libsequence  1.9.5
Alignment.hpp File Reference

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

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

Go to the source code of this file.

Namespaces

 Sequence::Alignment
 Routines fundamental to aligned data.
 
 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, const unsigned &n, std::istream &input_stream)
 
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)
 
template<typename T >
std::vector< T > Sequence::Alignment::TrimComplement (const std::vector< T > &data, const std::vector< int > &sites)
 
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)
 
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)
 
template<>
std::vector< std::string > Sequence::Alignment::TrimComplement (const std::vector< std::string > &data, const std::vector< int > &sites)
 

Detailed Description

Declaration of namespace Sequence::Alignment.

Definition in file Alignment.hpp.