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:

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

Private Attributes
const Sequence *	sequence_
unsigned int	currentPosition_

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 126 of file SequencePositionIterators.h.

Constructor & Destructor Documentation

SimpleSequencePositionIterator() [1/2]

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 143 of file SequencePositionIterators.h.

SimpleSequencePositionIterator() [2/2]

SimpleSequencePositionIterator::SimpleSequencePositionIterator

(

const SequencePositionIterator &

it

)

Copy constructor.

Parameters

it	A reference toward a SequencePositionIterator

Definition at line 65 of file SequencePositionIterators.cpp.

~SimpleSequencePositionIterator()

virtual bpp::SimpleSequencePositionIterator::~SimpleSequencePositionIterator ( )

inlinevirtual

Definition at line 151 of file SequencePositionIterators.h.

Member Function Documentation

getChar()

string AbstractSequencePositionIterator::getChar ( ) const

virtualinherited

Get the textual value of the Sequence at current position.

Implements bpp::SequencePositionIterator.

Definition at line 54 of file SequencePositionIterators.cpp.

getPosition()

unsigned int AbstractSequencePositionIterator::getPosition ( ) const

virtualinherited

Get the actual position of the iterator in the Sequence.

Implements bpp::SequencePositionIterator.

Definition at line 40 of file SequencePositionIterators.cpp.

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

getSequence()

const Sequence & AbstractSequencePositionIterator::getSequence ( ) const

virtualinherited

Get the Sequence on which the iterator loops.

Returns

A reference toward the Sequence object.

Implements bpp::SequencePositionIterator.

Definition at line 33 of file SequencePositionIterators.cpp.

Referenced by hasMorePositions().

getValue()

int AbstractSequencePositionIterator::getValue ( ) const

virtualinherited

Get the numerical value of the Sequence at current position.

Implements bpp::SequencePositionIterator.

Definition at line 47 of file SequencePositionIterators.cpp.

hasMorePositions()

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 127 of file SequencePositionIterators.cpp.

References bpp::AbstractSequencePositionIterator::getPosition(), bpp::AbstractSequencePositionIterator::getSequence(), and bpp::AbstractTemplateSymbolList< T >::size().

operator!=()

bool AbstractSequencePositionIterator::operator!= ( const SequencePositionIterator &  it ) const

virtualinherited

Implements bpp::SequencePositionIterator.

Definition at line 19 of file SequencePositionIterators.cpp.

References bpp::SequencePositionIterator::getPosition().

operator+()

SimpleSequencePositionIterator SimpleSequencePositionIterator::operator+ ( int  i ) const

virtual

Definition at line 111 of file SequencePositionIterators.cpp.

operator++() [1/2]

SimpleSequencePositionIterator & SimpleSequencePositionIterator::operator++ ( )

virtual

Implements bpp::SequencePositionIterator.

Definition at line 70 of file SequencePositionIterators.cpp.

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

operator++() [2/2]

SimpleSequencePositionIterator SimpleSequencePositionIterator::operator++ ( int  i )

virtual

Definition at line 78 of file SequencePositionIterators.cpp.

operator+=()

SimpleSequencePositionIterator & SimpleSequencePositionIterator::operator+= ( int  i )

virtual

Implements bpp::SequencePositionIterator.

Definition at line 87 of file SequencePositionIterators.cpp.

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

operator-()

SimpleSequencePositionIterator SimpleSequencePositionIterator::operator- ( int  i ) const

virtual

Definition at line 120 of file SequencePositionIterators.cpp.

operator-=()

SimpleSequencePositionIterator & SimpleSequencePositionIterator::operator-= ( int  i )

virtual

Implements bpp::SequencePositionIterator.

Definition at line 104 of file SequencePositionIterators.cpp.

operator==()

bool AbstractSequencePositionIterator::operator== ( const SequencePositionIterator &  it ) const

virtualinherited

Implements bpp::SequencePositionIterator.

Definition at line 12 of file SequencePositionIterators.cpp.

References bpp::SequencePositionIterator::getPosition().

setPosition()

void AbstractSequencePositionIterator::setPosition ( unsigned int  pos )

virtualinherited

Set the position of the iterator.

Parameters

pos	The position on the Sequence

Implements bpp::SequencePositionIterator.

Definition at line 26 of file SequencePositionIterators.cpp.

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

Member Data Documentation

currentPosition_

unsigned int bpp::AbstractSequencePositionIterator::currentPosition_

privateinherited

Definition at line 76 of file SequencePositionIterators.h.

Referenced by bpp::AbstractSequencePositionIterator::operator=().

sequence_

const Sequence* bpp::AbstractSequencePositionIterator::sequence_

privateinherited

Definition at line 75 of file SequencePositionIterators.h.

Referenced by bpp::AbstractSequencePositionIterator::operator=().

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

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