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

53  bool

ee_error_flag=

false

;

54  error

ee_error(

""

,0);

76  throw error

(

"Unexpected error\n"

,4);

93

_CrtMemCheckpoint( &

d_s1

);

97  Int4

number_of_AA_RR1;

98  Int4

number_of_AA_RR2;

107  throw error

(

"Error - number of letters in the scoring matrix file must be greater than 0\n"

,3);

146  throw error

(

"Number of letters is different for the scoring matrix and probabilities array\n"

,3);

151  throw error

(

"Number of letters is different for the scoring matrix and probabilities array\n"

,3);

176  Uint4

random_factor = 0;

181  if

(AdvancedParams_tmp.

Empty

())

184  #ifndef NCBI_OS_MSWIN 188

random_factor+=tv.tv_usec*10000000;

190  struct

_timeb timebuffer;

192

_ftime( &timebuffer );

193

timeline = ctime( & ( timebuffer.time ) );

194

random_factor+=timebuffer.millitm*10000000;

305  double

tmp_size=

Tmin

((

double

)(tmp_size1),

311

(

double

)(

sizeof

(

double

)*12)+(

double

)(

sizeof

(

Int4

)*17)

320

ee_error_flag=

true

;

326

ee_error_flag=

true

;

327

ee_error=

error

(

"Internal error in the program\n"

,4);

343 string

smatr_file_name_,

344 string

RR1_file_name_,

345 string

RR2_file_name_,

350 string

out_file_name_)

354  bool

ee_error_flag=

false

;

355  error

ee_error(

""

,0);

383  #ifndef NCBI_OS_MSWIN 386

_CrtMemCheckpoint( &

d_s1

);

390  Int4

number_of_AA_RR1;

391  Int4

number_of_AA_RR2;

422  throw error

(

"Number of letters is different in the files "

+smatr_file_name_+

" and "

+RR1_file_name_+

"\n"

,3);

427  throw error

(

"Number of letters is different in the files "

+smatr_file_name_+

" and "

+RR2_file_name_+

"\n"

,3);

431  for

(

t

=0;

t

<number_of_AA_RR1;

t

++)

457  Uint4

random_factor=rand_;

460  if

((

Int4

)random_factor<0)

463  #ifndef NCBI_OS_MSWIN 467

random_factor+=tv.tv_usec*10000000;

469  struct

_timeb timebuffer;

471

_ftime( &timebuffer );

472

timeline = ctime( & ( timebuffer.time ) );

473

random_factor+=timebuffer.millitm*10000000;

485

frand.open(rand_st.data(),

ios::in

);

502  throw error

(

"Unexpected error in randomization seed\n"

,3);

604  double

tmp_size=

Tmin

((

double

)(tmp_size1),

610

(

double

)(

sizeof

(

double

)*12)+(

double

)(

sizeof

(

Int4

)*17)

619

ee_error_flag=

true

;

625

ee_error_flag=

true

;

626

ee_error=

error

(

"Internal error in the program\n"

,4);

646  if

(value_<0||value_>1.0||dim_<=0)

648  throw error

(

"Unexpected error"

,4);

694  string

out_file_name_)

696  bool

ee_error_flag=

false

;

697  error

ee_error(

""

,0);

705  f

.open(out_file_name_.data(),

ios::in

);

711  bool

symmetric_case_flag;

715

str_ch=

new char

[

str

.length()+1];

718  throw error

(

"Memory allocation error\n"

,41);

722  for

(k=0;k<(

Int4

)

str

.length();k++)

726

str_ch[

str

.length()]=

'\0'

;

729  char

str_for_test0[]=

"number of realizations with killing"

;

730  char

*test_flag0= strstr(str_ch,str_for_test0);

734  throw error

(

"The output file "

+out_file_name_+

" exists and does not have correct format;\nplease delete the file and rerun the program\n"

,3);

737  char

str_for_test[]=

"0.5*"

;

739  char

*test_flag= strstr(str_ch,str_for_test);

742

symmetric_case_flag=

true

;

746

symmetric_case_flag=

false

;

752  if

(symmetric_case_flag)

756  throw error

(

"The output file "

+out_file_name_+

" exists and corresponds to symmetric case; \ncurrent calculation uses non-symmetric parameters;\nplease define another output file name\n"

,3);

760  if

(!symmetric_case_flag)

764  throw error

(

"The output file "

+out_file_name_+

" exists and corresponds to non-symmetric case; \ncurrent calculation uses symmetric parameters;\nplease define another output file name\n"

,3);

772

ee_error_flag=

true

;

778

ee_error_flag=

true

;

779

ee_error=

error

(

"Internal error in the program\n"

,4);

782  delete

[]str_ch;str_ch=

NULL

;

800  #ifndef NCBI_OS_MSWIN 805

_CrtMemCheckpoint( &

d_s2

);

811  for

(use = 0; use < _MAX_BLOCKS; use++)

813

total+=

d_s3

.lSizes[use];

816

total/=(double)1048576;

825 #if defined(NCBI_COMPILER_ICC) && defined(__OPTIMIZE__) \ 826  && NCBI_COMPILER_VERSION >= 1000 && NCBI_COMPILER_VERSION < 1100 827 # pragma optimization_level 1 832  Int4

d_number_of_AA=

data

->d_number_of_AA;

834  double

*d_RR1=

data

->d_RR1;

835  double

*d_RR2=

data

->d_RR2;

840  for

(

i

=0;

i

<d_number_of_AA;

i

++)

842  for

(j=0;j<d_number_of_AA;j++)

844

res+=d_RR1[

i

]*d_RR2[j]*exp(x_*d_smatr[

i

][j]);

852 string

smatr_file_name_,

854 Int4

&number_of_AA_smatr_)

856  bool

ee_error_flag=

false

;

857  error

ee_error(

""

,0);

866  f

.open(smatr_file_name_.data(),

ios::in

);

869  throw error

(

"Error - file "

+smatr_file_name_+

" is not found\n"

,3);

872  f

>>number_of_AA_smatr_;

874  if

(number_of_AA_smatr_<=0)

876  throw error

(

"Error - number of letters in the scoring matrix file must be greater than 0\n"

,3);

882  for

(

i

=0;

i

<number_of_AA_smatr_;

i

++)

884  for

(j=0;j<number_of_AA_smatr_;j++)

893  for

(

i

=0;

i

<number_of_AA_smatr_;

i

++)

897  if

(smatr_[

i

][j]!=smatr_[j][

i

])

911

ee_error_flag=

true

;

917

ee_error_flag=

true

;

918

ee_error=

error

(

"Internal error in the program\n"

,4);

935 string

RR_file_name_,

938 Int4

*&RR_sum_elements_,

939 Int4

&number_of_AA_RR_)

941  bool

ee_error_flag=

false

;

942  error

ee_error(

""

,0);

951  f

.open(RR_file_name_.data(),

ios::in

);

954  throw error

(

"Error - file "

+RR_file_name_+

" is not found\n"

,3);

957  f

>>number_of_AA_RR_;

959  if

(number_of_AA_RR_<=0)

961  throw error

(

"Error - number of letters in the probabilities file must be greater than 0\n"

,3);

964

RR_=

new double

[number_of_AA_RR_];

967

RR_sum_=

new double

[number_of_AA_RR_];

970

RR_sum_elements_=

new Int4

[number_of_AA_RR_];

976  for

(

i

=0;

i

<number_of_AA_RR_;

i

++)

982  throw error

(

"Error - input letter's probability number "

+

long_to_string

(

i

+1)+

" is negative\n"

,3);

987  throw error

(

"Error - input letter's probability number "

+

long_to_string

(

i

+1)+

" is greater than 1.0\n"

,3);

993

RR_sum_[

i

]=RR_sum_[

i

-1]+RR_[

i

];

997

RR_sum_[

i

]=RR_[

i

];

999

RR_sum_elements_[

i

]=

i

;

1002  if

(

fabs

(RR_sum_[number_of_AA_RR_-1]-1.0)>0.000000000001)

1012

ee_error_flag=

true

;

1018

ee_error_flag=

true

;

1019

ee_error=

error

(

"Internal error in the program\n"

,4);

1036 const

vector<double> &vector_,

1039 Int4

*&RR_sum_elements_,

1040 Int4

&number_of_AA_RR_)

1042  bool

ee_error_flag=

false

;

1043  error

ee_error(

""

,0);

1052

number_of_AA_RR_=vector_.size();

1054  if

(number_of_AA_RR_<=0)

1056  throw error

(

"Error - number of letters in the probabilities file must be greater than 0\n"

,3);

1059

RR_=

new double

[number_of_AA_RR_];

1062

RR_sum_=

new double

[number_of_AA_RR_];

1065

RR_sum_elements_=

new Int4

[number_of_AA_RR_];

1071  for

(

i

=0;

i

<number_of_AA_RR_;

i

++)

1073

RR_[

i

]=vector_[

i

];

1077  throw error

(

"Error - input letter's probability number "

+

long_to_string

(

i

+1)+

" is negative\n"

,3);

1082  throw error

(

"Error - input letter's probability number "

+

long_to_string

(

i

+1)+

" is greater than 1.0\n"

,3);

1088

RR_sum_[

i

]=RR_sum_[

i

-1]+RR_[

i

];

1092

RR_sum_[

i

]=RR_[

i

];

1094

RR_sum_elements_[

i

]=

i

;

1097  if

(

fabs

(RR_sum_[number_of_AA_RR_-1]-1.0)>0.000000000001)

1106

ee_error_flag=

true

;

1112

ee_error_flag=

true

;

1113

ee_error=

error

(

"Internal error in the program\n"

,4);

1144

number_=

abs

(number_);

1146  Int4

reminder=number_%10;

1147

number_=(number_-reminder)/10;

1156  return

tmp_string+res_;

1164  case

0:

return '0'

;

1165  case

1:

return '1'

;

1166  case

2:

return '2'

;

1167  case

3:

return '3'

;

1168  case

4:

return '4'

;

1169  case

5:

return '5'

;

1170  case

6:

return '6'

;

1171  case

7:

return '7'

;

1172  case

8:

return '8'

;

1173  case

9:

return '9'

;

1174  default

:

return '?'

;

1185  throw error

(

"Memory allocation error\n"

,41);

1192  double

x_floor=floor(x_);

1193  double

x_ceil=ceil(x_);

1194  if

(

fabs

(x_-x_floor)<0.5)

1221  throw error

(

"Unexpected error"

,4);

1224  bool

ee_error_flag=

false

;

1225  error

ee_error(

""

,0);

1240

tmp_ptr.

d_RR1

=RR1_;

1241

tmp_ptr.

d_RR2

=RR2_;

1245  Int4

smatr_max=smatr_[0][0];

1248  Int4

smatr_min=smatr_[0][0];

1254  double

threshold=DBL_MIN*10.0;

1256  double

aver_score=0;

1258  for

(

i

=0;

i

<number_of_AA_;

i

++)

1260  for

(j=0;j<number_of_AA_;j++)

1262  if

(RR1_[j]*RR2_[

i

]<=threshold)

1267

aver_score+=RR1_[

i

]*RR2_[j]*smatr_[

i

][j];

1269  if

(smatr_max<smatr_[

i

][j])

1271

smatr_max=smatr_[

i

][j];

1278  if

(smatr_[

i

][j]>0)

1283  if

(smatr_[

i

][j]<0)

1291  if

(aver_score>=-threshold)

1293  throw error

(

"Error - sum[i,j] RR1[i]*RR2[j]*smatr[i][j]>=0; the program cannot continue the calculation\n"

,3);

1298  throw error

(

"Error - at least one element of the scoring matrix must be positive\n"

,3);

1309  if

(

a

<threshold*100.0)

1311  throw error

(

"Error - the input parameters correspond to non-logarithmic regime\n"

,3);

1315  if

(

a

<threshold*100.0)

1317  throw error

(

"Error - the input parameters define the regime which is too close to the critical regime\n"

,3);

1323  double

tmp_pr=RR1_[smatr_max_i]*RR2_[smatr_max_j];

1324  double b

=(

log

(1+10*eps)-

log

(tmp_pr))/(

double

)smatr_max;

1328

std::vector<double> res_lambda;

1333

(

void

*)(&tmp_ptr),

1340  sort

(res_lambda.begin(),res_lambda.end());

1342  if

(res_lambda.size()==0)

1344  throw error

(

"Error - the program is not able to find the ungapped lambda\n"

,3);

1347  d_lambda

=res_lambda[res_lambda.size()-1];

1372  for

(

a

=0;

a

<number_of_AA_;

a

++)

1374  for

(

b

=0;

b

<number_of_AA_;

b

++)

1384  for

(

a

=0;

a

<number_of_AA_;

a

++)

1386  for

(

b

=0;

b

<number_of_AA_;

b

++)

1393  for

(ind=0;ind<number_of_AA_*number_of_AA_;ind++)

1399  for

(ind=1;ind<number_of_AA_*number_of_AA_;ind++)

1406  for

(

a

=0;

a

<number_of_AA_;

a

++)

1408  for

(

b

=0;

b

<number_of_AA_;

b

++)

1454

ee_error_flag=

true

;

1460

ee_error_flag=

true

;

1461

ee_error=

error

(

"Internal error in the program\n"

,4);

1491 #ifndef NCBI_OS_MSWIN 1500

seconds_=(double)(

t

)+(double)(tv.tv_usec) * 0.000001;

1504  struct

_timeb timebuffer;

1506

_ftime( &timebuffer );

1508

seconds_=timebuffer.time+(double)(timebuffer.millitm)/1000.0;

const TFrequencies & GetSeq2ResidueProbs(void) const

Get sequence 2 residue probabilities.

const TFrequencies & GetSeq1ResidueProbs(void) const

Get sequence 1 residue probabilities.

double GetMaxCalcMemory(void) const

Get maximum memory allowed for computation.

double GetMaxCalcTime(void) const

Get maximum calculation time allowed.

Int4 GetGapOpening(void) const

Get gap opening penalty.

double GetKAccuracy(void) const

Get relative error threshold for K parameter calculation for gapped alignment.

Int4 GetNumResidues(void) const

Get number of residues in utilized alphabet.

const Int4 ** GetScoreMatrix(void) const

Get score matrix.

double GetLambdaAccuracy(void) const

Get relative error threshold for lambda parameter calculation for gapped aligmment.

Int4 GetGapExtension(void) const

Get gap extention penalty.

Int4 GetTotalReNumber(void) const

Get total realizations number.

const vector< Int4 > & GetPrelimReNumbersKilling(void) const

Get perliminary realizations numbers killing array.

const vector< Int4 > & GetFirstStagePrelimReNumbers(void) const

Get first stage preliminary realizations numbers.

Int4 GetTotalReNumberKilling(void) const

Get total realizations number killing.

Uint4 GetRandomSeed(void) const

Get random seed.

const vector< Int4 > & GetPrelimReNumbers(void) const

Get preliminary realizations numbers.

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 void get_current_time(double &seconds_)

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 char digit_to_string(Int4 digit_)

void check_out_file(string out_file_name_)

double d_memory_size_in_MB

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_)

static void find_tetta_general(function_type *func_, void *func_pointer_, double a_, double b_, Int4 n_partition_, double eps_, std::vector< double > &res_)

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_)

static const char * str(char *buf, int n)

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

void SetSeed(TValue seed)

Seed the random number generator with "seed".

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

int gettimeofday(struct timeval *tp, void *unused)

std::istream & in(std::istream &in_, double &x_)

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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