bpp::LegacyAbstractMapping Class Reference

Partial implementation of the mapping interface. More...

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

Inheritance diagram for bpp::LegacyAbstractMapping:

Collaboration diagram for bpp::LegacyAbstractMapping:

Public Member Functions
	LegacyAbstractMapping (const Tree &tree)
	LegacyAbstractMapping (const LegacyAbstractMapping &absm)
LegacyAbstractMapping &	operator= (const LegacyAbstractMapping &absm)
LegacyAbstractMapping *	clone () const override=0
virtual	~LegacyAbstractMapping ()
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 mapping interface.

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

Definition at line 85 of file Mapping.h.

Constructor & Destructor Documentation

LegacyAbstractMapping() [1/2]

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

inline

Definition at line 96 of file Mapping.h.

References nbBranches_, nodes_, and tree_.

LegacyAbstractMapping() [2/2]

bpp::LegacyAbstractMapping::LegacyAbstractMapping ( const LegacyAbstractMapping &  absm )

inline

Definition at line 103 of file Mapping.h.

References nodes_, and tree_.

~LegacyAbstractMapping()

virtual bpp::LegacyAbstractMapping::~LegacyAbstractMapping ( )

inlinevirtual

Definition at line 127 of file Mapping.h.

Member Function Documentation

clone()

LegacyAbstractMapping* bpp::LegacyAbstractMapping::clone ( ) const

overridepure virtual

Implements bpp::LegacyMappingInterface.

Implemented in bpp::LegacyAbstractSubstitutionMapping, bpp::LegacyAbstractRewardMapping, bpp::LegacyProbabilisticSubstitutionMapping, and bpp::LegacyProbabilisticRewardMapping.

getBranchLengths()

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

inlineoverridevirtual

Returns

A vector with all tree branch lengths.

Implements bpp::LegacyMappingInterface.

Definition at line 174 of file Mapping.h.

References nbBranches_, and nodes_.

getNode()

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

inlinevirtual

Definition at line 162 of file Mapping.h.

References nodes_.

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

getNodeIndex()

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

inlineoverridevirtual

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

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

getNumberOfBranches()

size_t bpp::LegacyAbstractMapping::getNumberOfBranches ( ) const

inlineoverridevirtual

Returns

The number of branches mapped.

Implements bpp::LegacyMappingInterface.

Definition at line 160 of file Mapping.h.

References nbBranches_.

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

getNumberOfSites()

size_t bpp::LegacyAbstractMapping::getNumberOfSites ( ) const

inlineoverridevirtual

Returns

The number of sites mapped.

Implements bpp::LegacyMappingInterface.

Definition at line 158 of file Mapping.h.

References nbSites_.

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

getSitePosition()

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

inlineoverridevirtual

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 isEmpty(), and sitesPositions_.

isEmpty()

bool bpp::LegacyAbstractMapping::isEmpty ( ) const

inlineoverridevirtual

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 tree_.

Referenced by getSitePosition(), setSitePosition(), and tree().

operator=()

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

inline

Definition at line 114 of file Mapping.h.

References nbBranches_, nbSites_, nodes_, sitesPositions_, and tree_.

setNumberOfSites()

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

inlinevirtual

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

Definition at line 164 of file Mapping.h.

References nbSites_, and sitesPositions_.

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

setSitePosition()

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

inlineoverridevirtual

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 isEmpty(), and sitesPositions_.

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

setTree()

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

inline

Definition at line 138 of file Mapping.h.

References nbBranches_, nodes_, tree(), and tree_.

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

tree()

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

inlineoverridevirtual

Returns

Get the phylogenetic tree associated to this mapping.

Implements bpp::LegacyMappingInterface.

Definition at line 132 of file Mapping.h.

References isEmpty(), and tree_.

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

Member Data Documentation

nbBranches_

size_t bpp::LegacyAbstractMapping::nbBranches_

private

Definition at line 93 of file Mapping.h.

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

nbSites_

size_t bpp::LegacyAbstractMapping::nbSites_

private

Definition at line 92 of file Mapping.h.

Referenced by getNumberOfSites(), operator=(), and setNumberOfSites().

nodes_

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

private

Definition at line 91 of file Mapping.h.

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

sitesPositions_

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

private

Definition at line 90 of file Mapping.h.

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

tree_

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

private

Definition at line 89 of file Mapping.h.

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

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

• Bpp/Phyl/Legacy/Mapping/Mapping.h