jade::basic_selscan< TValue > Class Template Reference

A template for a class implementing the selscan program. More...

#include <jade.selscan.hpp>

Collaboration diagram for jade::basic_selscan< TValue >:

Public Types
typedef TValue	value_type
	The value type. More...
typedef basic_matrix< value_type >	matrix_type
	The matrix type. More...
typedef basic_verification< value_type >	verification_type
	The verification type. More...
typedef basic_genotype_matrix< value_type >	genotype_matrix_type
	The genotype matrix type. More...
typedef basic_genotype_matrix_factory< TValue >	genotype_matrix_factory_type
	The genotype matrix factory type. More...

Public Member Functions
	basic_selscan (args &a)
	Initializes a new instance of the class. More...
void	execute ()
	Executes the program. More...

Detailed Description

template<typename TValue>
class jade::basic_selscan< TValue >

A template for a class implementing the selscan program.

Definition at line 19 of file jade.selscan.hpp.

Member Typedef Documentation

genotype_matrix_factory_type

template<typename TValue >

typedef basic_genotype_matrix_factory<TValue> jade::basic_selscan< TValue >::genotype_matrix_factory_type

The genotype matrix factory type.

Definition at line 37 of file jade.selscan.hpp.

genotype_matrix_type

template<typename TValue >

typedef basic_genotype_matrix<value_type> jade::basic_selscan< TValue >::genotype_matrix_type

The genotype matrix type.

Definition at line 32 of file jade.selscan.hpp.

matrix_type

template<typename TValue >

typedef basic_matrix<value_type> jade::basic_selscan< TValue >::matrix_type

The matrix type.

Definition at line 26 of file jade.selscan.hpp.

value_type

template<typename TValue >

typedef TValue jade::basic_selscan< TValue >::value_type

The value type.

Definition at line 23 of file jade.selscan.hpp.

verification_type

template<typename TValue >

typedef basic_verification<value_type> jade::basic_selscan< TValue >::verification_type

The verification type.

Definition at line 29 of file jade.selscan.hpp.

Constructor & Destructor Documentation

basic_selscan()

template<typename TValue >

jade::basic_selscan< TValue >::basic_selscan ( args &  a )

inlineexplicit

Initializes a new instance of the class.

Parameters

a	The command-line arguments.

Definition at line 42 of file jade.selscan.hpp.

            : steps     (a.read("--steps", "-s", size_t(100)))
            , f_epsilon (_read_f_epsilon(a))
            , g_ptr     (genotype_matrix_factory_type::create(a.pop<std::string>()))
            , g         (*g_ptr)
            , fa        (a.pop<std::string>())
            , c1        (a.pop<std::string>())
            , c2        (_init_scaling_matrix(a, c1))
            , RK        (c1.get_width())
            , J         (g.get_width())
            , mu        (g.create_mu(f_epsilon))
            , rooted_fa (_compute_rooted_fa(fa))
            , c_inv     (RK, RK)
            , f_j_c_inv (RK, 1)
        {
            if (steps < 2)
                throw error() << "invalid value for --steps option ("
                              << steps << "); expected at least two steps";
 
            a.validate_empty();
 
            verification_type::validate_g(g);
            verification_type::validate_f(fa);
            verification_type::validate_c(c1);
            verification_type::validate_c(c2);
            verification_type::validate_gf_sizes(g, fa);
            verification_type::validate_fc_sizes(fa, c1);
            verification_type::validate_fc_sizes(fa, c2);
        }

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Member Function Documentation

execute()

template<typename TValue >

void jade::basic_selscan< TValue >::execute ( )

inline

Executes the program.

Definition at line 76 of file jade.selscan.hpp.

        {
            const auto K = fa.get_height();
 
            std::cout << "step\tlle-ratio\tglobal-lle\tlocal-lle";
 
            for (size_t k = 0; k < K; k++)
                std::cout << "\t" << "f-pop" << k;
 
            std::cout << std::endl;
 
            std::vector<record> records;
            records.reserve(J);
            for (size_t j = 0; j < J; j++)
                records.emplace_back(j, _compute_score(0, j));
 
            for (size_t si = 0; si < steps; si++)
                for (auto & r : records)
                    r.update(si, _compute_score(si, r.get_j()));
 
            for (const auto & r : records)
            {
                std::cout << r.get_step()                << '\t'
                          << _format(r.get_lle_ratio())  << '\t'
                          << _format(r.get_score())      << '\t'
                          << _format(r.get_best_score());
 
                for (size_t k = 0; k < K; k++)
                    std::cout << '\t' << _format(fa(k, r.get_j()));
 
                std::cout << std::endl;
            }
        }

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The documentation for this class was generated from the following file:

• jade.selscan.hpp