Record type for potentially long sequences, e.g. fasta entries. More...

Public Member Functions
	sequence_record (const sequence_record &other)

sequence_record &	operator= (const sequence_record &other)

const std::string &	get_header () const

const std::string &	get_id () const

const std::string &	get_supplement () const

long	enumerated () const

dna_iterator	seqbegin () const

dna_iterator	seqend () const

chardna_iterator	seqbegin_c () const

chardna_iterator	seqend_c () const

void	substr (std::string &res, const size_t ofs, size_t size=0) const

std::string	substr (const size_t ofs, const size_t size=0) const

char	operator[] (const size_t i) const

bool	compare (const size_t ofs, const size_t size, const std::string &str) const

bool	empty () const

size_t	size () const

std::string	md5sum () const

void	write_sequence (std::ostream &out) const

Detailed Description

Record type for potentially long sequences, e.g. fasta entries.

Member Function Documentation

bool shore::sequence_record::compare	(	const size_t	ofs,
		const size_t	size,
		const std::string &	str
	)		const

compare subsequence: eq=0, gt=1, lt=-1

long shore::sequence_record::enumerated ( ) const

integer id of this sequence

const std::string& shore::sequence_record::get_header ( ) const

fasta header of this sequence (id+supplement)

const std::string& shore::sequence_record::get_id ( ) const

string id of this sequence

const std::string& shore::sequence_record::get_supplement ( ) const

auxiliary info for the sequence

std::string shore::sequence_record::md5sum ( ) const

calculate / retrieve md5 checksum of the sequence

char shore::sequence_record::operator[] ( const size_t i) const

get (char encoded) base at a position of the sequence

dna_iterator shore::sequence_record::seqbegin ( ) const

iterator to the begin of the sequence in 4 bit encoding

chardna_iterator shore::sequence_record::seqbegin_c ( ) const

iterator to the begin of the sequence in char encoding

dna_iterator shore::sequence_record::seqend ( ) const

iterator to the end of the sequence in 4 bit encoding

chardna_iterator shore::sequence_record::seqend_c ( ) const

iterator to the end of the sequence in char encoding

size_t shore::sequence_record::size ( ) const

size of the sequence

void shore::sequence_record::substr	(	std::string &	res,
		const size_t	ofs,
		size_t	size = `0`
	)		const

get (char encoded) substring of the sequence

std::string shore::sequence_record::substr	(	const size_t	ofs,
		const size_t	size = `0`
	)		const

get (char encoded) substring of the sequence

void shore::sequence_record::write_sequence ( std::ostream & out) const

write the complete sequence to an output stream

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