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sls_alp_sim.cpp
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sls_alp_sim.cpp
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/* $Id: $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's offical duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================*/
/*****************************************************************************
File name: sls_alp_sim.cpp
Author: Sergey Sheetlin
Contents: Calculation of Gumbel parameters
******************************************************************************/
#include "sls_alp_sim.hpp"
using namespace Sls;
using namespace std;
static bool calculate_C_S_constant_flag=true;
static double dbl_max_log=log(DBL_MAX);
alp_sim::alp_sim(//constructor
alp_data *alp_data_)
{
d_alp_obj=NULL;
d_lambda_tmp=NULL;
d_lambda_tmp_errors=NULL;
d_C_tmp=NULL;
d_C_tmp_errors=NULL;
d_alp_data=alp_data_;
ofstream frand;
try
{
if(!d_alp_data)
{
throw error("Unexpected error\n",4);
};
d_alp_obj=new array_positive<alp*> (d_alp_data);
alp_data::assert_mem(d_alp_obj);
d_n_alp_obj=0;
d_alp_data->d_memory_size_in_MB+=(double)(sizeof(array_positive<alp*>))/mb_bytes;
double memory_before1=d_alp_data->d_memory_size_in_MB;
double time_before1;
alp_data::get_current_time(time_before1);
d_alp_data->d_time_before1=time_before1;
if(!d_alp_data->d_rand_flag)
{
d_alp_data->d_rand_all->d_random_seed=d_alp_data->d_random_seed;
};
//trial simulation for estimation time and memory
long int M_min;
long int nalp;
double time_after_tmp;
d_lambda_tmp=new array_positive<double>(d_alp_data);
alp_data::assert_mem(d_lambda_tmp);
d_lambda_tmp_errors=new array_positive<double>(d_alp_data);
alp_data::assert_mem(d_lambda_tmp_errors);
d_C_tmp=new array_positive<double>(d_alp_data);
alp_data::assert_mem(d_C_tmp);
d_C_tmp_errors=new array_positive<double>(d_alp_data);
alp_data::assert_mem(d_C_tmp_errors);
//quick tests
quick_test(
quick_tests_trials_number,
d_alp_data->d_max_time_for_quick_tests);
long int maximum_number_of_realizations_for_preliminary_simulation=1000;
bool loop_break_flag;
long int rand_i=-1;
bool lambda_accuracy_flag=true;
long int sim_number=1;
do{
long int nalp_lambda;
bool C_calculation=false;
long int number_tmp;
bool check_time_flag=true;
if(d_alp_data->d_rand_flag)
{
check_time_flag=false;
rand_i++;
number_tmp=d_alp_data->d_rand_all->d_first_stage_preliminary_realizations_numbers_ALP[rand_i];
}
else
{
number_tmp=alp_data::Tmin(maximum_number_of_realizations_for_preliminary_simulation-1,d_n_alp_obj+sim_number*d_alp_data->d_minimum_realizations_number-1);
};
get_minimal_simulation(
0,
number_tmp,
M_min,
nalp,
nalp_lambda,
C_calculation,
check_time_flag);
if(!d_alp_data->d_rand_flag)
{
d_alp_data->d_rand_all->d_first_stage_preliminary_realizations_numbers_ALP.push_back(number_tmp);
};
sim_number*=2;
if(d_lambda_tmp->d_elem[nalp]>=0)
{
if(d_lambda_tmp_errors->d_elem[nalp]/d_lambda_tmp->d_elem[nalp]<alp_data_->d_eps_lambda)
{
lambda_accuracy_flag=false;
};
};
alp_data::get_current_time(time_after_tmp);
if(number_tmp>=maximum_number_of_realizations_for_preliminary_simulation-1)
{
if(!d_alp_data->d_rand_flag)
{
break;
};
};
if(d_alp_data->d_rand_flag)
{
loop_break_flag=(rand_i>=(long int)(d_alp_data->d_rand_all->d_first_stage_preliminary_realizations_numbers_ALP.size()-1));
}
else
{
loop_break_flag=!(maximum_number_of_realizations_for_preliminary_simulation>d_n_alp_obj-1&&
lambda_accuracy_flag&&((time_after_tmp-time_before1)<=0||((time_after_tmp-time_before1)<0.01*d_alp_data->d_max_time&&d_alp_data->d_memory_size_in_MB<d_alp_data->d_max_mem)));
};
}
while(!loop_break_flag);
double memory_after1=d_alp_data->d_memory_size_in_MB;
double time_after1;
alp_data::get_current_time(time_after1);
if(memory_after1<=memory_before1)
{
delete d_alp_obj;d_alp_obj=NULL;
throw error("Unexpected error\n",4);
};
long int limit_by_memory=(long int)alp_data::Tmin((double)LONG_MAX-1,alp_data::round(d_alp_data->d_max_mem/2.0/(memory_after1-memory_before1)*d_n_alp_obj));
if(d_alp_data->d_memory_size_in_MB>d_alp_data->d_max_mem)
{
//cout<<"\nWarning: memory limit is reached.\nTo get the requested accuracy please\nincrease maximum allowed amount of memory if possible\n\n";
};
long int limit_by_time;
if(time_after1<=time_before1)
{
limit_by_time=LONG_MAX;
}
else
{
limit_by_time=(long int)alp_data::Tmin((double)LONG_MAX-1,alp_data::round(d_alp_data->d_max_time/3.0/4.0/(time_after1-time_before1)*d_n_alp_obj));
};
long int realizations_number2=alp_data::Tmin((long int)alp_data::round(limit_by_time)-1,limit_by_memory-1);
realizations_number2=alp_data::Tmin(maximum_number_of_realizations_for_preliminary_simulation-(long int)1,realizations_number2);
realizations_number2=alp_data::Tmax(d_n_alp_obj-(long int)1,realizations_number2);
delete d_lambda_tmp;d_lambda_tmp=NULL;
delete d_lambda_tmp_errors;d_lambda_tmp_errors=NULL;
delete d_C_tmp;d_C_tmp=NULL;
delete d_C_tmp_errors;d_C_tmp_errors=NULL;
//trial simulation for estimation M_min and nalp
d_lambda_tmp=new array_positive<double>(d_alp_data);
alp_data::assert_mem(d_lambda_tmp);
d_lambda_tmp_errors=new array_positive<double>(d_alp_data);
alp_data::assert_mem(d_lambda_tmp_errors);
d_C_tmp=new array_positive<double>(d_alp_data);
alp_data::assert_mem(d_C_tmp);
d_C_tmp_errors=new array_positive<double>(d_alp_data);
alp_data::assert_mem(d_C_tmp_errors);
long int nalp_lambda;
bool C_calculation=false;
double lambda;
double eps_K=d_alp_data->d_eps_K;
double K_C;
double K_C_error;
long int level;
long int diff_opt;
rand_i=-1;
loop_break_flag=false;
double time_before_ALP;
double time_during_ALP;
long int number_of_realizations_with_ALP=alp_data::Tmin(realizations_number2,d_n_alp_obj-(long int)1+d_alp_data->d_minimum_realizations_number);
long int number_of_realizations_with_ALP_pred;
alp_data::get_current_time(time_before_ALP);
do{
bool check_time_flag=true;
if(d_alp_data->d_rand_flag)
{
check_time_flag=false;
rand_i++;
number_of_realizations_with_ALP=d_alp_data->d_rand_all->d_preliminary_realizations_numbers_ALP[rand_i];
};
get_minimal_simulation(
0,
number_of_realizations_with_ALP,
M_min,
nalp,
nalp_lambda,
C_calculation,
check_time_flag);
if(!d_alp_data->d_rand_flag)
{
d_alp_data->d_rand_all->d_preliminary_realizations_numbers_ALP.push_back(number_of_realizations_with_ALP);
};
lambda=d_lambda_tmp->d_elem[nalp];
double tmp_lambda=2.0;
if(d_lambda_tmp->d_elem[nalp]>0)
{
tmp_lambda=((d_lambda_tmp_errors->d_elem[nalp]/d_lambda_tmp->d_elem[nalp])/d_alp_data->d_eps_lambda);
};
number_of_realizations_with_ALP_pred=number_of_realizations_with_ALP;
alp_data::get_current_time(time_during_ALP);
if(d_alp_data->d_rand_flag)
{
loop_break_flag=(rand_i>=(long int)(d_alp_data->d_rand_all->d_preliminary_realizations_numbers_ALP.size()-1));
if(loop_break_flag)
{
break;
};
};
if(time_during_ALP-time_before1>=d_alp_data->d_max_time*0.25||number_of_realizations_with_ALP>=realizations_number2||tmp_lambda<=1.0)
{
if(!d_alp_data->d_rand_flag)
{
break;
};
};
if(time_during_ALP<=time_before_ALP)
{
number_of_realizations_with_ALP=alp_data::Tmin(realizations_number2,number_of_realizations_with_ALP+d_alp_data->d_minimum_realizations_number);
}
else
{
long int max_number_of_realizations=(long int)floor(number_of_realizations_with_ALP*(d_alp_data->d_max_time*0.35-(time_before_ALP-time_before1))/(time_during_ALP-time_before_ALP));
number_of_realizations_with_ALP=alp_data::Tmin(realizations_number2,(long int)floor(0.5*number_of_realizations_with_ALP+0.5*max_number_of_realizations));
if(number_of_realizations_with_ALP>=max_number_of_realizations)
{
number_of_realizations_with_ALP=d_alp_data->Tmin(realizations_number2,number_of_realizations_with_ALP+d_alp_data->d_minimum_realizations_number);
};
if((double)(number_of_realizations_with_ALP-number_of_realizations_with_ALP_pred)/(double)number_of_realizations_with_ALP_pred<0.005)
{
number_of_realizations_with_ALP=number_of_realizations_with_ALP_pred;
if(!d_alp_data->d_rand_flag)
{
break;
};
};
};
}
while(!loop_break_flag);
realizations_number2=number_of_realizations_with_ALP;
long int realizations_number2_lambda=number_of_realizations_with_ALP;
rand_i=-1;
loop_break_flag=false;
double time_before_kill;
double time_during_kill;
long int number_of_realizations_with_killing=d_alp_data->Tmin(realizations_number2,d_alp_data->d_minimum_realizations_number-(long int)1);
long int number_of_realizations_with_killing_pred;
alp_data::get_current_time(time_before_kill);
do{
bool check_time_flag=false;
if(d_alp_data->d_rand_flag)
{
check_time_flag=false;
rand_i++;
number_of_realizations_with_killing=d_alp_data->d_rand_all->d_preliminary_realizations_numbers_killing[rand_i];
};
kill(
check_time_flag,
0,
number_of_realizations_with_killing,
M_min,
lambda,
eps_K,
K_C,
K_C_error,
level,
diff_opt);
if(!d_alp_data->d_rand_flag)
{
d_alp_data->d_rand_all->d_preliminary_realizations_numbers_killing.push_back(number_of_realizations_with_killing);
};
number_of_realizations_with_killing_pred=number_of_realizations_with_killing;
alp_data::get_current_time(time_during_kill);
double tmp_K=2.0;
if(K_C>0)
{
tmp_K=((K_C_error/K_C)/d_alp_data->d_eps_K);
};
if(d_alp_data->d_rand_flag)
{
loop_break_flag=(rand_i>=(long int)(d_alp_data->d_rand_all->d_preliminary_realizations_numbers_killing.size()-1));
if(loop_break_flag)
{
break;
};
};
if(time_during_kill-time_before1>=d_alp_data->d_max_time||number_of_realizations_with_killing>=realizations_number2||tmp_K<=1.0)
{
if(!d_alp_data->d_rand_flag)
{
break;
};
};
if(time_during_kill<=time_before_kill)
{
number_of_realizations_with_killing=d_alp_data->Tmin(realizations_number2,number_of_realizations_with_killing+d_alp_data->d_minimum_realizations_number);
}
else
{
long int max_number_of_realizations=(long int)floor(number_of_realizations_with_killing*(d_alp_data->d_max_time-(time_before_kill-time_before1))/(time_during_kill-time_before_kill));
number_of_realizations_with_killing=d_alp_data->Tmin(realizations_number2,(long int)floor(0.5*number_of_realizations_with_killing+0.5*max_number_of_realizations));
if(number_of_realizations_with_killing>=max_number_of_realizations)
{
number_of_realizations_with_killing=d_alp_data->Tmin(realizations_number2,number_of_realizations_with_killing+d_alp_data->d_minimum_realizations_number);
};
if((double)(number_of_realizations_with_killing-number_of_realizations_with_killing_pred)/(double)number_of_realizations_with_killing_pred<0.005)
{
number_of_realizations_with_killing=number_of_realizations_with_killing_pred;
if(!d_alp_data->d_rand_flag)
{
break;
};
};
};
}
while(!loop_break_flag);
long int k;
for(k=0;k<=number_of_realizations_with_killing;k++)
{
d_alp_obj->d_elem[k]->partially_release_memory();
};
realizations_number2=number_of_realizations_with_killing;
long int realizations_number2_K=number_of_realizations_with_killing;
d_alp_data->d_realizations_number2=realizations_number2_lambda;
if(K_C<=0)
{
throw error("Error - you have exceeded the calculation time or memory limit.\nThe error might indicate that the regime is linear or too close to linear to permit efficient computation.\nPossible solutions include changing the randomization seed, or increasing the allowed calculation time and the memory limit.\n",3);
};
double tmp=((K_C_error/K_C)/d_alp_data->d_eps_K);
tmp=alp_data::Tmin(ceil((realizations_number2_K+1)*tmp*tmp),(double)LONG_MAX);
long int realizations_number_killing=(long int)tmp;
tmp=((d_lambda_tmp_errors->d_elem[nalp]/d_lambda_tmp->d_elem[nalp])/d_alp_data->d_eps_lambda);
tmp=alp_data::Tmin(ceil((realizations_number2_lambda+1)*tmp*tmp),(double)LONG_MAX);
long int realizations_number_lambda=(long int)tmp;
double time_after2;
alp_data::get_current_time(time_after2);
time_after2=alp_data::Tmax(time_after2,time_after_tmp);
delete d_lambda_tmp;d_lambda_tmp=NULL;
delete d_lambda_tmp_errors;d_lambda_tmp_errors=NULL;
delete d_C_tmp;d_C_tmp=NULL;
delete d_C_tmp_errors;d_C_tmp_errors=NULL;
//main simulation
long int j;
j=1;
long int kill_j=0;
bool kill_flag=(realizations_number_killing>realizations_number2_K+1+j);
bool lambda_flag=(realizations_number_lambda>realizations_number2_lambda+1+j);
long int nalp_for_simulation=nalp;
//!!!!!!!!!!!!!!!!!!!!!!!
//cout<<"A number of ALPs\t"<<nalp_for_simulation<<endl;
if(d_alp_data->d_rand_flag)
{
lambda_flag=(d_alp_data->d_rand_all->d_total_realizations_number_with_ALP>realizations_number2_K+j-1);
kill_flag=(d_alp_data->d_rand_all->d_total_realizations_number_with_killing>realizations_number2_K+j-1);
};
if(kill_flag||lambda_flag)
{
long int step_for_time=1;
//long int number_of_unsuccesful_objects=0;
//!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
//cout<<"M_min="<<M_min<<endl;
while(d_n_alp_obj<LONG_MAX-realizations_number2_lambda-j)
{
kill_flag=(realizations_number_killing>realizations_number2_K+j);
lambda_flag=(realizations_number_lambda>realizations_number2_lambda+j);
if(d_alp_data->d_rand_flag)
{
lambda_flag=(d_alp_data->d_rand_all->d_total_realizations_number_with_ALP>realizations_number2_K+j-1);
kill_flag=(d_alp_data->d_rand_all->d_total_realizations_number_with_killing>realizations_number2_K+j-1);
};
if(!(kill_flag||lambda_flag))
{
if(!d_alp_data->d_rand_flag)
{
//cout<<"\nThe parameters were calculated with the required accuracy\n\n";
break;
}
else
{
break;
};
};
if(!kill_flag)
{
nalp_for_simulation=alp_data::Tmin(nalp_lambda,nalp);
};
bool sucess_flag=false;
if(realizations_number2_K+j<=realizations_number2_lambda)
{
}
else
{
d_alp_obj->set_elem(realizations_number2_K+j,NULL);
d_n_alp_obj++;
};
alp *&obj=d_alp_obj->d_elem[realizations_number2_K+j];
try
{
double eps_tmp;
while(!sucess_flag)
{
bool check_time_flag=true;
if(d_alp_data->d_rand_flag)
{
check_time_flag=false;
};
get_single_realization(
check_time_flag,
M_min,
nalp_for_simulation,
kill_flag,
level,
diff_opt,
obj,
sucess_flag,
eps_tmp);
if(!sucess_flag)
{
if(realizations_number2_K+j>realizations_number2_lambda)
{
d_n_alp_obj--;
};
//number_of_unsuccesful_objects++;
// if(number_of_unsuccesful_objects>/*5+*/0.5*alp_data::Tmin(d_alp_data->d_rand_all->d_total_realizations_number_with_killing,d_alp_data->d_rand_all->d_total_realizations_number_with_ALP)*eps_tmp)
// {
//if(realizations_number2_K+j>realizations_number2_lambda)
//{
// d_n_alp_obj--;
//};
//throw error("Error - you have exceeded the calculation time or memory limit.\nThe error might indicate that the regime is linear or too close to linear to permit efficient computation.\nPossible solutions include changing the randomization seed, or increasing the allowed calculation time and the memory limit.\n",3);
// };
};
};
}
catch (error_for_single_realization er)
{
if(d_alp_data->d_rand_flag)
{
throw error("Unexpected error in ramdomization\n",4);
};
//cout<<"\nWarning: time limit is reached.\nTo get the requested accuracy please\nincrease the allowed calculation time if possible\n\n";
if(realizations_number2_K+j>realizations_number2_lambda)
{
delete obj;obj=NULL;
d_n_alp_obj--;
};
break;
};
if(realizations_number2_K+j>realizations_number2_lambda)
{
if(kill_flag)
{
kill_j=j;
};
};
d_alp_obj->d_elem[realizations_number2_K+j]->partially_release_memory();
j++;
if(d_alp_data->d_memory_size_in_MB>d_alp_data->d_max_mem)
{
if(!d_alp_data->d_rand_flag)
{
//cout<<"\nWarning: memory limit is reached.\nTo get the requested accuracy please\nincrease the allowed amount of memory if possible\n\n";
break;
};
};
if(j%step_for_time==0)
{
double time_after3;
alp_data::get_current_time(time_after3);
if((time_after3-time_before1)>d_alp_data->d_max_time)
{
if(!d_alp_data->d_rand_flag)
{
//cout<<"\nWarning: time limit is reached.\nTo get the requested accuracy please\nincrease the allowed calculation time if possible\n\n";
break;
};
};
};
};
}
else
{
//cout<<"\nThe parameters were calculated with required accuracy\n\n";
};
long int final_realizations_number_killing=kill_j+realizations_number2_K+1;
long int final_realizations_number_lambda=alp_data::Tmax(realizations_number2_lambda+1,j+realizations_number2_K);
d_n_alp_obj=final_realizations_number_lambda;
double time_after100;
alp_data::get_current_time(time_after100);
//cout<<"\nActual calculation time is "<<time_after100-time_before1<<" seconds\n";
//cout<<"Actual memory usage is "<<d_alp_data->Tmax(memory_after2,memory_after3)<<" MBs\n\n";
if(!d_alp_data->d_rand_flag)
{
d_alp_data->d_rand_all->d_total_realizations_number_with_ALP=final_realizations_number_lambda-1;
d_alp_data->d_rand_all->d_total_realizations_number_with_killing=final_realizations_number_killing-1;
};
//!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
//output of a file with complete randomization information
if(!d_alp_data->d_rand_flag&&d_alp_data->d_randout!="")
{
//string rand_st="rand_"+alp_data::long_to_string(d_alp_data->d_rand_all->d_random_factor)+".out";
string rand_st=d_alp_data->d_randout;
frand.open(rand_st.data(),ios::out);
if(!frand)
{
throw error("Error - file "+rand_st+" cannot be created\n",3);
};
long int i;
frand<<d_alp_data->d_rand_all->d_random_seed<<endl;
frand<<d_alp_data->d_rand_all->d_first_stage_preliminary_realizations_numbers_ALP.size()<<"\t";
for(i=0;i<(long int)d_alp_data->d_rand_all->d_first_stage_preliminary_realizations_numbers_ALP.size();i++)
{
frand<<d_alp_data->d_rand_all->d_first_stage_preliminary_realizations_numbers_ALP[i]<<"\t";
};
frand<<endl;
frand<<d_alp_data->d_rand_all->d_preliminary_realizations_numbers_ALP.size()<<"\t";
for(i=0;i<(long int)d_alp_data->d_rand_all->d_preliminary_realizations_numbers_ALP.size();i++)
{
frand<<d_alp_data->d_rand_all->d_preliminary_realizations_numbers_ALP[i]<<"\t";
};
frand<<endl;
frand<<d_alp_data->d_rand_all->d_preliminary_realizations_numbers_killing.size()<<"\t";
for(i=0;i<(long int)d_alp_data->d_rand_all->d_preliminary_realizations_numbers_killing.size();i++)
{
frand<<d_alp_data->d_rand_all->d_preliminary_realizations_numbers_killing[i]<<"\t";
};
frand<<endl;
frand<<d_alp_data->d_rand_all->d_total_realizations_number_with_ALP<<endl;
frand<<d_alp_data->d_rand_all->d_total_realizations_number_with_killing<<endl;
frand.close();
};
//cout<<"A number of realizations\t"<<d_alp_data->d_rand_all->d_total_realizations_number_with_ALP<<endl;
bool inside_simulation_flag;
this->m_CalcTime=time_after100-time_before1;
output_main_parameters2m_new(
nalp_for_simulation,
level,
inside_simulation_flag,
final_realizations_number_lambda,
final_realizations_number_killing);
}
catch (...)
{
delete d_lambda_tmp;d_lambda_tmp=NULL;
delete d_lambda_tmp_errors;d_lambda_tmp_errors=NULL;
delete d_C_tmp;d_C_tmp=NULL;
delete d_C_tmp_errors;d_C_tmp_errors=NULL;
this->~alp_sim();
if(frand.is_open())
{
frand.close();
};
throw;
};
}
void alp_sim::symmetric_parameters_for_symmetric_scheme()
{
//check whether the scoring scheme is symmetric
bool symmetric_flag=true;
long int i,j;
for(i=0;i<d_alp_data->d_number_of_AA;i++)
{
for(j=0;j<i;j++)
{
if(d_alp_data->d_smatr[i][j]!=d_alp_data->d_smatr[j][i])
{
symmetric_flag=false;
break;
};
};
if(!symmetric_flag)
{
break;
};
};
if(symmetric_flag)
{
for(i=0;i<d_alp_data->d_number_of_AA;i++)
{
if(d_alp_data->d_RR1[i]!=d_alp_data->d_RR2[i])
{
symmetric_flag=false;
break;
};
};
};
if(symmetric_flag)
{
if(d_alp_data->d_epen1!=d_alp_data->d_epen2||d_alp_data->d_open1!=d_alp_data->d_open2)
{
symmetric_flag=false;
};
};
if(symmetric_flag)
{
m_AI=0.5*(m_AI+m_AJ);
m_AJ=m_AI;
m_AIError=0.5*(m_AIError+m_AJError);
m_AJError=m_AIError;
m_AlphaI=0.5*(m_AlphaI+m_AlphaJ);
m_AlphaJ=m_AlphaI;
m_AlphaIError=0.5*(m_AlphaIError+m_AlphaJError);
m_AlphaJError=m_AlphaIError;
};
}
void alp_sim::randomize_realizations(
long int final_realizations_number_lambda_,
long int final_realizations_number_killing_)
{
randomize_realizations_ind(0,final_realizations_number_killing_-1);
randomize_realizations_ind(final_realizations_number_killing_,final_realizations_number_lambda_-1);
}
void alp_sim::randomize_realizations_ind(
long int ind1_,
long int ind2_)
{
alp**array_ind=NULL;
long int *perm=NULL;
try
{
if(ind1_>=ind2_)
{
return;
};
if(ind2_>d_n_alp_obj-1)
{
throw error("Unexpected error\n",4);
};
long int total_number=ind2_-ind1_+1;
array_ind=new alp*[total_number];
alp_data::assert_mem(array_ind);
perm=new long int [total_number];
alp_data::assert_mem(perm);
generate_random_permulation(perm,total_number);
long int i;
for(i=0;i<total_number;i++)
{
array_ind[i]=d_alp_obj->d_elem[ind1_+perm[i]];
};
for(i=0;i<total_number;i++)
{
d_alp_obj->d_elem[ind1_+i]=array_ind[i];
};
delete[]array_ind;array_ind=NULL;
delete[]perm;perm=NULL;
}
catch (...)
{
delete[]array_ind;array_ind=NULL;
delete[]perm;perm=NULL;
throw;
};
}
void alp_sim::generate_random_permulation(
long int *perm_,
long int dim_)
{
long int i;
for(i=0;i<dim_;i++)
{
perm_[i]=i;
};
for(i=0;i<dim_-1;i++)
{
long int ind_swap=i+alp_data::random_long(d_alp_data->ran2(),dim_-i);
long int tmp=perm_[ind_swap];
perm_[ind_swap]=perm_[i];
perm_[i]=tmp;
};
}
void alp_sim::output_main_parameters2m_new(
long int nalp_for_lambda_simulation,
long int level,
bool &inside_simulation_flag,
long int final_realizations_number_lambda_,
long int final_realizations_number_killing_)
{
double lambda;
double lambda_error;
double test_difference;
double test_difference_error;
double C;
double C_error;
double K_C;
double K_C_error;
double a_I;
double a_I_error;
double a_J;
double a_J_error;
double sigma;
double sigma_error;
double alpha_I;
double alpha_I_error;
double alpha_J;
double alpha_J_error;
double K;
double K_error;
bool flag=false;