#include <Sequence/fastq.hpp>

Inheritance diagram for Sequence::fastq:

Public Types
typedef std::string::iterator	iterator

typedef std::string::const_iterator	const_iterator

typedef std::string::reference	reference

typedef std::string::const_reference	const_reference

typedef std::string::size_type	size_type

Public Member Functions
	fastq (const std::string &name, const std::string &seq, const std::string &qual)

	fastq (std::string &&name, std::string &&seq, std::string &&qual)

	fastq (const Seq &s)

	fastq (const fastq &s)=default

	fastq (fastq &&s)=default

	fastq (Seq &&s)

fastq &	operator= (const fastq &)=default

fastq &	operator= (fastq &&)=default

	~fastq ()

void	repname (const bool &)
	Set to true or false for repeating the seq name on third line of output.

std::istream &	read (std::istream &s)

std::ostream &	print (std::ostream &s) const

std::string	GetName (void) const

std::string	GetSeq (void) const

std::string	substr (std::string::size_type beg, std::string::size_type len) const

std::string	substr (std::string::size_type beg) const

iterator	begin ()

const_iterator	begin () const

iterator	end ()

const_iterator	end () const

const_iterator	cbegin () const

const_iterator	cend () const

void	Revcom (void)

void	Subseq (const unsigned &, const unsigned &)

void	Complement (void)

size_type	length (void) const

size_type	size (void) const

size_type	UngappedLength (void) const

bool	IsGapped (void) const

reference	operator[] (const size_type &i)

const_reference	operator[] (const size_type &i) const

bool	operator== (const Seq &rhs) const

bool	operator!= (const Seq &rhs) const

	operator std::string () const

const char *	c_str (void) const

Public Attributes
std::string	quality

std::string	name

std::string	seq

Detailed Description

Publicly derived from Sequence::Seq.

Definition at line 18 of file fastq.hpp.

Member Typedef Documentation

◆ const_iterator

typedef std::string::const_iterator Sequence::Seq::const_iterator

inherited

Const iterator to sequence elements. Iterators access the data, not the sequence name. Value type de-references to char

Definition at line 83 of file Seq.hpp.

◆ iterator

typedef std::string::iterator Sequence::Seq::iterator

inherited

Iterator to sequence elements. Iterators access the data, not the sequence name. Value type de-references to char

Definition at line 77 of file Seq.hpp.

Constructor & Destructor Documentation

◆ fastq() [1/2]

Sequence::fastq::fastq ( const Seq & s )

Warning: Quality string will be left empty

Definition at line 21 of file fastq.cc.

◆ fastq() [2/2]

Sequence::fastq::fastq ( Seq && s )

Warning: Quality string will be left empty

Definition at line 26 of file fastq.cc.

◆ ~fastq()

Sequence::fastq::~fastq ( )

inline

placeholder for vtable

Definition at line 39 of file fastq.hpp.

Member Function Documentation

◆ begin() [1/2]

Seq::iterator Sequence::Seq::begin ( )

inherited

Returns: an iterator to the beginning of the sequence

Examples:: valid_dna.cc.

Definition at line 189 of file Seq.cc.

◆ begin() [2/2]

Seq::const_iterator Sequence::Seq::begin ( ) const

inherited

Returns: a const iterator to the beginning of the sequence

Definition at line 207 of file Seq.cc.

◆ c_str()

const char * Sequence::Seq::c_str ( void ) const

inherited

Returns: the the C-style string representing the sequence as a cont char *

Definition at line 243 of file Seq.cc.

◆ cbegin()

Seq::const_iterator Sequence::Seq::cbegin ( ) const

inherited

Returns: a const iterator to the beginning of the sequence

Definition at line 225 of file Seq.cc.

◆ cend()

Seq::const_iterator Sequence::Seq::cend ( ) const

inherited

Returns: a const iterator to the end of the sequence

Definition at line 234 of file Seq.cc.

◆ Complement()

void Sequence::Seq::Complement ( void )

inherited

Complement the Sequence

Note: This modifies the data in the object by changing the std::string–if you want to keep the original sequence, you need to make a copy of the object first.

Definition at line 163 of file Seq.cc.

◆ end() [1/2]

Seq::iterator Sequence::Seq::end ( )

inherited

Returns: an iterator to the end of the sequence

Examples:: valid_dna.cc.

Definition at line 198 of file Seq.cc.

◆ end() [2/2]

Seq::const_iterator Sequence::Seq::end ( ) const

inherited

Returns: a const iterator to the end of the sequence

Definition at line 216 of file Seq.cc.

◆ GetName()

std::string Sequence::Seq::GetName ( void ) const

inherited

Deprecated:: Access first directly

◆ GetSeq()

std::string Sequence::Seq::GetSeq ( void ) const

inherited

Deprecated:: Access second directly

◆ IsGapped()

bool Sequence::Seq::IsGapped ( void ) const

inherited

Returns 1 if the sequence contaings the gap character '-', 0 otherwise

Definition at line 137 of file Seq.cc.

◆ length()

Seq::size_type Sequence::Seq::length ( void ) const

inherited

Return the total length of the sequence in bytes

Examples:: codons.cc.

Definition at line 58 of file Seq.cc.

◆ operator std::string()

Sequence::Seq::operator std::string ( ) const

inherited

allows (implict) cast to std::string

Definition at line 117 of file Seq.cc.

◆ operator!=()

bool Sequence::Seq::operator!= ( const Seq & rhs ) const

inherited

Returns: false if the sequences contain the same data, true otherwise.

Note: only the sequences (i.e. this->seq and rhs.seq) are compared

Definition at line 107 of file Seq.cc.

◆ operator==()

bool Sequence::Seq::operator== ( const Seq & rhs ) const

inherited

Returns: true if the sequences contain the same data, false otherwise.

Note: only the sequences (i.e. this->seq and rhs.seq) are compared

Definition at line 96 of file Seq.cc.

◆ operator[]() [1/2]

Seq::reference Sequence::Seq::operator[] ( const size_type & i )

inherited

Return the i-th element of the sequence.

Note: range-checking is done by assert()

Definition at line 75 of file Seq.cc.

◆ operator[]() [2/2]

Seq::const_reference Sequence::Seq::operator[] ( const size_type & i ) const

inherited

Return the i-th element of the sequence.

Note: range-checking is done by assert()

Definition at line 85 of file Seq.cc.

◆ print()

std::ostream & Sequence::fastq::print ( std::ostream & s ) const

virtual

Parameters

stream a std::ostream write the sequence in FASTQ format to stream

Implements Sequence::Seq.

Definition at line 66 of file fastq.cc.

◆ read()

std::istream & Sequence::fastq::read ( std::istream & s )

virtual

Exceptions

Sequence::SeqException	if memory can't be allocated. (This is because the data are temporarily read into char *, because that was found to be faster).
Sequence::badFormat	if the input stream is not in FASTQ format

Implements Sequence::Seq.

Definition at line 38 of file fastq.cc.

◆ Revcom()

void Sequence::Seq::Revcom ( void )

inherited

Reverse and complement the sequence.

Note: This function modifies the data in the object by changing the std::string–if you want to keep the original sequence, you need to make a copy of the object first.

Returns: *this

Definition at line 175 of file Seq.cc.

◆ size()

Seq::size_type Sequence::Seq::size ( void ) const

inherited

Return the total length of the sequence in bytes

Definition at line 67 of file Seq.cc.

◆ Subseq()

void Sequence::Seq::Subseq	(	const unsigned &	beg,
		const unsigned &	length
	)

inherited

Parameters

beg	the index along the sequence at which the substring begins
length	the length of the subseq Acts via std::string.substr(). Note that this modifies the data in the object by changing thestd::string–if you want to keep the original sequence, you need to make a copy of the object first.

Note: range-checking done by assert()

Definition at line 147 of file Seq.cc.

◆ substr() [1/2]

std::string Sequence::Seq::substr	(	std::string::size_type	beg,
		std::string::size_type	len
	)		const

inherited

Deprecated:: access .second.substr directly

Mimics the std::string member function of the same name.

Definition at line 40 of file Seq.cc.

◆ substr() [2/2]

std::string Sequence::Seq::substr ( std::string::size_type beg ) const

inherited

Deprecated:: access .second.substr directly

Mimics the standardstd::string member function of the same name.

Definition at line 49 of file Seq.cc.

◆ UngappedLength()

Seq::size_type Sequence::Seq::UngappedLength ( void ) const

inherited

Return length of sequence, excluding the gap character '-'

Definition at line 126 of file Seq.cc.

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

Public Types

Public Member Functions

Public Attributes

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ iterator

Constructor & Destructor Documentation

◆ fastq() [1/2]

◆ fastq() [2/2]

◆ ~fastq()

Member Function Documentation

◆ begin() [1/2]

◆ begin() [2/2]

◆ c_str()

◆ cbegin()

◆ cend()

◆ Complement()

◆ end() [1/2]

◆ end() [2/2]

◆ GetName()

◆ GetSeq()

◆ IsGapped()

◆ length()

◆ operator std::string()

◆ operator!=()

◆ operator==()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ print()

◆ read()

◆ Revcom()

◆ size()

◆ Subseq()

◆ substr() [1/2]

◆ substr() [2/2]

◆ UngappedLength()