bpp-seq3  3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::VectorMappedContainer< T > Class Template Referenceabstract

The template VectorMappedContainer class. More...

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

+ Inheritance diagram for bpp::VectorMappedContainer< T >:
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Public Member Functions

 VectorMappedContainer ()
 
 VectorMappedContainer (const VectorMappedContainer &vsc)
 
VectorMappedContainer< T > & operator= (const VectorMappedContainer &vsc)
 
virtual ~VectorMappedContainer ()
 
size_t getSize () const override
 Get the number of objects in the container. More...
 
size_t getNumberOfObjects () const
 
size_t getObjectPosition (const std::string &name) const override
 Link between position & name. More...
 
const std::string & getObjectName (size_t objectIndex) const override
 
std::vector< std::string > getObjectNames () const override
 
void setObjectNames (const std::vector< std::string > &names)
 
void setObjectName (size_t pos, const std::string &name)
 
void addObject (std::shared_ptr< T > newObject, size_t objectIndex, const std::string &name, bool check=false) override
 
void insertObject (std::shared_ptr< T > newObject, size_t objectIndex, const std::string &name) override
 
virtual void appendObject (std::shared_ptr< T > newObject, const std::string &name, bool checkNames=true)
 
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...
 
std::shared_ptr< T > removeObject (const std::string &name) override
 Remove and returns an object. More...
 
void deleteObject (const std::string &name) override
 Remove an object. More...
 
void addObject_ (std::shared_ptr< T > newObject, size_t objectIndex, const std::string &name, bool check=false) const
 
void clear () override
 Delete all objects in the container. More...
 
void nullify () override
 Nullify all elements. More...
 
virtual void setSize (size_t size)
 
virtual const std::shared_ptr< T > getObject (size_t objectIndex) const =0
 Retrieve an object from the container. More...
 
virtual std::shared_ptr< T > getObject (size_t objectIndex)=0
 Retrieve an object from the container. More...
 
virtual const T & object (size_t objectIndex) const =0
 Get a reference toward an object from the container. More...
 
virtual T & object (size_t objectIndex)=0
 Get a reference toward an object from the container. More...
 
const std::shared_ptr< T > getObject (const std::string &name) const override
 Retrieve an object from the container. More...
 
std::shared_ptr< T > getObject (const std::string &name) override
 
const T & object (const std::string &name) const override
 
T & object (const std::string &name) override
 
bool hasObject (const std::string &name) const override
 Check if a object with a given name is present in the container. More...
 
void addObject (std::shared_ptr< T > newObject, const std::string &name, bool checkName=false)
 Set an object. More...
 
void changeName (const std::string &okey, const std::string &nkey)
 change the key of an object. More...
 
bool isAvailableName (std::string objectName) const
 
void addObject_ (std::shared_ptr< T > newObject, const std::string &name, bool checkName=false) const
 
bool isAvailablePosition (size_t objectIndex) const
 
bool hasObjectWithPosition (size_t objectIndex) const
 
void setSize (size_t size) override
 
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...
 
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.
VectorMappedContainer< T > * clone () const override
 

Protected Member Functions

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 const T & object (const std::string &name) const =0
 
virtual T & object (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...
 

Protected Attributes

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

Private Attributes

std::vector< std::string > vNames_
 vector of the names, in same order as objects More...
 
std::map< std::string, size_t > mNames_
 map <string, size_t> for the positions of the names More...
 
std::map< std::string, std::shared_ptr< T > > mObjects_
 

Detailed Description

template<class T>
class bpp::VectorMappedContainer< T >

The template VectorMappedContainer class.

Objects are stored in a std::vector of shared pointers and in a map of shared pointers.

Object access is hence in $O(1)$ through indexes, and $O(log(n))$ through names.

Definition at line 31 of file VectorMappedContainer.h.

Constructor & Destructor Documentation

◆ VectorMappedContainer() [1/2]

template<class T >
bpp::VectorMappedContainer< T >::VectorMappedContainer ( )
inline

Definition at line 48 of file VectorMappedContainer.h.

Referenced by bpp::VectorMappedContainer< T >::clone().

◆ VectorMappedContainer() [2/2]

template<class T >
bpp::VectorMappedContainer< T >::VectorMappedContainer ( const VectorMappedContainer< T > &  vsc)
inline

Definition at line 55 of file VectorMappedContainer.h.

◆ ~VectorMappedContainer()

template<class T >
virtual bpp::VectorMappedContainer< T >::~VectorMappedContainer ( )
inlinevirtual

Definition at line 72 of file VectorMappedContainer.h.

Member Function Documentation

◆ addObject() [1/3]

template<class T >
void bpp::MappedNamedContainer< T >::addObject ( std::shared_ptr< T >  newObject,
const std::string &  name,
bool  checkName = false 
)
inlineinherited

Set an object.

Parameters
nameThe key of the object.
newObjectThe new object that will be associated to the key.
checkNameTell is the object name must be checked.

Definition at line 110 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::hasObject(), and bpp::MappedNamedContainer< T >::mObjects_.

Referenced by bpp::VectorMappedContainer< T >::addObject(), bpp::VectorMappedContainer< T >::appendObject(), and bpp::VectorMappedContainer< T >::insertObject().

◆ addObject() [2/3]

template<class T >
void bpp::VectorMappedContainer< T >::addObject ( std::shared_ptr< T >  newObject,
size_t  objectIndex,
const std::string &  name,
bool  check = false 
)
inlineoverridevirtual

Implements bpp::PositionedNamedContainerInterface< T >.

Definition at line 161 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::addObject(), bpp::VectorPositionedContainer< T >::addObject(), bpp::VectorMappedContainer< T >::mNames_, and bpp::VectorMappedContainer< T >::vNames_.

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequence(), bpp::TemplateVectorSequenceContainer< SequenceType >::setSequence(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::valueAt().

◆ addObject() [3/3]

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

Add an object.

Parameters
objectThe object to add.
objectIndexThe new position of the object
checkPositionLook 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_() [1/3]

template<class T >
void bpp::MappedNamedContainer< T >::addObject_ ( std::shared_ptr< T >  newObject,
const std::string &  name,
bool  checkName = false 
) const
inlineinherited

Definition at line 200 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::hasObject(), and bpp::MappedNamedContainer< T >::mObjects_.

Referenced by bpp::VectorMappedContainer< T >::addObject_().

◆ addObject_() [2/3]

template<class T >
void bpp::VectorMappedContainer< T >::addObject_ ( std::shared_ptr< T >  newObject,
size_t  objectIndex,
const std::string &  name,
bool  check = false 
) const
inline

Definition at line 232 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::addObject_(), bpp::VectorPositionedContainer< T >::addObject_(), bpp::VectorMappedContainer< T >::mNames_, and bpp::VectorMappedContainer< T >::vNames_.

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence().

◆ addObject_() [3/3]

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

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() [1/2]

template<class T >
virtual void bpp::VectorMappedContainer< T >::appendObject ( std::shared_ptr< T >  newObject,
const std::string &  name,
bool  checkNames = true 
)
inlinevirtual

Definition at line 185 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::addObject(), bpp::VectorPositionedContainer< T >::appendObject(), bpp::VectorMappedContainer< T >::mNames_, and bpp::VectorMappedContainer< T >::vNames_.

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

◆ appendObject() [2/2]

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

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().

◆ changeName()

template<class T >
void bpp::MappedNamedContainer< T >::changeName ( const std::string &  okey,
const std::string &  nkey 
)
inlineinherited

change the key of an object.

Parameters
okeyThe present key of the object.
nkeyThe next key of the object.

Definition at line 168 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::hasObject(), and bpp::MappedNamedContainer< T >::mObjects_.

Referenced by bpp::VectorMappedContainer< T >::setObjectName(), and bpp::VectorMappedContainer< T >::setObjectNames().

◆ clear()

template<class T >
void bpp::VectorMappedContainer< T >::clear ( )
inlineoverridevirtual

Delete all objects in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 240 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::clear(), bpp::VectorPositionedContainer< T >::clear(), bpp::VectorMappedContainer< T >::mNames_, and bpp::VectorMappedContainer< T >::vNames_.

Referenced by bpp::TemplateVectorSequenceContainer< SequenceType >::clear(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::clear().

◆ clone()

template<class T >
VectorMappedContainer<T>* bpp::VectorMappedContainer< T >::clone ( ) const
inlineoverridevirtual

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 80 of file VectorMappedContainer.h.

References bpp::VectorMappedContainer< T >::VectorMappedContainer().

◆ deleteObject() [1/2]

template<class T >
void bpp::VectorMappedContainer< T >::deleteObject ( const std::string &  name)
inlineoverridevirtual

Remove an object.

Parameters
nameThe key of the object.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 227 of file VectorMappedContainer.h.

References bpp::VectorMappedContainer< T >::deleteObject(), and bpp::VectorMappedContainer< T >::mNames_.

◆ deleteObject() [2/2]

template<class T >
void bpp::VectorMappedContainer< T >::deleteObject ( size_t  objectIndex)
inlineoverridevirtual

Delete an object from the container.

Parameters
objectIndexThe index of the object in the container.

Implements bpp::PositionedContainerInterface< T >.

Definition at line 207 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::deleteObject(), bpp::VectorPositionedContainer< T >::deleteObject(), bpp::VectorMappedContainer< T >::mNames_, and bpp::VectorMappedContainer< T >::vNames_.

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

◆ deleteObjects()

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

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().

◆ getNumberOfObjects()

template<class T >
size_t bpp::VectorMappedContainer< T >::getNumberOfObjects ( ) const
inline

Definition at line 101 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::getSize().

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getNumberOfSequences().

◆ getObject() [1/8]

template<class T >
virtual const std::shared_ptr<T> bpp::NamedContainerInterface< T >::getObject ( const std::string &  name) const
protectedpure virtualinherited

Retrieve an object from the container.

Parameters
nameThe name of the object.
Returns
A reference toward the Object with corresponding name.

Implemented in bpp::MappedNamedContainer< T >.

◆ getObject() [2/8]

template<class T >
const std::shared_ptr<T> bpp::MappedNamedContainer< T >::getObject ( const std::string &  name) const
inlineoverridevirtualinherited

Retrieve an object from the container.

Parameters
nameThe name of the object.
Returns
A reference toward the Object with corresponding name.

Implements bpp::NamedContainerInterface< T >.

Definition at line 61 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::mObjects_.

Referenced by bpp::MappedNamedContainer< T >::isAvailableName(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequence(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence().

◆ getObject() [3/8]

template<class T >
std::shared_ptr<T> bpp::MappedNamedContainer< T >::getObject ( const std::string &  name)
inlineoverridevirtualinherited

Implements bpp::NamedContainerInterface< T >.

Definition at line 70 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::mObjects_.

◆ getObject() [4/8]

template<class T >
virtual std::shared_ptr<T> bpp::NamedContainerInterface< T >::getObject ( const std::string &  name)
protectedpure virtualinherited

Implemented in bpp::MappedNamedContainer< T >.

◆ getObject() [5/8]

template<class T >
virtual const std::shared_ptr<T> bpp::PositionedContainerInterface< T >::getObject ( size_t  objectIndex) const
pure virtualinherited

Retrieve an object from the container.

Parameters
objectIndexThe position of the object.
Returns
A shared pointer toward the Object object with corresponding name.

Implemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< bpp::Site >, and bpp::VectorPositionedContainer< SiteType >.

◆ getObject() [6/8]

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

Retrieve an object from the container.

Parameters
objectIndexThe 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() [7/8]

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

Retrieve an object from the container.

Parameters
objectIndexThe 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() [8/8]

template<class T >
virtual std::shared_ptr<T> bpp::PositionedContainerInterface< T >::getObject ( size_t  objectIndex)
pure virtualinherited

Retrieve an object from the container.

Parameters
objectIndexThe position of the object.
Returns
A shared pointer toward the Object object with corresponding name.

Implemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< bpp::Site >, and bpp::VectorPositionedContainer< SiteType >.

◆ getObject_()

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

Definition at line 221 of file VectorPositionedContainer.h.

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

◆ getObjectName()

template<class T >
const std::string& bpp::VectorMappedContainer< T >::getObjectName ( size_t  objectIndex) const
inlineoverridevirtual

Implements bpp::PositionedNamedContainerInterface< T >.

Definition at line 115 of file VectorMappedContainer.h.

References bpp::VectorMappedContainer< T >::getSize(), and bpp::VectorMappedContainer< T >::vNames_.

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence(), bpp::TemplateVectorSequenceContainer< SequenceType >::sequenceKey(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequenceKey(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequence(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::valueAt().

◆ getObjectNames()

template<class T >
std::vector<std::string> bpp::VectorMappedContainer< T >::getObjectNames ( ) const
inlineoverridevirtual
Returns
All objects keys.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 133 of file VectorMappedContainer.h.

References bpp::VectorMappedContainer< T >::vNames_.

Referenced by bpp::TemplateVectorSequenceContainer< SequenceType >::getSequenceKeys(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequenceKeys().

◆ getObjectPosition()

template<class T >
size_t bpp::VectorMappedContainer< T >::getObjectPosition ( const std::string &  name) const
inlineoverridevirtual

Link between position & name.

Implements bpp::PositionedNamedContainerInterface< T >.

Definition at line 106 of file VectorMappedContainer.h.

References bpp::VectorMappedContainer< T >::mNames_.

Referenced by bpp::TemplateVectorSequenceContainer< SequenceType >::getSequencePosition(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::getSequencePosition().

◆ getSize()

template<class T >
size_t bpp::VectorMappedContainer< T >::getSize ( ) const
inlineoverridevirtual

Get the number of objects in the container.

Returns
The number of objects in the container.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 92 of file VectorMappedContainer.h.

References bpp::VectorPositionedContainer< T >::getSize().

Referenced by bpp::TemplateVectorSequenceContainer< SequenceType >::getNumberOfSequences(), and bpp::VectorMappedContainer< T >::getObjectName().

◆ hasObject() [1/2]

template<class T >
virtual bool bpp::NamedContainerInterface< T >::hasObject ( const std::string &  name) const
protectedpure virtualinherited

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

Parameters
nameThe name of the object.
Returns
True if a object with the given name is present in the container.

Implemented in bpp::MappedNamedContainer< T >.

◆ hasObject() [2/2]

template<class T >
bool bpp::MappedNamedContainer< T >::hasObject ( const std::string &  name) const
inlineoverridevirtualinherited

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

Parameters
nameThe name of the object.
Returns
True if a object with the given name is present in the container.

Implements bpp::NamedContainerInterface< T >.

Definition at line 97 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::mObjects_.

Referenced by bpp::MappedNamedContainer< T >::addObject(), bpp::MappedNamedContainer< T >::addObject_(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSequence(), bpp::MappedNamedContainer< T >::changeName(), bpp::MappedNamedContainer< T >::deleteObject(), bpp::TemplateVectorSequenceContainer< SequenceType >::hasSequence(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::hasSequence(), bpp::MappedNamedContainer< T >::isAvailableName(), and bpp::MappedNamedContainer< T >::removeObject().

◆ hasObjectWithPosition()

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

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() [1/2]

template<class T >
void bpp::VectorMappedContainer< T >::insertObject ( std::shared_ptr< T >  newObject,
size_t  objectIndex,
const std::string &  name 
)
inlineoverridevirtual

Implements bpp::PositionedNamedContainerInterface< T >.

Definition at line 171 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::addObject(), bpp::VectorPositionedContainer< T >::insertObject(), bpp::VectorMappedContainer< T >::mNames_, and bpp::VectorMappedContainer< T >::vNames_.

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::insertSequence(), and bpp::TemplateVectorSequenceContainer< SequenceType >::insertSequence().

◆ insertObject() [2/2]

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

Insert an object.

Parameters
objectThe object to add.
objectIndexThe 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().

◆ isAvailableName()

template<class T >
bool bpp::MappedNamedContainer< T >::isAvailableName ( std::string  objectName) const
inlineinherited
Returns
whether the name is in the map keys and the mapped object is nullptr or empty.

Definition at line 195 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::getObject(), and bpp::MappedNamedContainer< T >::hasObject().

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::sequence().

◆ isAvailablePosition()

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

Definition at line 92 of file VectorPositionedContainer.h.

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

◆ nullify()

template<class T >
void bpp::VectorMappedContainer< T >::nullify ( )
inlineoverridevirtual

Nullify all elements.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 248 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::nullify(), and bpp::VectorPositionedContainer< T >::nullify().

Referenced by bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::addSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::deleteSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::removeSite(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequenceNames(), and bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSite().

◆ object() [1/8]

template<class T >
virtual const T& bpp::NamedContainerInterface< T >::object ( const std::string &  name) const
protectedpure virtualinherited

Implemented in bpp::MappedNamedContainer< T >.

◆ object() [2/8]

template<class T >
const T& bpp::MappedNamedContainer< T >::object ( const std::string &  name) const
inlineoverridevirtualinherited

Implements bpp::NamedContainerInterface< T >.

Definition at line 79 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::mObjects_.

Referenced by bpp::TemplateVectorSequenceContainer< SequenceType >::sequence_().

◆ object() [3/8]

template<class T >
T& bpp::MappedNamedContainer< T >::object ( const std::string &  name)
inlineoverridevirtualinherited

Implements bpp::NamedContainerInterface< T >.

Definition at line 88 of file MappedNamedContainer.h.

References bpp::MappedNamedContainer< T >::mObjects_.

◆ object() [4/8]

template<class T >
virtual T& bpp::NamedContainerInterface< T >::object ( const std::string &  name)
protectedpure virtualinherited

Implemented in bpp::MappedNamedContainer< T >.

◆ object() [5/8]

template<class T >
virtual const T& bpp::PositionedContainerInterface< T >::object ( size_t  objectIndex) const
pure virtualinherited

Get a reference toward an object from the container.

Parameters
objectIndexThe position of the object.
Returns
A reference toward the Object object with corresponding name.

Implemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< bpp::Site >, and bpp::VectorPositionedContainer< SiteType >.

◆ object() [6/8]

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

Get a reference toward an object from the container.

Parameters
objectIndexThe 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() [7/8]

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

Get a reference toward an object from the container.

Parameters
objectIndexThe 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_.

◆ object() [8/8]

template<class T >
virtual T& bpp::PositionedContainerInterface< T >::object ( size_t  objectIndex)
pure virtualinherited

Get a reference toward an object from the container.

Parameters
objectIndexThe position of the object.
Returns
A reference toward the Object object with corresponding name.

Implemented in bpp::VectorPositionedContainer< T >, bpp::VectorPositionedContainer< bpp::Site >, and bpp::VectorPositionedContainer< SiteType >.

◆ operator=()

template<class T >
VectorMappedContainer<T>& bpp::VectorMappedContainer< T >::operator= ( const VectorMappedContainer< T > &  vsc)
inline

Definition at line 62 of file VectorMappedContainer.h.

References bpp::VectorMappedContainer< T >::mNames_, bpp::MappedNamedContainer< T >::operator=(), bpp::VectorPositionedContainer< T >::operator=(), and bpp::VectorMappedContainer< T >::vNames_.

◆ removeObject() [1/2]

template<class T >
std::shared_ptr<T> bpp::VectorMappedContainer< T >::removeObject ( const std::string &  name)
inlineoverridevirtual

Remove and returns an object.

Parameters
nameThe key of the object.
Returns
The object previously associated to the given key.

Reimplemented from bpp::MappedNamedContainer< T >.

Definition at line 222 of file VectorMappedContainer.h.

References bpp::VectorMappedContainer< T >::mNames_, and bpp::VectorMappedContainer< T >::removeObject().

◆ removeObject() [2/2]

template<class T >
std::shared_ptr<T> bpp::VectorMappedContainer< T >::removeObject ( size_t  objectIndex)
inlineoverridevirtual

Extract and remove a object from the container.

Parameters
objectIndexThe position of the object.
Returns
A smart pointer toward the removed object.

Implements bpp::PositionedContainerInterface< T >.

Definition at line 193 of file VectorMappedContainer.h.

References bpp::VectorMappedContainer< T >::mNames_, bpp::MappedNamedContainer< T >::removeObject(), bpp::VectorPositionedContainer< T >::removeObject(), and bpp::VectorMappedContainer< T >::vNames_.

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

◆ setObjectName()

template<class T >
void bpp::VectorMappedContainer< T >::setObjectName ( size_t  pos,
const std::string &  name 
)
inline

Definition at line 154 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::changeName(), bpp::VectorMappedContainer< T >::mNames_, and bpp::VectorMappedContainer< T >::vNames_.

◆ setObjectNames()

template<class T >
void bpp::VectorMappedContainer< T >::setObjectNames ( const std::vector< std::string > &  names)
inline

Definition at line 138 of file VectorMappedContainer.h.

References bpp::MappedNamedContainer< T >::changeName(), bpp::VectorMappedContainer< T >::mNames_, and bpp::VectorMappedContainer< T >::vNames_.

Referenced by bpp::TemplateVectorSequenceContainer< SequenceType >::setSequenceKeys(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::setSequenceKeys(), and bpp::TemplateVectorSequenceContainer< SequenceType >::setSequenceNames().

◆ setSize() [1/2]

template<class T >
virtual void bpp::PositionedContainerInterface< T >::setSize ( size_t  size)
inlinevirtualinherited

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

Definition at line 40 of file PositionedContainer.h.

◆ setSize() [2/2]

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

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

◆ mNames_

template<class T >
std::map<std::string, size_t> bpp::VectorMappedContainer< T >::mNames_
private

map <string, size_t> for the positions of the names

Definition at line 45 of file VectorMappedContainer.h.

Referenced by bpp::VectorMappedContainer< T >::addObject(), bpp::VectorMappedContainer< T >::addObject_(), bpp::VectorMappedContainer< T >::appendObject(), bpp::VectorMappedContainer< T >::clear(), bpp::VectorMappedContainer< T >::deleteObject(), bpp::VectorMappedContainer< T >::getObjectPosition(), bpp::VectorMappedContainer< T >::insertObject(), bpp::VectorMappedContainer< T >::operator=(), bpp::VectorMappedContainer< T >::removeObject(), bpp::VectorMappedContainer< T >::setObjectName(), and bpp::VectorMappedContainer< T >::setObjectNames().

◆ mObjects_

template<class T >
std::map<std::string, std::shared_ptr<T> > bpp::MappedNamedContainer< T >::mObjects_
privateinherited

Definition at line 28 of file MappedNamedContainer.h.

Referenced by bpp::MappedNamedContainer< T >::addObject(), bpp::MappedNamedContainer< T >::addObject_(), bpp::MappedNamedContainer< T >::changeName(), bpp::MappedNamedContainer< T >::clear(), bpp::MappedNamedContainer< T >::deleteObject(), bpp::MappedNamedContainer< T >::getObject(), bpp::MappedNamedContainer< T >::getObjectNames(), bpp::MappedNamedContainer< T >::getSize(), bpp::MappedNamedContainer< T >::hasObject(), bpp::MappedNamedContainer< T >::nullify(), bpp::MappedNamedContainer< T >::object(), bpp::MappedNamedContainer< T >::operator=(), and bpp::MappedNamedContainer< T >::removeObject().

◆ positions_

template<class T >
std::vector< std::shared_ptr<T> > bpp::VectorPositionedContainer< T >::positions_
protectedinherited

Definition at line 34 of file VectorPositionedContainer.h.

Referenced by bpp::VectorPositionedContainer< T >::addObject(), bpp::VectorPositionedContainer< T >::addObject_(), bpp::VectorPositionedContainer< T >::appendObject(), bpp::VectorPositionedContainer< T >::clear(), bpp::VectorPositionedContainer< T >::deleteObject(), bpp::VectorPositionedContainer< T >::deleteObjects(), bpp::VectorPositionedContainer< T >::getObject(), bpp::VectorPositionedContainer< T >::getObject_(), bpp::VectorPositionedContainer< T >::getSize(), bpp::VectorPositionedContainer< T >::hasObjectWithPosition(), bpp::VectorPositionedContainer< T >::insertObject(), bpp::VectorPositionedContainer< T >::isAvailablePosition(), bpp::VectorPositionedContainer< T >::nullify(), bpp::VectorPositionedContainer< T >::object(), bpp::VectorPositionedContainer< T >::operator=(), bpp::VectorPositionedContainer< T >::removeObject(), bpp::VectorPositionedContainer< T >::setSize(), and bpp::VectorPositionedContainer< T >::~VectorPositionedContainer().

◆ vNames_

template<class T >
std::vector<std::string> bpp::VectorMappedContainer< T >::vNames_
private

vector of the names, in same order as objects

Definition at line 40 of file VectorMappedContainer.h.

Referenced by bpp::VectorMappedContainer< T >::addObject(), bpp::VectorMappedContainer< T >::addObject_(), bpp::VectorMappedContainer< T >::appendObject(), bpp::VectorMappedContainer< T >::clear(), bpp::VectorMappedContainer< T >::deleteObject(), bpp::VectorMappedContainer< T >::getObjectName(), bpp::VectorMappedContainer< T >::getObjectNames(), bpp::VectorMappedContainer< T >::insertObject(), bpp::VectorMappedContainer< T >::operator=(), bpp::VectorMappedContainer< T >::removeObject(), bpp::VectorMappedContainer< T >::setObjectName(), and bpp::VectorMappedContainer< T >::setObjectNames().

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