bpp::PositionedContainer< T > Class Template Reference

The PositionedContainer interface. More...

#include <Bpp/Seq/Container/PositionedContainer.h>

Inheritance diagram for bpp::PositionedContainer< T >:

Public Member Functions
	PositionedContainer ()
virtual	~PositionedContainer ()
virtual size_t	getSize () const =0
	the size More...
virtual void	setSize (size_t size)
virtual void	clear ()=0

Protected Member Functions
virtual const std::shared_ptr< T >	getObject (size_t objectIndex) const =0
	Retrieve an object from the container. Set as protected since they will be public under T specific names. More...
virtual std::shared_ptr< T >	getObject (size_t objectIndex)=0
virtual std::shared_ptr< T >	removeObject (size_t objectIndex)=0
	Extract and remove a object from the container. More...
virtual void	deleteObject (size_t objectIndex)=0
	Delete an object from the container. More...

Detailed Description

template<class T>
class bpp::PositionedContainer< T >

The PositionedContainer interface.

Interface to manage indexed containers, where Objects may be accessed via their indice, i.e. their position in the container.

All Objects must have a position, accessible through getPosition and setPosition methods (see Site class).

Definition at line 62 of file PositionedContainer.h.

Constructor & Destructor Documentation

PositionedContainer()

template<class T >

bpp::PositionedContainer< T >::PositionedContainer ( )

inline

Definition at line 65 of file PositionedContainer.h.

~PositionedContainer()

template<class T >

virtual bpp::PositionedContainer< T >::~PositionedContainer ( )

inlinevirtual

Definition at line 66 of file PositionedContainer.h.

Member Function Documentation

clear()

template<class T >

virtual void bpp::PositionedContainer< T >::clear ( )

pure virtual

Implemented in bpp::VectorSiteContainer, bpp::VectorSequenceContainer, bpp::VectorProbabilisticSiteContainer, bpp::VectorProbabilisticSequenceContainer, bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< ProbabilisticSite >, bpp::VectorPositionedContainer< Site >, bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, bpp::VectorMappedContainer< ProbabilisticSequence >, bpp::CompressedVectorSiteContainer, and bpp::AlignedSequenceContainer.

deleteObject()

template<class T >

virtual void bpp::PositionedContainer< T >::deleteObject ( size_t  objectIndex )

protectedpure virtual

Delete an object from the container.

Parameters

objectIndex

The index of the object in the container.

Implemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< ProbabilisticSite >, bpp::VectorPositionedContainer< Site >, bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, and bpp::VectorMappedContainer< ProbabilisticSequence >.

getObject() [1/2]

template<class T >

virtual const std::shared_ptr<T> bpp::PositionedContainer< T >::getObject ( size_t  objectIndex ) const

protectedpure virtual

Retrieve an object from the container. Set as protected since they will be public under T specific names.

Parameters

objectIndex

The position of the object.

Returns

A reference toward the Object object with corresponding name.

Implemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< ProbabilisticSite >, bpp::VectorPositionedContainer< Site >, bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, and bpp::VectorMappedContainer< ProbabilisticSequence >.

getObject() [2/2]

template<class T >

virtual std::shared_ptr<T> bpp::PositionedContainer< T >::getObject ( size_t  objectIndex )

protectedpure virtual

Implemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< ProbabilisticSite >, bpp::VectorPositionedContainer< Site >, bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, and bpp::VectorMappedContainer< ProbabilisticSequence >.

getSize()

template<class T >

virtual size_t bpp::PositionedContainer< T >::getSize ( ) const

pure virtual

the size

Implemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< ProbabilisticSite >, bpp::VectorPositionedContainer< Site >, bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, and bpp::VectorMappedContainer< ProbabilisticSequence >.

removeObject()

template<class T >

virtual std::shared_ptr<T> bpp::PositionedContainer< T >::removeObject ( size_t  objectIndex )

protectedpure virtual

Extract and remove a object from the container.

Parameters

objectIndex

The position of the object.

Returns

A smart pointer toward the removed object.

Implemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< ProbabilisticSite >, bpp::VectorPositionedContainer< Site >, bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, and bpp::VectorMappedContainer< ProbabilisticSequence >.

setSize()

template<class T >

virtual void bpp::PositionedContainer< T >::setSize ( size_t  size )

inlinevirtual

Reimplemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< ProbabilisticSite >, and bpp::VectorPositionedContainer< Site >.

Definition at line 76 of file PositionedContainer.h.

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

• Bpp/Seq/Container/PositionedContainer.h