Sequence Class Reference

#include <genesis/sequence/sequence.hpp>

Detailed Description

Definition at line 40 of file sequence/sequence.hpp.

Public Member Functions
	Sequence ()=default
	Sequence (Sequence &&)=default
	Sequence (Sequence const &)=default
	Sequence (std::string const &label, std::string const &sites, size_t abundance=1)
	~Sequence ()=default
size_t	abundance () const
void	abundance (size_t value)
iterator	begin ()
const_iterator	begin () const
const_iterator	cbegin () const
const_iterator	cend () const
void	clear ()
iterator	end ()
const_iterator	end () const
std::string &	label ()
std::string const &	label () const
void	label (std::string &&value)
void	label (std::string const &value)
size_t	length () const
	Return the length (number of sites) of this sequence. More...
Sequence &	operator= (Sequence &&)=default
Sequence &	operator= (Sequence const &)=default
char &	operator[] (size_t index)
char	operator[] (size_t index) const
std::vector< unsigned char > &	phred_scores ()
std::vector< unsigned char > const &	phred_scores () const
void	phred_scores (std::vector< unsigned char > &&value)
void	phred_scores (std::vector< unsigned char > const &value)
char &	site_at (size_t index)
char	site_at (size_t index) const
std::string &	sites ()
std::string const &	sites () const
void	sites (std::string &&value)
void	sites (std::string const &value)
size_t	size () const
	Alias for length(). More...
void	swap (Sequence &other)

Public Types
typedef std::string::const_iterator	const_iterator
typedef std::string::iterator	iterator

Constructor & Destructor Documentation

Sequence() [1/4]

Sequence ( )

default

Sequence() [2/4]

Sequence ( std::string const &  label, std::string const &  sites, size_t  abundance = 1  )

inline

Definition at line 57 of file sequence/sequence.hpp.

~Sequence()

~Sequence ( )

default

Sequence() [3/4]

Sequence ( Sequence const &  )

default

Sequence() [4/4]

Sequence ( Sequence &&  )

default

Member Function Documentation

abundance() [1/2]

size_t abundance ( ) const

inline

Definition at line 150 of file sequence/sequence.hpp.

abundance() [2/2]

void abundance ( size_t  value )

inline

Definition at line 155 of file sequence/sequence.hpp.

begin() [1/2]

iterator begin ( )

inline

Definition at line 204 of file sequence/sequence.hpp.

begin() [2/2]

const_iterator begin ( ) const

inline

Definition at line 214 of file sequence/sequence.hpp.

cbegin()

const_iterator cbegin ( ) const

inline

Definition at line 224 of file sequence/sequence.hpp.

cend()

const_iterator cend ( ) const

inline

Definition at line 229 of file sequence/sequence.hpp.

clear()

void clear ( )

inline

Definition at line 78 of file sequence/sequence.hpp.

end() [1/2]

iterator end ( )

inline

Definition at line 209 of file sequence/sequence.hpp.

end() [2/2]

const_iterator end ( ) const

inline

Definition at line 219 of file sequence/sequence.hpp.

label() [1/4]

std::string& label ( )

inline

Definition at line 90 of file sequence/sequence.hpp.

label() [2/4]

std::string const& label ( ) const

inline

Definition at line 95 of file sequence/sequence.hpp.

label() [3/4]

void label ( std::string &&  value )

inline

Definition at line 105 of file sequence/sequence.hpp.

label() [4/4]

void label ( std::string const &  value )

inline

Definition at line 100 of file sequence/sequence.hpp.

length()

size_t length ( ) const

inline

Return the length (number of sites) of this sequence.

Definition at line 167 of file sequence/sequence.hpp.

operator=() [1/2]

Sequence& operator= ( Sequence &&  )

default

operator=() [2/2]

Sequence& operator= ( Sequence const &  )

default

operator[]() [1/2]

char& operator[] ( size_t  index )

inline

Definition at line 190 of file sequence/sequence.hpp.

operator[]() [2/2]

char operator[] ( size_t  index ) const

inline

Definition at line 195 of file sequence/sequence.hpp.

phred_scores() [1/4]

std::vector<unsigned char>& phred_scores ( )

inline

Definition at line 130 of file sequence/sequence.hpp.

phred_scores() [2/4]

std::vector<unsigned char> const& phred_scores ( ) const

inline

Definition at line 135 of file sequence/sequence.hpp.

phred_scores() [3/4]

void phred_scores ( std::vector< unsigned char > &&  value )

inline

Definition at line 145 of file sequence/sequence.hpp.

phred_scores() [4/4]

void phred_scores ( std::vector< unsigned char > const &  value )

inline

Definition at line 140 of file sequence/sequence.hpp.

site_at() [1/2]

char& site_at ( size_t  index )

inline

Definition at line 180 of file sequence/sequence.hpp.

site_at() [2/2]

char site_at ( size_t  index ) const

inline

Definition at line 185 of file sequence/sequence.hpp.

sites() [1/4]

std::string& sites ( )

inline

Definition at line 110 of file sequence/sequence.hpp.

sites() [2/4]

std::string const& sites ( ) const

inline

Definition at line 115 of file sequence/sequence.hpp.

sites() [3/4]

void sites ( std::string &&  value )

inline

Definition at line 125 of file sequence/sequence.hpp.

sites() [4/4]

void sites ( std::string const &  value )

inline

Definition at line 120 of file sequence/sequence.hpp.

size()

size_t size ( ) const

inline

Alias for length().

Definition at line 175 of file sequence/sequence.hpp.

swap()

void swap ( Sequence &  other )

inline

Definition at line 71 of file sequence/sequence.hpp.

Member Typedef Documentation

const_iterator

typedef std::string::const_iterator const_iterator

Definition at line 49 of file sequence/sequence.hpp.

iterator

typedef std::string::iterator iterator

Definition at line 48 of file sequence/sequence.hpp.

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The documentation for this class was generated from the following file:

• sequence/sequence.hpp