The template VectorPositionedContainer class. More...

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

Inheritance diagram for bpp::VectorPositionedContainer< T >:

Collaboration diagram for bpp::VectorPositionedContainer< T >:

Public Member Functions
	VectorPositionedContainer (const std::vector< std::shared_ptr< T >> &vs)
	Build a new container from a set of positions. More...

	VectorPositionedContainer (size_t size=0)
	Build a new empty container with specified size. More...

	VectorPositionedContainer (const VectorPositionedContainer< T > &vsc)

VectorPositionedContainer< T > &	operator= (const VectorPositionedContainer< T > &vsc)
	copy where shared_ptr elements are shared More...

virtual	~VectorPositionedContainer ()

size_t	getSize () const override
	the size More...

bool	isAvailablePosition (size_t objectIndex) const

bool	hasObjectWithPosition (size_t objectIndex) const

void	setSize (size_t size) override

void	clear () override
	Destroys the vector. More...

virtual void	nullify ()
	Nullify all elements. More...

const std::shared_ptr< T >	getObject (size_t objectIndex) const override
	Retrieve an object from the container. More...

std::shared_ptr< T >	getObject (size_t objectIndex) override
	Retrieve an object from the container. More...

const T &	object (size_t objectIndex) const override
	Get a reference toward an object from the container. More...

T &	object (size_t objectIndex) override
	Get a reference toward an object from the container. More...

void	addObject (std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false)
	Add an object. More...

void	insertObject (std::shared_ptr< T > object, size_t objectIndex)
	Insert an object. More...

std::shared_ptr< T >	removeObject (size_t objectIndex) override
	Extract and remove a object from the container. More...

void	deleteObject (size_t objectIndex) override
	Delete an object from the container. More...

void	deleteObjects (size_t objectIndex, size_t length)

void	appendObject (std::shared_ptr< T > object)

std::shared_ptr< T >	getObject_ (size_t objectIndex) const

void	addObject_ (std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false) const

The Clonable interface.
VectorPositionedContainer< T > *	clone () const override

Protected Attributes
std::vector< std::shared_ptr< T > >	positions_

Detailed Description

template<class T>
class bpp::VectorPositionedContainer< T >

The template VectorPositionedContainer class.

Objects are stored in a std::vector of shared pointers. Object access is hence in .

Definition at line 29 of file VectorPositionedContainer.h.

Constructor & Destructor Documentation

◆ VectorPositionedContainer() [1/3]

template<class T >

bpp::VectorPositionedContainer< T >::VectorPositionedContainer ( const std::vector< std::shared_ptr< T >> & vs )

inline

Build a new container from a set of positions.

Parameters

vs	A std::vector of objects.

Definition at line 42 of file VectorPositionedContainer.h.

◆ VectorPositionedContainer() [2/3]

template<class T >

bpp::VectorPositionedContainer< T >::VectorPositionedContainer ( size_t size = 0 )

inline

Build a new empty container with specified size.

Parameters

size	Number of sequences in the container.

Definition at line 51 of file VectorPositionedContainer.h.

◆ VectorPositionedContainer() [3/3]

template<class T >

bpp::VectorPositionedContainer< T >::VectorPositionedContainer ( const VectorPositionedContainer< T > & vsc )

inline

Definition at line 56 of file VectorPositionedContainer.h.

◆ ~VectorPositionedContainer()

template<class T >

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

inlinevirtual

Definition at line 69 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Member Function Documentation

◆ addObject()

template<class T >

void bpp::VectorPositionedContainer< T >::addObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		bool	checkPosition = `false`
	)

inline

Add an object.

Parameters

object	The object to add.
objectIndex	The new position of the object
checkPosition	Look if the position is empty.

Definition at line 162 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), bpp::VectorPositionedContainer< T >::object(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::VectorMappedContainer< T >::addObject(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::setSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSite(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::valueAt().

◆ addObject_()

template<class T >

void bpp::VectorPositionedContainer< T >::addObject_	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		bool	checkPosition = `false`
	)		const

inline

Definition at line 228 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::VectorMappedContainer< T >::addObject_(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::site().

◆ appendObject()

template<class T >

void bpp::VectorPositionedContainer< T >::appendObject ( std::shared_ptr< T > object )

inline

Definition at line 216 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::addSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), and bpp::VectorMappedContainer< T >::appendObject().

◆ clear()

template<class T >

void bpp::VectorPositionedContainer< T >::clear ( )

inlineoverridevirtual

Destroys the vector.

Implements bpp::PositionedContainerInterface< T >.

Reimplemented in bpp::VectorMappedContainer< bpp::Sequence >, and bpp::VectorMappedContainer< SequenceType >.

Definition at line 113 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::clear(), bpp::VectorMappedContainer< T >::clear(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::clear().

◆ clone()

template<class T >

VectorPositionedContainer<T>* bpp::VectorPositionedContainer< T >::clone ( ) const

inlineoverridevirtual

Implements bpp::Clonable.

Reimplemented in bpp::VectorMappedContainer< bpp::Sequence >, and bpp::VectorMappedContainer< SequenceType >.

Definition at line 80 of file VectorPositionedContainer.h.

◆ deleteObject()

template<class T >

void bpp::VectorPositionedContainer< T >::deleteObject ( size_t objectIndex )

inlineoverridevirtual

Delete an object from the container.

Parameters

objectIndex The index of the object in the container.

Implements bpp::PositionedContainerInterface< T >.

Reimplemented in bpp::VectorMappedContainer< bpp::Sequence >, and bpp::VectorMappedContainer< SequenceType >.

Definition at line 200 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::VectorMappedContainer< T >::deleteObject(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::deleteSite(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSite().

◆ deleteObjects()

template<class T >

void bpp::VectorPositionedContainer< T >::deleteObjects	(	size_t	objectIndex,
		size_t	length
	)

inline

Definition at line 208 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::deleteSites(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSites().

◆ getObject() [1/2]

template<class T >

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

inlineoverridevirtual

Retrieve an object from the container.

Parameters

objectIndex The position of the object.

Returns: A shared pointer toward the Object object with corresponding name.

Implements bpp::PositionedContainerInterface< T >.

Definition at line 127 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::site(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::site_().

◆ getObject() [2/2]

template<class T >

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

inlineoverridevirtual

Retrieve an object from the container.

Parameters

objectIndex The position of the object.

Returns: A shared pointer toward the Object object with corresponding name.

Implements bpp::PositionedContainerInterface< T >.

Definition at line 134 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

◆ getObject_()

template<class T >

std::shared_ptr<T> bpp::VectorPositionedContainer< T >::getObject_ ( size_t objectIndex ) const

inline

Definition at line 221 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

◆ getSize()

template<class T >

size_t bpp::VectorPositionedContainer< T >::getSize ( ) const

inlineoverridevirtual

the size

Implements bpp::PositionedContainerInterface< T >.

Reimplemented in bpp::VectorMappedContainer< bpp::Sequence >, and bpp::VectorMappedContainer< SequenceType >.

Definition at line 87 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

◆ hasObjectWithPosition()

template<class T >

bool bpp::VectorPositionedContainer< T >::hasObjectWithPosition ( size_t objectIndex ) const

inline

Definition at line 97 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::site().

◆ insertObject()

template<class T >

void bpp::VectorPositionedContainer< T >::insertObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex
	)

inline

Insert an object.

Parameters

object	The object to add.
objectIndex	The new position of the object

Definition at line 179 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::addSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), and bpp::VectorMappedContainer< T >::insertObject().

◆ isAvailablePosition()

template<class T >

bool bpp::VectorPositionedContainer< T >::isAvailablePosition ( size_t objectIndex ) const

inline

Definition at line 92 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

◆ nullify()

template<class T >

virtual void bpp::VectorPositionedContainer< T >::nullify ( )

inlinevirtual

Nullify all elements.

Reimplemented in bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< bpp::Sequence >, and bpp::VectorMappedContainer< SequenceType >.

Definition at line 122 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::insertSequence(), bpp::VectorMappedContainer< T >::nullify(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::operator=(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::setSequence().

◆ object() [1/2]

template<class T >

const T& bpp::VectorPositionedContainer< T >::object ( size_t objectIndex ) const

inlineoverridevirtual

Get a reference toward an object from the container.

Parameters

objectIndex The position of the object.

Returns: A reference toward the Object object with corresponding name.

Implements bpp::PositionedContainerInterface< T >.

Definition at line 141 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::VectorPositionedContainer< T >::addObject().

◆ object() [2/2]

template<class T >

T& bpp::VectorPositionedContainer< T >::object ( size_t objectIndex )

inlineoverridevirtual

Get a reference toward an object from the container.

Parameters

objectIndex The position of the object.

Returns: A reference toward the Object object with corresponding name.

Implements bpp::PositionedContainerInterface< T >.

Definition at line 148 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

◆ operator=()

template<class T >

VectorPositionedContainer<T>& bpp::VectorPositionedContainer< T >::operator= ( const VectorPositionedContainer< T > & vsc )

inline

copy where shared_ptr elements are shared

Definition at line 63 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::VectorMappedContainer< T >::operator=().

◆ removeObject()

template<class T >

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

inlineoverridevirtual

Extract and remove a object from the container.

Parameters

objectIndex The position of the object.

Returns: A smart pointer toward the removed object.

Implements bpp::PositionedContainerInterface< T >.

Reimplemented in bpp::VectorMappedContainer< bpp::Sequence >, and bpp::VectorMappedContainer< SequenceType >.

Definition at line 188 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize(), and bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::VectorMappedContainer< T >::removeObject(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::removeSite(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::removeSite().

◆ setSize()

template<class T >

void bpp::VectorPositionedContainer< T >::setSize ( size_t size )

inlineoverridevirtual

Reimplemented from bpp::PositionedContainerInterface< T >.

Definition at line 102 of file VectorPositionedContainer.h.

References bpp::VectorPositionedContainer< T >::positions_.

Referenced by bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::addSequence(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::operator=(), and bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer().

Member Data Documentation

◆ positions_

template<class T >

std::vector< std::shared_ptr<T> > bpp::VectorPositionedContainer< T >::positions_

protected

Definition at line 34 of file VectorPositionedContainer.h.

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

Bpp/Seq/Container/VectorPositionedContainer.h

Public Member Functions

Protected Attributes

Detailed Description

template<class T> class bpp::VectorPositionedContainer< T >

Constructor & Destructor Documentation

◆ VectorPositionedContainer() [1/3]

◆ VectorPositionedContainer() [2/3]

◆ VectorPositionedContainer() [3/3]

◆ ~VectorPositionedContainer()

Member Function Documentation

◆ addObject()

◆ addObject_()

◆ appendObject()

◆ clear()

◆ clone()

◆ deleteObject()

◆ deleteObjects()

◆ getObject() [1/2]

◆ getObject() [2/2]

◆ getObject_()

◆ getSize()

◆ hasObjectWithPosition()

◆ insertObject()

◆ isAvailablePosition()

◆ nullify()

◆ object() [1/2]

◆ object() [2/2]

◆ operator=()

◆ removeObject()

◆ setSize()

Member Data Documentation

◆ positions_

template<class T>
class bpp::VectorPositionedContainer< T >