Partial implementation of the substitution mapping interface. More...

#include <Bpp/Phyl/Legacy/Mapping/SubstitutionMapping.h>

Inheritance diagram for bpp::LegacyAbstractSubstitutionMapping:

Collaboration diagram for bpp::LegacyAbstractSubstitutionMapping:

Public Member Functions
	LegacyAbstractSubstitutionMapping (const Tree &tree)

	LegacyAbstractSubstitutionMapping (const LegacyAbstractSubstitutionMapping &absm)=default

LegacyAbstractSubstitutionMapping *	clone () const override=0

LegacyAbstractSubstitutionMapping &	operator= (const LegacyAbstractSubstitutionMapping &absm)=default

virtual	~LegacyAbstractSubstitutionMapping ()

virtual size_t	getNumberOfSubstitutionTypes () const =0

virtual double &	operator() (size_t nodeIndex, size_t siteIndex, size_t type)=0

virtual const double &	operator() (size_t nodeIndex, size_t siteIndex, size_t type) const =0

virtual const Tree &	tree () const =0

virtual bool	isEmpty () const =0

virtual size_t	getNumberOfSites () const =0

virtual size_t	getNumberOfBranches () const =0

virtual int	getSitePosition (size_t index) const =0

virtual std::vector< double >	getBranchLengths () const =0

virtual size_t	getNodeIndex (int nodeId) const =0

virtual void	setSitePosition (size_t index, int position)=0
	Set the position of a given site. More...

bool	isEmpty () const override

const TreeTemplate< Node > &	tree () const override

void	setTree (const Tree &tree)

int	getSitePosition (size_t index) const override

void	setSitePosition (size_t index, int position) override
	Set the position of a given site. More...

size_t	getNumberOfSites () const override

size_t	getNumberOfBranches () const override

virtual const Node *	getNode (size_t nodeIndex) const

virtual void	setNumberOfSites (size_t numberOfSites)

virtual std::vector< double >	getBranchLengths () const override

virtual size_t	getNodeIndex (int nodeId) const override

Private Attributes
std::unique_ptr< const TreeTemplate< Node > >	tree_

std::vector< int >	sitesPositions_

std::vector< const Node * >	nodes_

size_t	nbSites_

size_t	nbBranches_

Detailed Description

Partial implementation of the substitution mapping interface.

This implementation copies the input tree in a TreeTemplate<Node> object.

Definition at line 54 of file SubstitutionMapping.h.

Constructor & Destructor Documentation

◆ LegacyAbstractSubstitutionMapping() [1/2]

bpp::LegacyAbstractSubstitutionMapping::LegacyAbstractSubstitutionMapping ( const Tree & tree )

inline

Definition at line 59 of file SubstitutionMapping.h.

◆ LegacyAbstractSubstitutionMapping() [2/2]

bpp::LegacyAbstractSubstitutionMapping::LegacyAbstractSubstitutionMapping ( const LegacyAbstractSubstitutionMapping & absm )

default

◆ ~LegacyAbstractSubstitutionMapping()

virtual bpp::LegacyAbstractSubstitutionMapping::~LegacyAbstractSubstitutionMapping ( )

inlinevirtual

Definition at line 67 of file SubstitutionMapping.h.

Member Function Documentation

◆ clone()

LegacyAbstractSubstitutionMapping * bpp::LegacyAbstractSubstitutionMapping::clone ( ) const

overridepure virtual

Implements bpp::LegacyAbstractMapping.

Implemented in bpp::LegacyProbabilisticSubstitutionMapping.

◆ getBranchLengths() [1/2]

virtual std::vector< double > bpp::LegacyMappingInterface::getBranchLengths ( ) const

pure virtualinherited

Returns: A vector with all tree branch lengths.

Implemented in bpp::LegacyAbstractMapping.

◆ getBranchLengths() [2/2]

virtual std::vector< double > bpp::LegacyAbstractMapping::getBranchLengths ( ) const

inlineoverridevirtualinherited

Returns: A vector with all tree branch lengths.

Implements bpp::LegacyMappingInterface.

Definition at line 174 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbBranches_, and bpp::LegacyAbstractMapping::nodes_.

◆ getNode()

virtual const Node * bpp::LegacyAbstractMapping::getNode ( size_t nodeIndex ) const

inlinevirtualinherited

Definition at line 162 of file Mapping.h.

References bpp::LegacyAbstractMapping::nodes_.

Referenced by bpp::LegacyRewardMappingTools::writeToStream(), and bpp::LegacySubstitutionMappingTools::writeToStream().

◆ getNodeIndex() [1/2]

virtual size_t bpp::LegacyMappingInterface::getNodeIndex ( int nodeId ) const

pure virtualinherited

Parameters

nodeId An id of the node to look for in the map.

Returns: The mapping index for the specified node id.

Implemented in bpp::LegacyAbstractMapping.

◆ getNodeIndex() [2/2]

virtual size_t bpp::LegacyAbstractMapping::getNodeIndex ( int nodeId ) const

inlineoverridevirtualinherited

Parameters

nodeId An id of the node to look for in the map.

Returns: The mapping index for the specified node id.

Implements bpp::LegacyMappingInterface.

Definition at line 184 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbBranches_, bpp::LegacyAbstractMapping::nodes_, and bpp::TextTools::toString().

Referenced by bpp::LegacyProbabilisticSubstitutionMapping::getNumberOfSubstitutions(), bpp::LegacyProbabilisticRewardMapping::getReward(), bpp::LegacyRewardMappingTools::readFromStream(), and bpp::LegacySubstitutionMappingTools::readFromStream().

◆ getNumberOfBranches() [1/2]

virtual size_t bpp::LegacyMappingInterface::getNumberOfBranches ( ) const

pure virtualinherited

Returns: The number of branches mapped.

Implemented in bpp::LegacyAbstractMapping.

Referenced by bpp::LegacySubstitutionMappingTools::computeNormForSite(), bpp::LegacyRewardMappingTools::computeSumForSite(), bpp::LegacySubstitutionMappingTools::computeSumForSite(), bpp::LegacySubstitutionMappingTools::computeTotalSubstitutionVectorForSitePerBranch(), and bpp::LegacySubstitutionMappingTools::computeTotalSubstitutionVectorForSitePerType().

◆ getNumberOfBranches() [2/2]

size_t bpp::LegacyAbstractMapping::getNumberOfBranches ( ) const

inlineoverridevirtualinherited

Returns: The number of branches mapped.

Implements bpp::LegacyMappingInterface.

Definition at line 160 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbBranches_.

Referenced by bpp::LegacyProbabilisticRewardMapping::setNumberOfSites(), bpp::LegacyProbabilisticSubstitutionMapping::setNumberOfSites(), bpp::LegacyProbabilisticRewardMapping::setTree(), bpp::LegacyProbabilisticSubstitutionMapping::setTree(), bpp::LegacyRewardMappingTools::writeToStream(), and bpp::LegacySubstitutionMappingTools::writeToStream().

◆ getNumberOfSites() [1/2]

virtual size_t bpp::LegacyMappingInterface::getNumberOfSites ( ) const

pure virtualinherited

Returns: The number of sites mapped.

Implemented in bpp::LegacyAbstractMapping.

Referenced by bpp::LegacyRewardMappingTools::computeSumForBranch(), and bpp::LegacySubstitutionMappingTools::computeSumForBranch().

◆ getNumberOfSites() [2/2]

size_t bpp::LegacyAbstractMapping::getNumberOfSites ( ) const

inlineoverridevirtualinherited

Returns: The number of sites mapped.

Implements bpp::LegacyMappingInterface.

Definition at line 158 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbSites_.

Referenced by bpp::LegacyProbabilisticRewardMapping::setTree(), bpp::LegacyProbabilisticSubstitutionMapping::setTree(), bpp::LegacyRewardMappingTools::writeToStream(), and bpp::LegacySubstitutionMappingTools::writeToStream().

◆ getNumberOfSubstitutionTypes()

virtual size_t bpp::LegacySubstitutionMappingInterface::getNumberOfSubstitutionTypes ( ) const

pure virtualinherited

Returns: The number of distinct types of substitutions mapped.

Implemented in bpp::LegacyProbabilisticSubstitutionMapping.

Referenced by bpp::LegacySubstitutionMappingTools::computeNormForSite(), bpp::LegacySubstitutionMappingTools::computeSumForBranch(), bpp::LegacySubstitutionMappingTools::computeSumForSite(), bpp::LegacySubstitutionMappingTools::computeTotalSubstitutionVectorForSitePerBranch(), and bpp::LegacySubstitutionMappingTools::computeTotalSubstitutionVectorForSitePerType().

◆ getSitePosition() [1/2]

virtual int bpp::LegacyMappingInterface::getSitePosition ( size_t index ) const

pure virtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implemented in bpp::LegacyAbstractMapping.

◆ getSitePosition() [2/2]

int bpp::LegacyAbstractMapping::getSitePosition ( size_t index ) const

inlineoverridevirtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implements bpp::LegacyMappingInterface.

Definition at line 146 of file Mapping.h.

References bpp::LegacyAbstractMapping::isEmpty(), and bpp::LegacyAbstractMapping::sitesPositions_.

◆ isEmpty() [1/2]

virtual bool bpp::LegacyMappingInterface::isEmpty ( ) const

pure virtualinherited

Returns: True is the map is empty, that is, if no tree is associated to the map yet.

Implemented in bpp::LegacyAbstractMapping.

◆ isEmpty() [2/2]

bool bpp::LegacyAbstractMapping::isEmpty ( ) const

inlineoverridevirtualinherited

Returns: True is the map is empty, that is, if no tree is associated to the map yet.

Implements bpp::LegacyMappingInterface.

Definition at line 130 of file Mapping.h.

References bpp::LegacyAbstractMapping::tree_.

Referenced by bpp::LegacyAbstractMapping::getSitePosition(), bpp::LegacyAbstractMapping::setSitePosition(), and bpp::LegacyAbstractMapping::tree().

◆ operator()() [1/2]

virtual const double & bpp::LegacySubstitutionMappingInterface::operator()	(	size_t	nodeIndex,
		size_t	siteIndex,
		size_t	type
	)		const

pure virtualinherited

Implemented in bpp::LegacyProbabilisticSubstitutionMapping.

◆ operator()() [2/2]

virtual double & bpp::LegacySubstitutionMappingInterface::operator()	(	size_t	nodeIndex,
		size_t	siteIndex,
		size_t	type
	)

pure virtualinherited

Implemented in bpp::LegacyProbabilisticSubstitutionMapping.

◆ operator=()

LegacyAbstractSubstitutionMapping & bpp::LegacyAbstractSubstitutionMapping::operator= ( const LegacyAbstractSubstitutionMapping & absm )

default

◆ setNumberOfSites()

virtual void bpp::LegacyAbstractMapping::setNumberOfSites ( size_t numberOfSites )

inlinevirtualinherited

Reimplemented in bpp::LegacyProbabilisticRewardMapping, and bpp::LegacyProbabilisticSubstitutionMapping.

Definition at line 164 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbSites_, and bpp::LegacyAbstractMapping::sitesPositions_.

Referenced by bpp::LegacyProbabilisticRewardMapping::setNumberOfSites(), and bpp::LegacyProbabilisticSubstitutionMapping::setNumberOfSites().

◆ setSitePosition() [1/2]

void bpp::LegacyAbstractMapping::setSitePosition	(	size_t	index,
		int	position
	)

inlineoverridevirtualinherited

Set the position of a given site.

Warning: No index checking is performed, use with care!

Parameters

index	The site index.
position	The position of the site.

Implements bpp::LegacyMappingInterface.

Definition at line 152 of file Mapping.h.

References bpp::LegacyAbstractMapping::isEmpty(), and bpp::LegacyAbstractMapping::sitesPositions_.

Referenced by bpp::LegacyRewardMappingTools::readFromStream(), and bpp::LegacySubstitutionMappingTools::readFromStream().

◆ setSitePosition() [2/2]

virtual void bpp::LegacyMappingInterface::setSitePosition	(	size_t	index,
		int	position
	)

pure virtualinherited

Set the position of a given site.

Warning: No index checking is performed, use with care!

Parameters

index	The site index.
position	The position of the site.

Implemented in bpp::LegacyAbstractMapping.

◆ setTree()

void bpp::LegacyAbstractMapping::setTree ( const Tree & tree )

inlineinherited

Definition at line 138 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbBranches_, bpp::LegacyAbstractMapping::nodes_, bpp::LegacyAbstractMapping::tree(), and bpp::LegacyAbstractMapping::tree_.

Referenced by bpp::LegacyProbabilisticRewardMapping::setTree(), and bpp::LegacyProbabilisticSubstitutionMapping::setTree().

◆ tree() [1/2]

virtual const Tree & bpp::LegacyMappingInterface::tree ( ) const

pure virtualinherited

Returns: Get the phylogenetic tree associated to this mapping.

Implemented in bpp::LegacyAbstractMapping.

◆ tree() [2/2]

const TreeTemplate< Node > & bpp::LegacyAbstractMapping::tree ( ) const

inlineoverridevirtualinherited

Returns: Get the phylogenetic tree associated to this mapping.

Implements bpp::LegacyMappingInterface.

Definition at line 132 of file Mapping.h.

References bpp::LegacyAbstractMapping::isEmpty(), and bpp::LegacyAbstractMapping::tree_.

Referenced by bpp::LegacyAbstractMapping::setTree(), bpp::LegacyProbabilisticRewardMapping::setTree(), and bpp::LegacyProbabilisticSubstitutionMapping::setTree().

Member Data Documentation

◆ nbBranches_

size_t bpp::LegacyAbstractMapping::nbBranches_

privateinherited

Definition at line 93 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::getBranchLengths(), bpp::LegacyAbstractMapping::getNodeIndex(), bpp::LegacyAbstractMapping::getNumberOfBranches(), bpp::LegacyAbstractMapping::LegacyAbstractMapping(), bpp::LegacyAbstractMapping::operator=(), and bpp::LegacyAbstractMapping::setTree().

◆ nbSites_

size_t bpp::LegacyAbstractMapping::nbSites_

privateinherited

Definition at line 92 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::getNumberOfSites(), bpp::LegacyAbstractMapping::operator=(), and bpp::LegacyAbstractMapping::setNumberOfSites().

◆ nodes_

std::vector<const Node*> bpp::LegacyAbstractMapping::nodes_

privateinherited

Definition at line 91 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::getBranchLengths(), bpp::LegacyAbstractMapping::getNode(), bpp::LegacyAbstractMapping::getNodeIndex(), bpp::LegacyAbstractMapping::LegacyAbstractMapping(), bpp::LegacyAbstractMapping::operator=(), and bpp::LegacyAbstractMapping::setTree().

◆ sitesPositions_

std::vector<int> bpp::LegacyAbstractMapping::sitesPositions_

privateinherited

Definition at line 90 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::getSitePosition(), bpp::LegacyAbstractMapping::operator=(), bpp::LegacyAbstractMapping::setNumberOfSites(), and bpp::LegacyAbstractMapping::setSitePosition().

◆ tree_

std::unique_ptr<const TreeTemplate<Node> > bpp::LegacyAbstractMapping::tree_

privateinherited

Definition at line 89 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::isEmpty(), bpp::LegacyAbstractMapping::LegacyAbstractMapping(), bpp::LegacyAbstractMapping::operator=(), bpp::LegacyAbstractMapping::setTree(), and bpp::LegacyAbstractMapping::tree().

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

Bpp/Phyl/Legacy/Mapping/SubstitutionMapping.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ LegacyAbstractSubstitutionMapping() [1/2]

◆ LegacyAbstractSubstitutionMapping() [2/2]

◆ ~LegacyAbstractSubstitutionMapping()

Member Function Documentation

◆ clone()

◆ getBranchLengths() [1/2]

◆ getBranchLengths() [2/2]

◆ getNode()

◆ getNodeIndex() [1/2]

◆ getNodeIndex() [2/2]

◆ getNumberOfBranches() [1/2]

◆ getNumberOfBranches() [2/2]

◆ getNumberOfSites() [1/2]

◆ getNumberOfSites() [2/2]

◆ getNumberOfSubstitutionTypes()

◆ getSitePosition() [1/2]

◆ getSitePosition() [2/2]

◆ isEmpty() [1/2]

◆ isEmpty() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=()

◆ setNumberOfSites()

◆ setSitePosition() [1/2]

◆ setSitePosition() [2/2]

◆ setTree()

◆ tree() [1/2]

◆ tree() [2/2]

Member Data Documentation

◆ nbBranches_

◆ nbSites_

◆ nodes_

◆ sitesPositions_

◆ tree_