Alignment.hpp File Reference

Declaration of namespace Sequence::Alignment. More...

#include <iosfwd>
#include <fstream>
#include <vector>
#include <string>
#include <Sequence/SeqExceptions.hpp>
#include <Sequence/bits/Alignment.tcc>

Go to the source code of this file.

Namespaces
namespace	Sequence::Alignment
	Routines fundamental to aligned data.
namespace	Sequence
	The namespace in which this library resides.
Functions
template<typename T >
void	Sequence::Alignment::GetData (std::vector< T > &seqarray, const char *infilename)
template<typename T >
std::istream &	Sequence::Alignment::GetData (std::vector< T > &seqarray, std::istream &input_stream)
template<typename T >
std::istream &	Sequence::Alignment::ReadNObjects (std::vector< T > &seqarray, unsigned n, std::istream &input_stream)
template<typename T >
void	Sequence::Alignment::EmptyVector (std::vector< T * > &seqarray)
template<typename T >
bool	Sequence::Alignment::Gapped (const std::vector< T > &data)
template<typename T >
bool	Sequence::Alignment::IsAlignment (const std::vector< T > &data)
template<typename Iterator >
bool	Sequence::Alignment::validForPolyAnalysis (Iterator beg, Iterator end)
template<typename T >
unsigned	Sequence::Alignment::UnGappedLength (const std::vector< T > &data)
template<typename T >
void	Sequence::Alignment::RemoveGaps (std::vector< T > &data)
template<typename T >
void	Sequence::Alignment::RemoveTerminalGaps (std::vector< T > &data)
template<typename T >
void	Sequence::Alignment::RemoveFixedOutgroupInsertions (std::vector< T > &data, unsigned site, const unsigned &ref)
template<typename T >
std::vector< T >	Sequence::Alignment::Trim (const std::vector< T > &data, const std::vector< int > &sites) throw (Sequence::SeqException)
template<typename T >
std::vector< T >	Sequence::Alignment::TrimComplement (const std::vector< T > &data, const std::vector< int > &sites) throw (Sequence::SeqException)
template<>
bool	Sequence::Alignment::Gapped (const std::vector< std::string > &data)
template<>
bool	Sequence::Alignment::IsAlignment (const std::vector< std::string > &data)
template<>
bool	Sequence::Alignment::validForPolyAnalysis (std::vector< std::string >::const_iterator beg, std::vector< std::string >::const_iterator end)
template<>
bool	Sequence::Alignment::validForPolyAnalysis (std::vector< std::string >::iterator beg, std::vector< std::string >::iterator end)
template<>
unsigned	Sequence::Alignment::UnGappedLength (const std::vector< std::string > &data) throw (Sequence::SeqException)
template<>
void	Sequence::Alignment::RemoveGaps (std::vector< std::string > &data)
template<>
void	Sequence::Alignment::RemoveTerminalGaps (std::vector< std::string > &data)
template<>
void	Sequence::Alignment::RemoveFixedOutgroupInsertions (std::vector< std::string > &data, unsigned site, const unsigned &ref)
template<>
std::vector< std::string >	Sequence::Alignment::Trim (const std::vector< std::string > &data, const std::vector< int > &sites) throw (Sequence::SeqException)
template<>
std::vector< std::string >	Sequence::Alignment::TrimComplement (const std::vector< std::string > &data, const std::vector< int > &sites) throw (Sequence::SeqException)

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Detailed Description

Declaration of namespace Sequence::Alignment.

Definition in file Alignment.hpp.