bpp::SimpleSequencePositionIterator Class Reference

Loop over all positions in a Sequence. More...

#include <Bpp/Seq/SequencePositionIterators.h>

Inheritance diagram for bpp::SimpleSequencePositionIterator:

Collaboration diagram for bpp::SimpleSequencePositionIterator:

List of all members.

Public Member Functions
bool	hasMorePositions () const
	Tells if there is more positions in the Sequence.
unsigned int	getPosition () const
	Get the actual position of the iterator in the Sequence.
void	setPosition (unsigned int pos)
	Set the position of the iterator.
int	getValue () const
	Get the numerical value of the Sequence at current position.
std::string	getChar () const
	Get the textual value of the Sequence at current position.
const Sequence &	getSequence () const
	Get the Sequence on which the iterator loops.
Constructors and destructor
	SimpleSequencePositionIterator (const Sequence &seq, unsigned int pos=0)
	General constructor.
	SimpleSequencePositionIterator (const SequencePositionIterator &it)
	Copie constructor.
virtual	~SimpleSequencePositionIterator ()
Operators
SimpleSequencePositionIterator &	operator++ ()
virtual SimpleSequencePositionIterator	operator++ (int i)
SimpleSequencePositionIterator &	operator+= (int i)
SimpleSequencePositionIterator &	operator-= (int i)
virtual SimpleSequencePositionIterator	operator+ (int i) const
virtual SimpleSequencePositionIterator	operator- (int i) const
Comparison operators
bool	operator== (const SequencePositionIterator &it) const
bool	operator!= (const SequencePositionIterator &it) const

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Detailed Description

Loop over all positions in a Sequence.

This is the simplest implementation of SequencePositionIterator. It just loops over all positions of a Sequence.

 Sequence seq = Sequence("seq1", "ATTCGATCCG-G", &AlphabetTools::DNA_ALPHABET);
 for (SimpleSequencePositionIterator it(seq) ; it.hasMorePositions() ; ++it) {
   cout << it.getPosition() << " : " << it.getValue() << " (" << it.getChar() << ")" << endl;
 }

Author:

Sylvain Gaillard

Definition at line 163 of file SequencePositionIterators.h.

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Constructor & Destructor Documentation

bpp::SimpleSequencePositionIterator::SimpleSequencePositionIterator	(	const Sequence &	seq,
		unsigned int	pos = 0
	)		[inline]

General constructor.

Parameters:

seq	A reference toward the Sequence object we want to loop over
pos	Optional integer where to start on the Sequence object

Definition at line 180 of file SequencePositionIterators.h.

SimpleSequencePositionIterator::SimpleSequencePositionIterator

(

const SequencePositionIterator &

it

)

Copie constructor.

Parameters:

it	A reference toward a SequencePositionIterator

Definition at line 96 of file SequencePositionIterators.cpp.

virtual bpp::SimpleSequencePositionIterator::~SimpleSequencePositionIterator

(

)

[inline, virtual]

Definition at line 188 of file SequencePositionIterators.h.

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Member Function Documentation

string AbstractSequencePositionIterator::getChar

(

)

const [virtual, inherited]

Get the textual value of the Sequence at current position.

Implements bpp::SequencePositionIterator.

Definition at line 86 of file SequencePositionIterators.cpp.

unsigned int AbstractSequencePositionIterator::getPosition

(

)

const [virtual, inherited]

Get the actual position of the iterator in the Sequence.

Implements bpp::SequencePositionIterator.

Definition at line 74 of file SequencePositionIterators.cpp.

Referenced by hasMorePositions(), operator++(), and operator+=().

const Sequence & AbstractSequencePositionIterator::getSequence

(

)

const [virtual, inherited]

Get the Sequence on which the iterator loops.

Returns:

A reference toward the Sequence object.

Implements bpp::SequencePositionIterator.

Definition at line 68 of file SequencePositionIterators.cpp.

Referenced by hasMorePositions().

int AbstractSequencePositionIterator::getValue

(

)

const [virtual, inherited]

Get the numerical value of the Sequence at current position.

Implements bpp::SequencePositionIterator.

Definition at line 80 of file SequencePositionIterators.cpp.

bool SimpleSequencePositionIterator::hasMorePositions

(

)

const [virtual]

Tells if there is more positions in the Sequence.

Returns:

true if there is more positions in the Sequence

Implements bpp::SequencePositionIterator.

Definition at line 143 of file SequencePositionIterators.cpp.

References bpp::AbstractSequencePositionIterator::getPosition(), and bpp::AbstractSequencePositionIterator::getSequence().

bool AbstractSequencePositionIterator::operator!=

(

const SequencePositionIterator &

it

)

const [virtual, inherited]

Implements bpp::SequencePositionIterator.

Definition at line 56 of file SequencePositionIterators.cpp.

References bpp::SequencePositionIterator::getPosition().

SimpleSequencePositionIterator SimpleSequencePositionIterator::operator+

(

int

i

)

const [virtual]

Definition at line 129 of file SequencePositionIterators.cpp.

SimpleSequencePositionIterator & SimpleSequencePositionIterator::operator++

(

)

[virtual]

Implements bpp::SequencePositionIterator.

Definition at line 101 of file SequencePositionIterators.cpp.

References bpp::AbstractSequencePositionIterator::getPosition(), and bpp::AbstractSequencePositionIterator::setPosition().

SimpleSequencePositionIterator SimpleSequencePositionIterator::operator++

(

int

i

)

[virtual]

Definition at line 108 of file SequencePositionIterators.cpp.

SimpleSequencePositionIterator & SimpleSequencePositionIterator::operator+=

(

int

i

)

[virtual]

Implements bpp::SequencePositionIterator.

Definition at line 116 of file SequencePositionIterators.cpp.

References bpp::AbstractSequencePositionIterator::getPosition(), and bpp::AbstractSequencePositionIterator::setPosition().

SimpleSequencePositionIterator SimpleSequencePositionIterator::operator-

(

int

i

)

const [virtual]

Definition at line 137 of file SequencePositionIterators.cpp.

SimpleSequencePositionIterator & SimpleSequencePositionIterator::operator-=

(

int

i

)

[virtual]

Implements bpp::SequencePositionIterator.

Definition at line 123 of file SequencePositionIterators.cpp.

bool AbstractSequencePositionIterator::operator==

(

const SequencePositionIterator &

it

)

const [virtual, inherited]

Implements bpp::SequencePositionIterator.

Definition at line 50 of file SequencePositionIterators.cpp.

References bpp::SequencePositionIterator::getPosition().

void AbstractSequencePositionIterator::setPosition

(

unsigned int

pos

)

[virtual, inherited]

Set the position of the iterator.

Parameters:

pos	The position on the Sequence

Implements bpp::SequencePositionIterator.

Definition at line 62 of file SequencePositionIterators.cpp.

Referenced by operator++(), and operator+=().

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

• Bpp/Seq/SequencePositionIterators.h
• Bpp/Seq/SequencePositionIterators.cpp