jade::basic_genotype_matrix< TValue > Class Template Reference

A template for an abstract class implementing operations for a genotype matrix. More...

#include <jade.genotype_matrix.hpp>

Inheritance diagram for jade::basic_genotype_matrix< TValue >:

Collaboration diagram for jade::basic_genotype_matrix< TValue >:

Public Types
typedef TValue	value_type
	The value type. More...
typedef basic_matrix< TValue >	matrix_type
	The matrix type. More...
typedef basic_discrete_genotype_matrix< value_type >	dgm_type
	The discrete genotype matrix type. More...
typedef basic_likelihood_genotype_matrix< value_type >	lgm_type
	The likelihood genotype matrix type. More...

Public Member Functions
virtual	~basic_genotype_matrix ()
	Reclaims resources used by the class and derived classes. More...
virtual void	compute_derivatives_f (const matrix_type &q, const matrix_type &fa, const matrix_type &fb, const matrix_type &qfa, const matrix_type &qfb, const size_t j, matrix_type &d_vec, matrix_type &h_mat) const =0
	Computes the derivative vector and hessian matrix for a specified marker of the F matrix. More...
virtual void	compute_derivatives_q (const matrix_type &q, const matrix_type &fa, const matrix_type &fb, const matrix_type &qfa, const matrix_type &qfb, const size_t i, matrix_type &d_vec, matrix_type &h_mat) const =0
	Computes the derivative vector and hessian matrix for a specified individual of the Q matrix. More...
virtual value_type	compute_lle (const matrix_type &q, const matrix_type &fa, const matrix_type &fb, const matrix_type &qfa, const matrix_type &qfb) const =0
virtual matrix_type	create_mu (const value_type f_epsilon) const =0
virtual size_t	get_height () const =0
virtual std::string	get_size_str () const =0
virtual size_t	get_width () const =0
virtual std::string	str () const =0

Protected Member Functions
	basic_genotype_matrix ()
	Initializes a new instance of the class. More...

Detailed Description

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

A template for an abstract class implementing operations for a genotype matrix.

Definition at line 25 of file jade.genotype_matrix.hpp.

Member Typedef Documentation

dgm_type

template<typename TValue >

typedef basic_discrete_genotype_matrix<value_type> jade::basic_genotype_matrix< TValue >::dgm_type

The discrete genotype matrix type.

Definition at line 35 of file jade.genotype_matrix.hpp.

lgm_type

template<typename TValue >

typedef basic_likelihood_genotype_matrix<value_type> jade::basic_genotype_matrix< TValue >::lgm_type

The likelihood genotype matrix type.

Definition at line 38 of file jade.genotype_matrix.hpp.

matrix_type

template<typename TValue >

typedef basic_matrix<TValue> jade::basic_genotype_matrix< TValue >::matrix_type

The matrix type.

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

value_type

template<typename TValue >

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

The value type.

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

Constructor & Destructor Documentation

~basic_genotype_matrix()

template<typename TValue >

virtual jade::basic_genotype_matrix< TValue >::~basic_genotype_matrix ( )

inlinevirtual

Reclaims resources used by the class and derived classes.

Definition at line 43 of file jade.genotype_matrix.hpp.

        {
        }

basic_genotype_matrix()

template<typename TValue >

jade::basic_genotype_matrix< TValue >::basic_genotype_matrix ( )

inlineprotected

Initializes a new instance of the class.

Definition at line 145 of file jade.genotype_matrix.hpp.

        {
        }

Member Function Documentation

compute_derivatives_f()

template<typename TValue >

virtual void jade::basic_genotype_matrix< TValue >::compute_derivatives_f ( const matrix_type &  q, const matrix_type &  fa, const matrix_type &  fb, const matrix_type &  qfa, const matrix_type &  qfb, const size_t  j, matrix_type &  d_vec, matrix_type &  h_mat  ) const

pure virtual

Computes the derivative vector and hessian matrix for a specified marker of the F matrix.

Parameters

q	The Q matrix.
fa	The F matrix.
fb	The 1-F matrix.
qfa	The Q*F product.
qfb	The Q*(1-F) product.
j	The marker.
d_vec	The derivative vector.
h_mat	The hessian matrix.

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compute_derivatives_q()

template<typename TValue >

virtual void jade::basic_genotype_matrix< TValue >::compute_derivatives_q ( const matrix_type &  q, const matrix_type &  fa, const matrix_type &  fb, const matrix_type &  qfa, const matrix_type &  qfb, const size_t  i, matrix_type &  d_vec, matrix_type &  h_mat  ) const

pure virtual

Computes the derivative vector and hessian matrix for a specified individual of the Q matrix.

Parameters

q	The Q matrix.
fa	The F matrix.
fb	The 1-F matrix.
qfa	The Q*F product.
qfb	The Q*(1-F) product.
i	The individual.
d_vec	The derivative vector.
h_mat	The hessian matrix.

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compute_lle()

template<typename TValue >

virtual value_type jade::basic_genotype_matrix< TValue >::compute_lle ( const matrix_type &  q, const matrix_type &  fa, const matrix_type &  fb, const matrix_type &  qfa, const matrix_type &  qfb  ) const

pure virtual

Returns

The log of the likelihood function.

Parameters

q	The Q matrix.
fa	The F matrix for major alleles.
fb	The F matrix for minor alleles.
qfa	The Q*Fa product.
qfb	The Q*Fb product.

create_mu()

template<typename TValue >

virtual matrix_type jade::basic_genotype_matrix< TValue >::create_mu ( const value_type  f_epsilon ) const

pure virtual

Returns

A new mu matrix.

Parameters

f_epsilon

The F matrix boundary epsilon.

Implemented in jade::basic_discrete_genotype_matrix< TValue >.

get_height()

template<typename TValue >

virtual size_t jade::basic_genotype_matrix< TValue >::get_height ( ) const

pure virtual

Returns

The height of the matrix.

Implemented in jade::basic_discrete_genotype_matrix< TValue >.

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get_size_str()

template<typename TValue >

virtual std::string jade::basic_genotype_matrix< TValue >::get_size_str ( ) const

pure virtual

Returns

The string representation of the size of the matrix.

Implemented in jade::basic_discrete_genotype_matrix< TValue >.

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get_width()

template<typename TValue >

virtual size_t jade::basic_genotype_matrix< TValue >::get_width ( ) const

pure virtual

Returns

The width of the matrix.

Implemented in jade::basic_discrete_genotype_matrix< TValue >.

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str()

template<typename TValue >

virtual std::string jade::basic_genotype_matrix< TValue >::str ( ) const

pure virtual

Returns

The string representation of the matrix.

Implemented in jade::basic_discrete_genotype_matrix< TValue >.

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

• jade.genotype_matrix.hpp