The template PositionedNamedContainer class, that links position & name containers. More...

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

Inheritance diagram for bpp::PositionedNamedContainer< T >:

Collaboration diagram for bpp::PositionedNamedContainer< T >:

Public Member Functions
virtual	~PositionedNamedContainer ()

The Clonable interface.
virtual PositionedNamedContainer< T > *	clone () const =0

Protected Member Functions
virtual void	addObject (std::shared_ptr< T > object, size_t objectIndex, const std::string &name, bool check=false)=0

virtual void	insertObject (std::shared_ptr< T > object, size_t objectIndex, const std::string &name)=0

virtual size_t	getObjectPosition (const std::string &name) const =0
	Link between position & name. More...

virtual std::string	getObjectName (size_t objectIndex) const =0

Private Member Functions
virtual size_t	getSize () const =0
	the size More...

virtual void	setSize (size_t size)

virtual void	clear ()=0

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...

virtual const std::shared_ptr< T >	getObject (const std::string &name) const =0
	Retrieve an object from the container. More...

virtual std::shared_ptr< T >	getObject (const std::string &name)=0

virtual bool	hasObject (const std::string &name) const =0
	Check if a object with a given name is present in the container. More...

virtual std::shared_ptr< T >	removeObject (const std::string &name)=0
	Extract and remove a object from the container. More...

virtual void	deleteObject (const std::string &name)=0
	Remove a object from the container. More...

virtual std::vector< std::string >	getObjectNames () const =0
	Get all the names of the objects in the container. More...

virtual size_t	getSize () const =0
	Get the number of objects in the container. More...

virtual void	clear ()=0
	Delete all objects in the container. More...

Detailed Description

template<class T>
class bpp::PositionedNamedContainer< T >

The template PositionedNamedContainer class, that links position & name containers.

Definition at line 62 of file PositionedNamedContainer.h.

Constructor & Destructor Documentation

◆ ~PositionedNamedContainer()

template<class T >

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

inlinevirtual

Definition at line 77 of file PositionedNamedContainer.h.

Member Function Documentation

◆ addObject()

template<class T >

virtual void bpp::PositionedNamedContainer< T >::addObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		const std::string &	name,
		bool	check = `false`
	)

protectedpure virtual

Implemented in bpp::VectorMappedContainer< T >.

◆ clear() [1/2]

template<class T >

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

pure virtualinherited

Delete all objects in the container.

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

◆ clear() [2/2]

template<class T >

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

pure virtualinherited

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.

◆ clone()

template<class T >

virtual PositionedNamedContainer<T>* bpp::PositionedNamedContainer< T >::clone ( ) const

pure virtual

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

◆ deleteObject() [1/2]

template<class T >

virtual void bpp::NamedContainer< T >::deleteObject ( const std::string & name )

protectedpure virtualinherited

Remove a object from the container.

Parameters

name	The name of the object.

Implemented in bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, bpp::VectorMappedContainer< ProbabilisticSequence >, and bpp::MappedNamedContainer< T >.

◆ deleteObject() [2/2]

template<class T >

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

protectedpure virtualinherited

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() [1/4]

template<class T >

virtual const std::shared_ptr<T> bpp::NamedContainer< T >::getObject ( const std::string & name ) const

protectedpure virtualinherited

Retrieve an object from the container.

Parameters

name	The name of the object.

Returns: A reference toward the Object with corresponding name.

Implemented in bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, bpp::VectorMappedContainer< ProbabilisticSequence >, and bpp::MappedNamedContainer< T >.

◆ getObject() [2/4]

template<class T >

virtual std::shared_ptr<T> bpp::NamedContainer< T >::getObject ( const std::string & name )

protectedpure virtualinherited

Implemented in bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, bpp::VectorMappedContainer< ProbabilisticSequence >, and bpp::MappedNamedContainer< T >.

◆ getObject() [3/4]

template<class T >

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

protectedpure virtualinherited

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() [4/4]

template<class T >

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

protectedpure virtualinherited

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

◆ getObjectName()

template<class T >

virtual std::string bpp::PositionedNamedContainer< T >::getObjectName ( size_t objectIndex ) const

protectedpure virtual

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

◆ getObjectNames()

template<class T >

virtual std::vector<std::string> bpp::NamedContainer< T >::getObjectNames ( ) const

protectedpure virtualinherited

Get all the names of the objects in the container.

Returns: A vector of strings with all object names.

Implemented in bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, bpp::VectorMappedContainer< ProbabilisticSequence >, and bpp::MappedNamedContainer< T >.

◆ getObjectPosition()

template<class T >

virtual size_t bpp::PositionedNamedContainer< T >::getObjectPosition ( const std::string & name ) const

protectedpure virtual

Link between position & name.

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

◆ getSize() [1/2]

template<class T >

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

pure virtualinherited

Get the number of objects in the container.

Returns: The number of objects in the container.

Implemented in bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, bpp::VectorMappedContainer< ProbabilisticSequence >, and bpp::MappedNamedContainer< T >.

◆ getSize() [2/2]

template<class T >

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

pure virtualinherited

the size

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

◆ hasObject()

template<class T >

virtual bool bpp::NamedContainer< T >::hasObject ( const std::string & name ) const

protectedpure virtualinherited

Check if a object with a given name is present in the container.

Parameters

name	The name of the object.

Returns: True if a object with the given name is present in the container.

Implemented in bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, bpp::VectorMappedContainer< ProbabilisticSequence >, and bpp::MappedNamedContainer< T >.

◆ insertObject()

template<class T >

virtual void bpp::PositionedNamedContainer< T >::insertObject	(	std::shared_ptr< T >	object,
		size_t	objectIndex,
		const std::string &	name
	)

protectedpure virtual

Implemented in bpp::VectorMappedContainer< T >.

◆ removeObject() [1/2]

template<class T >

virtual std::shared_ptr<T> bpp::NamedContainer< T >::removeObject ( const std::string & name )

protectedpure virtualinherited

Extract and remove a object from the container.

Parameters

name	The name of the object.

Implemented in bpp::VectorMappedContainer< T >, bpp::VectorMappedContainer< Sequence >, bpp::VectorMappedContainer< ProbabilisticSequence >, and bpp::MappedNamedContainer< T >.

◆ removeObject() [2/2]

template<class T >

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

protectedpure virtualinherited

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 )

inlinevirtualinherited

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

Definition at line 76 of file PositionedContainer.h.

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

Bpp/Seq/Container/PositionedNamedContainer.h

Public Member Functions

Protected Member Functions

Private Member Functions

Detailed Description

template<class T> class bpp::PositionedNamedContainer< T >

Constructor & Destructor Documentation

◆ ~PositionedNamedContainer()

Member Function Documentation

◆ addObject()

◆ clear() [1/2]

◆ clear() [2/2]

◆ clone()

◆ deleteObject() [1/2]

◆ deleteObject() [2/2]

◆ getObject() [1/4]

◆ getObject() [2/4]

◆ getObject() [3/4]

◆ getObject() [4/4]

◆ getObjectName()

◆ getObjectNames()

◆ getObjectPosition()

◆ getSize() [1/2]

◆ getSize() [2/2]

◆ hasObject()

◆ insertObject()

◆ removeObject() [1/2]

◆ removeObject() [2/2]

◆ setSize()

template<class T>
class bpp::PositionedNamedContainer< T >