libsequence
1.9.5
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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) |
Declaration of namespace Sequence::Alignment.
Definition in file Alignment.hpp.