libsequence  1.9.5
Public Types | Public Member Functions | Public Attributes | Static Public Attributes | List of all members
Sequence::VariantMatrix Class Reference
Molecular Population Genetics » Variant Matrix

Matrix representation of variation data. More...

#include <VariantMatrix.hpp>

Public Types

using value_type = std::int8_t
 

Public Member Functions

template<typename data_input , typename positions_input >
 VariantMatrix (data_input &&data_, positions_input &&positions_, const std::int8_t max_allele_value=-1)
 "Perfect-forwarding" constructor. More...
 
std::int8_t & get (const std::size_t site, const std::size_t haplotype)
 Get data from marker site and haplotype haplotype. No range-checking is done.
 
const std::int8_t & get (const std::size_t site, const std::size_t haplotype) const
 Get data from marker site and haplotype haplotype. No range-checking is done.
 
std::int8_t & at (const std::size_t site, const std::size_t haplotype)
 Get data from marker site and haplotype haplotype. std::out_of_range is thrown if indexes are invalid.
 
const std::int8_t & at (const std::size_t site, const std::size_t haplotype) const
 Get data from marker site and haplotype haplotype. std::out_of_range is thrown if indexes are invalid.
 

Public Attributes

std::vector< std::int8_t > data
 Data stored in matrix form with rows as sites.
 
std::vector< double > positions
 Position of sites.
 
std::size_t nsites
 Number of sites in data set.
 
std::size_t nsam
 Sample size of data set.
 
const std::int8_t max_allele
 Max allelic value stored in matrix.
 

Static Public Attributes

static const std::int8_t mask = std::numeric_limits<std::int8_t>::min()
 Reserved value for masked data.
 

Detailed Description

Matrix representation of variation data.

The data structure is a row-major matrix. Variants are represented by 8-bit integers. Negative values represent missing data, thus allowing up to 128 non-missing states per variable site.

Rows are sites, columns are either haplotypes or are populated as necessary in the case of genotype (unphased) data. Storing variable sites in rows places the performance priority on sites over haplotypes.

The only reserved character state is std::numeric_limits<std::int8_t>::min(), which is used to represent masked data. That reserved value is VariantMatrix::mask, which is a static constant.

\version 1.9.2

Definition at line 22 of file VariantMatrix.hpp.

Member Typedef Documentation

◆ value_type

using Sequence::VariantMatrix::value_type = std::int8_t

The value type of the data. Helpful for generic programming

Definition at line 78 of file VariantMatrix.hpp.

Constructor & Destructor Documentation

◆ VariantMatrix()

template<typename data_input , typename positions_input >
Sequence::VariantMatrix::VariantMatrix ( data_input &&  data_,
positions_input &&  positions_,
const std::int8_t  max_allele_value = -1 
)
inline

"Perfect-forwarding" constructor.

std::invalid_argument will be thrown if data.size() % positions.size() != 0.0.

Definition at line 82 of file VariantMatrix.hpp.

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