Alignment.tcc File Reference

implementation of routines declared in Alignment.hpp More...

#include <Sequence/Alignment.hpp>
#include <Sequence/SeqConstants.hpp>
#include <Sequence/SeqProperties.hpp>
#include <boost/static_assert.hpp>
#include <boost/type_traits.hpp>
#include <iterator>
#include <algorithm>

Go to the source code of this file.

Namespaces
namespace	Sequence
	The namespace in which this library resides.
namespace	Sequence::Alignment
	Routines fundamental to aligned data.
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)

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Detailed Description

implementation of routines declared in Alignment.hpp

The static assertion that is used throughout this file ensures that the template type parameter T is either std::pair<std::string,std::string> or derived from that type, which includes Sequence::Seq (see Sequence/Seq.hpp).

Definition in file Alignment.tcc.