Sequence::Seq Class Reference

Abstract interface to sequence objects. More...

#include <Sequence/Seq.hpp>

Inheritance diagram for Sequence::Seq:

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
	Seq (void)
template<typename T >
	Seq (T &&name_, T &&seq_)
	Seq (const char *n, const char *s)
	Seq (const Seq &seq)=default
	Seq (Seq &&seq)=default
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 ()
iterator	end ()
const_iterator	begin () const
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
Seq &	operator= (const Seq &rhs)=default
Seq &	operator= (Seq &&rhs)=default
	operator std::string () const
const char *	c_str (void) const
virtual std::istream &	read (std::istream &s)=0
virtual std::ostream &	print (std::ostream &s) const =0

Public Attributes
std::string	name
std::string	seq

Detailed Description

Abstract interface to sequence objects.

Abstract interface to sequence objects. A sequence consists of a name and a sequence, both of which are stored as C++ std::strings. Most of the rest of the member functions of this class are to make the behavior of Sequence::Seq more "std::string"-like.

Definition at line 46 of file Seq.hpp.

Member Typedef Documentation

const_iterator

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

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

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

Seq()

Sequence::Seq::Seq

(

void

)

creates an empty sequence

Definition at line 32 of file Seq.cc.

Member Function Documentation

begin() [1/2]

Seq::iterator Sequence::Seq::begin

(

)

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

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

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

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

Returns

a const iterator to the end of the sequence

Definition at line 234 of file Seq.cc.

Complement()

void Sequence::Seq::Complement

(

void

)

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

(

)

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

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

Deprecated:

Access first directly

GetSeq()

std::string Sequence::Seq::GetSeq

(

void

)

const

Deprecated:

Access second directly

IsGapped()

bool Sequence::Seq::IsGapped

(

void

)

const

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

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

allows (implict) cast to std::string

Definition at line 117 of file Seq.cc.

operator!=()

bool Sequence::Seq::operator!=

(

const Seq &

rhs

)

const

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

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

)

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

Return the i-th element of the sequence.

Note

range-checking is done by assert()

Definition at line 85 of file Seq.cc.

print()

virtual std::ostream& Sequence::Seq::print ( std::ostream &  s ) const

pure virtual

read an object of type Sequence::Seq from an istream

Implemented in Sequence::Fasta, and Sequence::fastq.

read()

virtual std::istream& Sequence::Seq::read ( std::istream &  s )

pure virtual

read an object of type Sequence::Seq from an istream

Implemented in Sequence::Fasta, and Sequence::fastq.

Revcom()

void Sequence::Seq::Revcom

(

void

)

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

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
	)

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

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

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

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

Definition at line 126 of file Seq.cc.

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

• Seq.hpp
• Seq.cc