Sequence::StateCounts Struct Reference

Track character state occurrence at a site in a VariantMatrix. More...

#include <StateCounts.hpp>

Public Member Functions
	StateCounts (const std::int8_t refstate_)
void	operator() (ConstRowView &)
void	operator() (const RowView &)

Public Attributes
std::vector< std::int32_t >	counts
	Keep track of (state, count) pairs.
std::size_t	max_allele_idx
	The max allelic value seen.
std::uint32_t	n
	The sample size at this site. Excluded missing data.
std::int8_t	refstate

Static Public Attributes
static constexpr VariantMatrix::value_type	max_allele = std::numeric_limits<VariantMatrix::value_type>::max()

Detailed Description

Track character state occurrence at a site in a VariantMatrix.

This class keeps track of how many times each character state occurs at a variable site in a VariantMatrix. All missing data (negative state values) are considered equivalent and collapsed into the single missing value of -1.

When constructed, the sample size at a site is considered to be the sum of the number of occurrences of all non-missing states.

Definition at line 11 of file StateCounts.hpp.

Constructor & Destructor Documentation

StateCounts()

Sequence::StateCounts::StateCounts

(

const std::int8_t

refstate_

)

Construct with a ConstRowView and a reference state, which defaults to 0.

Definition at line 13 of file StateCounts.cc.

Member Data Documentation

refstate

std::int8_t Sequence::StateCounts::refstate

The reference state for this site. Needed for certain summary statistics. Default is -1 (missing).

Definition at line 34 of file StateCounts.hpp.

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

• StateCounts.hpp
• StateCounts.cc