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sls_basic.hpp
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sls_basic.hpp
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#ifndef INCLUDED_SLS_BASIC
#define INCLUDED_SLS_BASIC
/* $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_basic.hpp
Author: Sergey Sheetlin
Contents: Some basic functions and types
******************************************************************************/
#ifndef _MSC_VER //UNIX program
#else
#define _CRT_SECURE_NO_WARNINGS
#endif
#ifndef _MSC_VER //UNIX program
#include <sys/time.h>
#else
#include <sys/timeb.h>
#endif
#include <iomanip>
#include <cmath>
#include <string>
namespace Sls {
const double pi=3.1415926535897932384626433832795;
const double const_val=1/sqrt(2.0*pi);
const long int quick_tests_trials_number=100;
struct error//struct to handle exceptions
{
std::string st;
error(std::string st_,long int error_code_){st=st_;error_code=error_code_;};
long int error_code;
};
//structure for user-defined Gumbel parameters without errors
struct AlignmentEvaluerParameters
{
double d_lambda;
double d_k;
double d_a1;
double d_b1;
double d_a2;
double d_b2;
double d_alpha1;
double d_beta1;
double d_alpha2;
double d_beta2;
double d_sigma;
double d_tau;
};
//structure for user-defined Gumbel parameters with errors
struct AlignmentEvaluerParametersWithErrors
{
double d_lambda;
double d_lambda_error;
double d_k;
double d_k_error;
double d_a1;
double d_a1_error;
double d_b1;
double d_b1_error;
double d_a2;
double d_a2_error;
double d_b2;
double d_b2_error;
double d_alpha1;
double d_alpha1_error;
double d_beta1;
double d_beta1_error;
double d_alpha2;
double d_alpha2_error;
double d_beta2;
double d_beta2_error;
double d_sigma;
double d_sigma_error;
double d_tau;
double d_tau_error;
};
class sls_basic{
public:
template<class T>
static inline T Tmax(T i_, T j_)
{
if(i_>j_)
{
return i_;
};
return j_;
}
template<class T>
static inline T Tmin(T i_, T j_)
{
if(i_<j_)
{
return i_;
};
return j_;
}
template<class T>
static inline T Tmax(T x_,T y_,T z_)
{
return Tmax(Tmax(x_,y_),z_);
}
template<class T>
static inline T Tmin(T x_,T y_,T z_)
{
return Tmin(Tmin(x_,y_),z_);
}
template<class T>
static inline T Tmax(T x_,T y_,T z_,T w_)
{
return Tmax(Tmax(x_,y_),Tmax(z_,w_));
}
template<class T>
static inline T Tmin(T x_,T y_,T z_,T w_)
{
return Tmin(Tmin(x_,y_),Tmin(z_,w_));
}
static inline void assert_mem(void *pointer_)
{
if(!pointer_)
{
throw error("Memory allocation error\n",41);
};
}
static double round(//returns nearest integer to x_
const double &x_);
static void get_current_time(
double &seconds_);
static double one_minus_exp_function(
double y_);
static double normal_probability(
double x_,
double eps_);
static double normal_probability(
double a_,
double b_,
double h_,
long int N_,
double *p_,
double x_,
double eps_);
static double ln_one_minus_val(
double val_);
};
}
#endif