static void get_current_time(double &seconds_)

static T Tmin(T i_, T j_)

static Int4 random_long(double value_, Int4 dim_)

Int4 * d_RR1_sum_elements

static void assert_mem(void *pointer_)

double d_memory_size_in_MB

static double degree(double x_, double n_)

double John2_weight_calculation(Int4 length_)

void release_and_calculate_memory(T *&pointer_, Int4 dim_)

double * d_WD_j_const_next

double * d_WS_j_const_next

void increment_sequences()

double * d_WD_i_const_next

void simulate_alp_upto_the_given_level(Int4 M_min_)

void increment_H_weights_with_sentinels(Int4 diff_opt_)

void partially_release_memory()

array_positive< Int4 > * d_alp_pos

array_positive< Int4 > * d_H_J

array_positive< Int4 > * d_alp

void save_state(state *&state_)

void kill_upto_level(Int4 M_min_, Int4 M_level_)

double * d_WS_j_const_pred

double * d_WS_i_const_next

void increment_H_matrix()

double * d_WI_j_const_pred

void increment_W_matrix()

double * d_WI_i_const_pred

array_positive< double > * d_alp_weights

void check_time_function(Int4 ff_=0)

bool one_step_of_importance_sampling_without_weight_calculation(Int4 d_dim1_, Int4 d_dim2_)

void swap(T &a1_, T &a2_)

array_positive< state * > * d_alp_states

bool d_single_realiztion_calculation_flag

double * d_WI_j_const_next

void restore_state(Int4 nalp_, state *&state_)

array< Int4 > * d_cells_counts

void increment_H_weights()

double * d_WI_i_const_next

array_positive< Int4 > * d_H_I

void increment_W_weights()

double * d_WS_i_const_pred

double * d_WD_j_const_pred

void simulate_alp_upto_the_given_number(Int4 nalp_)

double * d_WD_i_const_pred

void set_elem(Int4 ind_, T elem_)

void increase_elem_by_1(Int4 ind_)

void set_elem(Int4 ind_, T elem_)

double * d_elements_values

array< Int4 > * d_cells_counts

int32_t Int4

4-byte (32-bit) signed integer

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