jade::basic_verification< TValue > Class Template Reference

A template for a class that performs validation on various types of matrices. More...

#include <jade.verification.hpp>

Collaboration diagram for jade::basic_verification< TValue >:

Public Types
typedef TValue	value_type
	The value type. More...
typedef basic_matrix< value_type >	matrix_type
	The matrix type. More...
typedef basic_genotype_matrix< value_type >	genotype_matrix_type
	The genotype matrix type. More...

Static Public Member Functions
static bool	validate_c (const matrix_type &c)
	Validates the C matrix and throws an exception if validation fails. More...
static bool	validate_f (const matrix_type &f)
	Validates the F matrix and throws an exception if validation fails. More...
static bool	validate_fc_sizes (const matrix_type &f, const matrix_type &c)
	Validates the sizes of the F and C matrices and throws an exception if validation fails. More...
static bool	validate_fif_size (const matrix_type &fif, const size_t k, const size_t j)
	Validates the size of the Fin-force matrix and throws an exception if validation fails. More...
static bool	validate_g (const genotype_matrix_type &g)
	Validates the G matrix and throws an exception if validation fails. More...
static bool	validate_gf_sizes (const genotype_matrix_type &g, const matrix_type &f)
	Validates the sizes of the G and F matrices and throws an exception if validation fails. More...
static bool	validate_gq_sizes (const genotype_matrix_type &g, const matrix_type &q)
	Validates the sizes of the G and Q matrices and throws an exception if validation fails. More...
static bool	validate_gqf_sizes (const genotype_matrix_type &g, const matrix_type &q, const matrix_type &f)
	Validates the sizes of the G, Q, and F matrices and throws an exception if validation fails. More...
static bool	validate_q (const matrix_type &q)
	Validates the Q matrix and throws an exception if validation fails. More...
static bool	validate_qf_sizes (const matrix_type &q, const matrix_type &f)
	Validates the sizes of the Q and F matrices and throws an exception if validation fails. More...

Static Public Attributes
static constexpr value_type	epsilon = value_type(0.000001)
	The epsilon value. More...

Detailed Description

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

A template for a class that performs validation on various types of matrices.

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

Member Typedef Documentation

genotype_matrix_type

template<typename TValue >

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

The genotype matrix type.

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

matrix_type

template<typename TValue >

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

The matrix type.

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

value_type

template<typename TValue >

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

The value type.

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

Member Function Documentation

validate_c()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_c ( const matrix_type &  c )

inlinestatic

Validates the C matrix and throws an exception if validation fails.

Returns

True.

Parameters

c	The C matrix to validate.

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

        {
            if (!c.is_square())
                throw error() << "invalid C matrix size " << c.get_size_str()
                              << " is not square";
 
            const auto rk = c.get_height();
            if (0 == rk)
                throw error() << "invalid C matrix size " << c.get_size_str()
                              << " does not contain any components";
 
            for (size_t y = 0; y < rk; y++)
                for (size_t x = y + 1; x < rk; x++)
                    if (std::fabs(c(y, x) - c(x, y)) > epsilon)
                        throw error()
                            << "invalid C matrix cell [" << y+1 << ","
                            << x+1 << "] (" << c(y, x)
                            << ") is not equal to symmetric cell ["
                            << x+1 << "," << y+1 << "] (" << c(x, y) << ")";
 
 
            // Create a copy of C before LAPACK replaces it with the
            // Cholesky square root and then its inverse.
            matrix_type cholesky (c);
            if (!cholesky.potrf_lower() || !cholesky.potri_lower())
                throw error("invalid C matrix is not positive semidefinite");
 
            return true;
        }

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validate_f()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_f ( const matrix_type &  f )

inlinestatic

Validates the F matrix and throws an exception if validation fails.

Returns

True.

Parameters

f	The F matrix to validate.

Definition at line 73 of file jade.verification.hpp.

        {
            static const auto epsilon = value_type(1.0e-6);
            static const auto min     = value_type(0.0) + epsilon;
            static const auto max     = value_type(1.0) - epsilon;
 
            const auto K = f.get_height();
            const auto J = f.get_width();
 
            if (0 == K)
                throw error() << "invalid F matrix size " << f.get_size_str()
                              << " does not contain any components";
 
            if (0 == J)
                throw error() << "invalid F matrix size " << f.get_size_str()
                              << " does not contain any markers";
 
            for (size_t k = 0; k < K; k++)
            {
                for (size_t j = 0; j < J; j++)
                {
                    const auto f_kj = f(k, j);
 
                    if (f_kj >= min && f_kj <= max)
                        continue;
 
                    throw error()
                        << "invalid F matrix cell [" << k+1 << "," << j+1
                        << "] (" << f_kj << ") is not between 0 and 1";
                }
            }
 
            return true;
        }

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validate_fc_sizes()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_fc_sizes ( const matrix_type &  f, const matrix_type &  c  )

inlinestatic

Validates the sizes of the F and C matrices and throws an exception if validation fails.

Returns

True.

Parameters

f	The F matrix to validate.
c	The C matrix to validate.

Definition at line 114 of file jade.verification.hpp.

        {
            if (f.get_height() != c.get_height() + 1)
                throw error()
                    << "inconsistent F matrix size " << f.get_size_str()
                    << " and C matrix size " << c.get_size_str();
 
            return true;
        }

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validate_fif_size()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_fif_size ( const matrix_type &  fif, const size_t  k, const size_t  j  )

inlinestatic

Validates the size of the Fin-force matrix and throws an exception if validation fails.

Returns

True.

Parameters

fif	The Fin-force matrix.
k	The component count.
j	The marker count.

Definition at line 131 of file jade.verification.hpp.

        {
            const auto fif_height = fif.get_height();
            const auto fif_width  = fif.get_width();
 
            if (fif_width != j)
                throw error()
                    << "inconsistent marker count (" << j
                    << ") and width of matrix specified for --fin-force "
                    << "option (" << fif_width << ")";
 
            if (fif_height >= k)
                throw error()
                    << "inconsistent component count (" << k << ") and "
                    << "height of matrix specified for --fin-force "
                    << "option (" << fif_height << ")";
 
            return true;
        }

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validate_g()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_g ( const genotype_matrix_type &  g )

inlinestatic

Validates the G matrix and throws an exception if validation fails.

Returns

True.

Parameters

g	The G matrix to validate.

Definition at line 158 of file jade.verification.hpp.

        {
            if (0 == g.get_height())
                throw error() << "invalid G matrix size " << g.get_size_str()
                              << " does not contain any individuals";
 
            if (0 == g.get_width())
                throw error() << "invalid G matrix size " << g.get_size_str()
                              << " does not contain any markers";
 
            return true;
        }

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validate_gf_sizes()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_gf_sizes ( const genotype_matrix_type &  g, const matrix_type &  f  )

inlinestatic

Validates the sizes of the G and F matrices and throws an exception if validation fails.

Returns

True.

Parameters

g	The G matrix to validate.
f	The F matrix to validate.

Definition at line 177 of file jade.verification.hpp.

        {
            if (g.get_width() != f.get_width())
                throw error()
                    << "inconsistent G matrix size " << g.get_size_str()
                    << " and F matrix size " << f.get_size_str();
 
            return true;
        }

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validate_gq_sizes()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_gq_sizes ( const genotype_matrix_type &  g, const matrix_type &  q  )

inlinestatic

Validates the sizes of the G and Q matrices and throws an exception if validation fails.

Returns

True.

Parameters

g	The G matrix to validate.
q	The Q matrix to validate.

Definition at line 194 of file jade.verification.hpp.

        {
            if (g.get_height() != q.get_height())
                throw error()
                    << "inconsistent G matrix size " << g.get_size_str()
                    << " and Q matrix size " << q.get_size_str();
 
            return true;
        }

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validate_gqf_sizes()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_gqf_sizes ( const genotype_matrix_type &  g, const matrix_type &  q, const matrix_type &  f  )

inlinestatic

Validates the sizes of the G, Q, and F matrices and throws an exception if validation fails.

Returns

True.

Parameters

g	The G matrix to validate.
q	The Q matrix to validate.
f	The F matrix to validate.

Definition at line 211 of file jade.verification.hpp.

        {
            return validate_gq_sizes(g, q)
                && validate_gf_sizes(g, f)
                && validate_qf_sizes(q, f);
        }

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validate_q()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_q ( const matrix_type &  q )

inlinestatic

Validates the Q matrix and throws an exception if validation fails.

Returns

True.

Parameters

q	The Q matrix to validate.

Definition at line 225 of file jade.verification.hpp.

        {
            const auto I = q.get_height();
            const auto K = q.get_width();
 
            if (0 == I)
                throw error() << "invalid Q matrix size " << q.get_size_str()
                              << " does not contain any individuals";
 
            if (0 == K)
                throw error() << "invalid Q matrix size " << q.get_size_str()
                              << " does not contain any components";
 
            for (size_t i = 0; i < I; i++)
            {
                auto sum = value_type(0);
 
                for (size_t k = 0; k < K; k++)
                {
                    const auto q_ik = q(i, k);
 
                    if (q_ik < value_type(0) || q_ik > value_type(1))
                        throw error()
                            << "invalid Q matrix cell [" << i+1 << "," << k+1
                            << "] (" << q_ik << ") is not between 0 and 1";
 
                    sum += q_ik;
                }
 
                if (std::fabs(sum - value_type(1)) > epsilon)
                    throw error() << "invalid Q matrix row " << i+1
                                << " does not sum to 1 (" << sum << ")";
            }
 
            return true;
        }

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validate_qf_sizes()

template<typename TValue >

static bool jade::basic_verification< TValue >::validate_qf_sizes ( const matrix_type &  q, const matrix_type &  f  )

inlinestatic

Validates the sizes of the Q and F matrices and throws an exception if validation fails.

Returns

True.

Parameters

q	The Q matrix to validate.
f	The F matrix to validate.

Definition at line 268 of file jade.verification.hpp.

        {
            if (q.get_width() != f.get_height())
                throw error()
                    << "inconsistent Q matrix size " << q.get_size_str()
                    << " and F matrix size " << f.get_size_str();
 
            return true;
        }

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Field Documentation

epsilon

template<typename TValue >

constexpr value_type jade::basic_verification< TValue >::epsilon = value_type(0.000001)

staticconstexpr

The epsilon value.

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

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

• jade.verification.hpp