Sequence::Alignment Namespace Reference

Routines fundamental to aligned data. More...

Functions
template<typename T >
void	GetData (std::vector< T > &seqarray, const char *infilename)
template<typename T >
std::istream &	GetData (std::vector< T > &seqarray, std::istream &input_stream)
template<typename T >
std::istream &	ReadNObjects (std::vector< T > &seqarray, const unsigned &n, std::istream &input_stream)
template<typename T >
bool	Gapped (const std::vector< T > &data)
template<typename T >
bool	IsAlignment (const std::vector< T > &data)
template<typename Iterator >
bool	validForPolyAnalysis (Iterator beg, Iterator end)
template<typename T >
unsigned	UnGappedLength (const std::vector< T > &data)
template<typename T >
void	RemoveGaps (std::vector< T > &data)
template<typename T >
void	RemoveTerminalGaps (std::vector< T > &data)
template<typename T >
void	RemoveFixedOutgroupInsertions (std::vector< T > &data, unsigned site, const unsigned &ref)
template<typename T >
std::vector< T >	Trim (const std::vector< T > &data, const std::vector< int > &sites)
template<typename T >
std::vector< T >	TrimComplement (const std::vector< T > &data, const std::vector< int > &sites)
template<>
bool	Gapped (const std::vector< std::string > &data)
template<>
bool	IsAlignment (const std::vector< std::string > &data)
template<>
bool	validForPolyAnalysis (std::vector< std::string >::const_iterator beg, std::vector< std::string >::const_iterator end)
template<>
bool	validForPolyAnalysis (std::vector< std::string >::iterator beg, std::vector< std::string >::iterator end)
template<>
unsigned	UnGappedLength (const std::vector< std::string > &data)
template<>
void	RemoveGaps (std::vector< std::string > &data)
template<>
void	RemoveTerminalGaps (std::vector< std::string > &data)
template<>
void	RemoveFixedOutgroupInsertions (std::vector< std::string > &data, unsigned site, const unsigned &ref)
template<>
std::vector< std::string >	Trim (const std::vector< std::string > &data, const std::vector< int > &sites)
template<>
std::vector< std::string >	TrimComplement (const std::vector< std::string > &data, const std::vector< int > &sites)

Detailed Description

Routines fundamental to aligned data.

#include<Sequence/Alignment.hpp>
This namespace defines a series of template routines used for manipulating aligned sequence data. The routines may be used on their own, and are also the building blocks for alignment I/O as defined in Sequence::AlignStream.

Note

Valid types for instantiation of these templates are the following: std::pair<std::string,std::string>, or anything derived from there, which include Sequence::Seq, etc. This requirment is checked at compile time via compile-time assertions using the static_assert function. There are also specializations such that std::string is also a valid type.

Function Documentation

Gapped()

template<>

bool Sequence::Alignment::Gapped

(

const std::vector< std::string > &

data

)

specialization for std::string

Definition at line 35 of file Specializations.cc.

IsAlignment()

template<>

bool Sequence::Alignment::IsAlignment

(

const std::vector< std::string > &

data

)

specialization for std::string

Definition at line 50 of file Specializations.cc.

RemoveGaps()

template<>

void Sequence::Alignment::RemoveGaps

(

std::vector< std::string > &

data

)

a specialization for std::string

Definition at line 128 of file Specializations.cc.

RemoveTerminalGaps()

template<>

void Sequence::Alignment::RemoveTerminalGaps

(

std::vector< std::string > &

data

)

a specialization for std::string

Definition at line 159 of file Specializations.cc.

Trim()

template<>

std::vector< std::string > Sequence::Alignment::Trim	(	const std::vector< std::string > &	data,
		const std::vector< int > &	sites
	)

a specialization for std::string

Definition at line 241 of file Specializations.cc.

TrimComplement()

template<>

std::vector< std::string > Sequence::Alignment::TrimComplement	(	const std::vector< std::string > &	data,
		const std::vector< int > &	sites
	)

a specialization for std::string

Definition at line 276 of file Specializations.cc.

UnGappedLength()

template<>

unsigned Sequence::Alignment::UnGappedLength

(

const std::vector< std::string > &

data

)

specialization for std::string

Definition at line 100 of file Specializations.cc.

validForPolyAnalysis()

template<>

bool Sequence::Alignment::validForPolyAnalysis	(	std::vector< std::string >::const_iterator	beg,
		std::vector< std::string >::const_iterator	end
	)

specialization for std::string

Definition at line 63 of file Specializations.cc.