Representation and manipulation of variation data. More...

Classes
struct	Sequence::col_view_iterator< POINTER >
	Iterator for column views. More...

struct	Sequence::internal::row_view_< T >
	Implementation details for Sequence::RowView and Sequence::ConstRowView. More...

struct	Sequence::internal::col_view_< T >
	Implementation details for Sequence::ColView and Sequence::ConstColView. More...

struct	Sequence::StateCounts
	Track character state occurrence at a site in a VariantMatrix. More...

class	Sequence::VariantMatrix
	Matrix representation of variation data. More...

Typedefs
using	Sequence::RowView = internal::row_view_< std::int8_t * >
	View of a VariantMatrix row (a variable site)

using	Sequence::ConstRowView = internal::row_view_< const std::int8_t * >
	Const view of a VariantMatrix row (a variable site)

using	Sequence::ColView = internal::col_view_< std::int8_t * >
	View of a VariantMatrix column ("haplotype")

using	Sequence::ConstColView = internal::col_view_< const std::int8_t * >
	Const view of a VariantMatrix column ("haplotype")

Functions
template<typename POINTER >
col_view_iterator< POINTER >	Sequence::operator+ (col_view_iterator< POINTER > i, typename col_view_iterator< POINTER >::difference_type d)

template<typename POINTER >
col_view_iterator< POINTER >	Sequence::operator+ (typename col_view_iterator< POINTER >::difference_type d, col_view_iterator< POINTER > i)

template<typename POINTER >
col_view_iterator< POINTER > &	Sequence::operator++ (col_view_iterator< POINTER > &i)

template<typename POINTER >
col_view_iterator< POINTER >	Sequence::operator- (col_view_iterator< POINTER > i, typename col_view_iterator< POINTER >::difference_type d)

template<typename POINTER >
col_view_iterator< POINTER >	Sequence::operator- (typename col_view_iterator< POINTER >::difference_type d, col_view_iterator< POINTER > i)

template<typename POINTER >
col_view_iterator< POINTER > &	Sequence::operator-- (col_view_iterator< POINTER > &i)

template<typename POINTER >
col_view_iterator< POINTER > &	Sequence::operator+= (col_view_iterator< POINTER > &i, typename col_view_iterator< POINTER >::difference_type d)

template<typename POINTER >
col_view_iterator< POINTER > &	Sequence::operator-= (col_view_iterator< POINTER > &i, typename col_view_iterator< POINTER >::difference_type d)

template<typename POINTER >
col_view_iterator< POINTER >::difference_type	Sequence::operator- (col_view_iterator< POINTER > i, col_view_iterator< POINTER > j)

std::vector< StateCounts >	Sequence::process_variable_sites (const VariantMatrix &m, const std::vector< std::int8_t > &refstates)

std::vector< StateCounts >	Sequence::process_variable_sites (const VariantMatrix &m, const std::int8_t refstate)

std::vector< StateCounts >	Sequence::process_variable_sites (const VariantMatrix &m)

template<typename streamtype >
VariantMatrix	Sequence::from_msformat (streamtype &input_stream)
	Create VariantMatrix from "ms"-like input format. More...

template<typename output_stream >
void	Sequence::to_msformat (const VariantMatrix &m, output_stream &o)
	Write VariantMatrix in "ms" format. More...

ConstRowView	Sequence::get_RowView (const VariantMatrix &m, const std::size_t row)
	Return a ConstRowView from VariantMatrix `m` at row `row`. std::out_of_range is thrown if `row` is out of range.

RowView	Sequence::get_RowView (VariantMatrix &m, const std::size_t row)

ConstRowView	Sequence::get_ConstRowView (const VariantMatrix &m, const std::size_t row)
	Return a ConstRowView from VariantMatrix `m` at row `row`. std::out_of_range is thrown if `row` is out of range.

ConstRowView	Sequence::get_ConstRowView (VariantMatrix &m, const std::size_t row)
	Return a ConstRowView from VariantMatrix `m` at row `row`. std::out_of_range is thrown if `row` is out of range.

ColView	Sequence::get_ColView (VariantMatrix &m, const std::size_t col)
	Return a ColView from VariantMatrix `m` at col `col`. std::out_of_range is thcoln if `col` is out of range.

ConstColView	Sequence::get_ColView (const VariantMatrix &m, const std::size_t col)
	Return a ConstColView from VariantMatrix `m` at col `col`. std::out_of_range is thcoln if `col` is out of range.

ConstColView	Sequence::get_ConstColView (VariantMatrix &m, const std::size_t col)
	Return a ConstColView from VariantMatrix `m` at col `col`. std::out_of_range is thcoln if `col` is out of range.

ConstColView	Sequence::get_ConstColView (const VariantMatrix &m, const std::size_t col)
	Return a ConstColView from VariantMatrix `m` at col `col`. std::out_of_range is thcoln if `col` is out of range.

Detailed Description

Representation and manipulation of variation data.

Function Documentation

◆ from_msformat()

template<typename streamtype >

VariantMatrix Sequence::from_msformat ( streamtype & input_stream )

inline

Create VariantMatrix from "ms"-like input format.

Parameters

input_stream A model of std::istream

Returns: A VariantMatrix

See ms_to_VariantMatrix.cc for example.

Examples:: ms_to_VariantMatrix.cc, and nSL_from_ms.cc.

Definition at line 20 of file msformat.hpp.

◆ get_RowView()

RowView Sequence::get_RowView	(	VariantMatrix &	m,
		const std::size_t	row
	)

Return a RowView from VariantMatrix m at row row. std::out_of_range is thrown if row is out of range.

Definition at line 38 of file VariantMatrixViews.cc.

◆ operator+() [1/2]

template<typename POINTER >

col_view_iterator<POINTER> Sequence::operator+	(	col_view_iterator< POINTER >	i,
		typename col_view_iterator< POINTER >::difference_type	d
	)

inline

Add to an iterator

Definition at line 113 of file col_view_iterator.hpp.

◆ operator+() [2/2]

template<typename POINTER >

col_view_iterator<POINTER> Sequence::operator+	(	typename col_view_iterator< POINTER >::difference_type	d,
		col_view_iterator< POINTER >	i
	)

inline

Add to an iterator

Definition at line 125 of file col_view_iterator.hpp.

◆ operator++()

template<typename POINTER >

col_view_iterator<POINTER>& Sequence::operator++ ( col_view_iterator< POINTER > & i )

inline

Increment an iterator by one

Definition at line 135 of file col_view_iterator.hpp.

◆ operator+=()

template<typename POINTER >

col_view_iterator<POINTER>& Sequence::operator+=	(	col_view_iterator< POINTER > &	i,
		typename col_view_iterator< POINTER >::difference_type	d
	)

inline

Increment an iterator

Definition at line 177 of file col_view_iterator.hpp.

◆ operator-() [1/3]

template<typename POINTER >

col_view_iterator<POINTER> Sequence::operator-	(	col_view_iterator< POINTER >	i,
		typename col_view_iterator< POINTER >::difference_type	d
	)

inline

Subtract from an iterator

Definition at line 145 of file col_view_iterator.hpp.

◆ operator-() [2/3]

template<typename POINTER >

col_view_iterator<POINTER> Sequence::operator-	(	typename col_view_iterator< POINTER >::difference_type	d,
		col_view_iterator< POINTER >	i
	)

inline

Subtract from an iterator

Definition at line 157 of file col_view_iterator.hpp.

◆ operator-() [3/3]

template<typename POINTER >

col_view_iterator<POINTER>::difference_type Sequence::operator-	(	col_view_iterator< POINTER >	i,
		col_view_iterator< POINTER >	j
	)

inline

Distance between two iterators

Definition at line 199 of file col_view_iterator.hpp.

◆ operator--()

template<typename POINTER >

col_view_iterator<POINTER>& Sequence::operator-- ( col_view_iterator< POINTER > & i )

inline

Decrement iterator by one

Definition at line 167 of file col_view_iterator.hpp.

◆ operator-=()

template<typename POINTER >

col_view_iterator<POINTER>& Sequence::operator-=	(	col_view_iterator< POINTER > &	i,
		typename col_view_iterator< POINTER >::difference_type	d
	)

inline

Decrement an iterator

Definition at line 188 of file col_view_iterator.hpp.

◆ process_variable_sites() [1/3]

std::vector< StateCounts > Sequence::process_variable_sites	(	const VariantMatrix &	m,
		const std::vector< std::int8_t > &	refstates
	)

Create a vector of StateCounts from a VariantMatrix. If refstates is not empty and differs in length from m.nsites, then std::invalid_argument is thrown.

Definition at line 68 of file StateCounts.cc.

◆ process_variable_sites() [2/3]

std::vector< StateCounts > Sequence::process_variable_sites	(	const VariantMatrix &	m,
		const std::int8_t	refstate
	)

Create a vector of StateCounts with a specific reference state used for all sites

Definition at line 94 of file StateCounts.cc.

◆ process_variable_sites() [3/3]

std::vector< StateCounts > Sequence::process_variable_sites ( const VariantMatrix & m )

Create a vector of StateCounts with a reference state of -1 used for all sites

Definition at line 113 of file StateCounts.cc.

◆ to_msformat()

template<typename output_stream >

void Sequence::to_msformat	(	const VariantMatrix &	m,
		output_stream &	o
	)

inline

Write VariantMatrix in "ms" format.

Parameters

m	A VariantMatrix
o	A model of std::ostream

See ms_to_VariantMatrix.cc for example.

Examples:: ms_to_VariantMatrix.cc.

Definition at line 62 of file msformat.hpp.

Classes

Typedefs

Functions

Detailed Description

Function Documentation

◆ from_msformat()

◆ get_RowView()

◆ operator+() [1/2]

◆ operator+() [2/2]

◆ operator++()

◆ operator+=()

◆ operator-() [1/3]

◆ operator-() [2/3]

◆ operator-() [3/3]

◆ operator--()

◆ operator-=()

◆ process_variable_sites() [1/3]

◆ process_variable_sites() [2/3]

◆ process_variable_sites() [3/3]

◆ to_msformat()