Basic implementation of the the Reward interface. More...

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

Inheritance diagram for bpp::AbstractReward:

Collaboration diagram for bpp::AbstractReward:

Public Member Functions
	AbstractReward (std::shared_ptr< const AlphabetIndex1 > alphIndex)

	AbstractReward (const AbstractReward &ar)

AbstractReward &	operator= (const AbstractReward &ar)

virtual	~AbstractReward ()

bool	hasAlphabetIndex () const

void	setAlphabetIndex (std::shared_ptr< const AlphabetIndex1 > alphIndex)
	attribution of an AlphabetIndex1 More...

std::shared_ptr< const AlphabetIndex1 >	getAlphabetIndex () const

const AlphabetIndex1 &	alphabetIndex () const

virtual Reward *	clone () const =0

virtual std::shared_ptr< const Alphabet >	getAlphabet () const
	Short cut function, equivalent to getSubstitutionRegister()->getAlphabet(). More...

virtual size_t	getNumberOfStates () const
	Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize(). More...

virtual double	getReward (size_t initialState, size_t finalState, double length) const =0
	Get the reward of susbstitutions on a branch, given the initial and final states, and the branch length. More...

virtual Matrix< double > *	getAllRewards (double length) const =0
	Get the rewards on a branch, for each initial and final states, and given the branch length. More...

virtual void	storeAllRewards (double length, Eigen::MatrixXd &mat) const =0
	Store the rewards on a branch, for each initial and final states, and given the branch length. More...

virtual void	setSubstitutionModel (std::shared_ptr< const SubstitutionModelInterface > model)=0
	Set the substitution model associated with this reward, if relevant. More...

Protected Member Functions
virtual void	alphabetIndexHasChanged ()=0

Protected Attributes
std::shared_ptr< const AlphabetIndex1 >	alphIndex_

Detailed Description

Basic implementation of the the Reward interface.

This partial implementation deals with the AlphabetIndex1 gestion, by owning a pointer.

Definition at line 122 of file Reward.h.

Constructor & Destructor Documentation

◆ AbstractReward() [1/2]

bpp::AbstractReward::AbstractReward ( std::shared_ptr< const AlphabetIndex1 > alphIndex )

inline

Definition at line 129 of file Reward.h.

◆ AbstractReward() [2/2]

bpp::AbstractReward::AbstractReward ( const AbstractReward & ar )

inline

Definition at line 133 of file Reward.h.

◆ ~AbstractReward()

virtual bpp::AbstractReward::~AbstractReward ( )

inlinevirtual

Definition at line 143 of file Reward.h.

Member Function Documentation

◆ alphabetIndex()

const AlphabetIndex1& bpp::AbstractReward::alphabetIndex ( ) const

inline

Definition at line 161 of file Reward.h.

References alphIndex_.

◆ alphabetIndexHasChanged()

virtual void bpp::AbstractReward::alphabetIndexHasChanged ( )

protectedpure virtual

Implemented in bpp::DecompositionReward.

Referenced by setAlphabetIndex().

◆ clone()

virtual Reward* bpp::Reward::clone ( ) const

pure virtualinherited

Implements bpp::Clonable.

Implemented in bpp::DecompositionReward.

Referenced by bpp::RewardMappingTools::computeRewardVectors().

◆ getAllRewards()

virtual Matrix<double>* bpp::Reward::getAllRewards ( double length ) const

pure virtualinherited

Get the rewards on a branch, for each initial and final states, and given the branch length.

Parameters

length The length of the branch.

Returns: A matrix with all rewards for each initial and final states.

Implemented in bpp::DecompositionReward.

◆ getAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::Reward::getAlphabet ( ) const

inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet().

Returns: The alphabet associated to this substitution count.

Definition at line 65 of file Reward.h.

References bpp::Reward::getAlphabetIndex().

Referenced by bpp::Reward::getNumberOfStates().

◆ getAlphabetIndex()

std::shared_ptr<const AlphabetIndex1> bpp::AbstractReward::getAlphabetIndex ( ) const

inlinevirtual

Returns: The AlphabetIndex1 object associated to this instance. The alphabet index contains the value associated to each state.

Implements bpp::Reward.

Definition at line 159 of file Reward.h.

References alphIndex_.

Referenced by bpp::DecompositionReward::fillBMatrice_().

◆ getNumberOfStates()

virtual size_t bpp::Reward::getNumberOfStates ( ) const

inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize().

Returns: The number of states in the model/alphabet.

Definition at line 75 of file Reward.h.

References bpp::Reward::getAlphabet().

◆ getReward()

virtual double bpp::Reward::getReward	(	size_t	initialState,
		size_t	finalState,
		double	length
	)		const

pure virtualinherited

Get the reward of susbstitutions on a branch, given the initial and final states, and the branch length.

Parameters

initialState	The initial state.
finalState	The final state.
length	The length of the branch.

Returns: The reward of the function on a branch of specified length and according to initial and final states.

Implemented in bpp::DecompositionReward.

◆ hasAlphabetIndex()

bool bpp::AbstractReward::hasAlphabetIndex ( ) const

inlinevirtual

Returns: Tell if an alphabet index has been attached to this class.

Implements bpp::Reward.

Definition at line 146 of file Reward.h.

References alphIndex_.

◆ operator=()

AbstractReward& bpp::AbstractReward::operator= ( const AbstractReward & ar )

inline

Definition at line 137 of file Reward.h.

References alphIndex_.

Referenced by bpp::DecompositionReward::operator=().

◆ setAlphabetIndex()

void bpp::AbstractReward::setAlphabetIndex ( std::shared_ptr< const AlphabetIndex1 > alphIndex )

inlinevirtual

attribution of an AlphabetIndex1

Parameters

alphIndex pointer to a AlphabetIndex1

Implements bpp::Reward.

Definition at line 153 of file Reward.h.

References alphabetIndexHasChanged(), and alphIndex_.

◆ setSubstitutionModel()

virtual void bpp::Reward::setSubstitutionModel ( std::shared_ptr< const SubstitutionModelInterface > model )

pure virtualinherited

Set the substitution model associated with this reward, if relevant.

Parameters

model The substitution model to use with this reward.

Implemented in bpp::DecompositionReward.

◆ storeAllRewards()

virtual void bpp::Reward::storeAllRewards	(	double	length,
		Eigen::MatrixXd &	mat
	)		const

pure virtualinherited

Store the rewards on a branch, for each initial and final states, and given the branch length.

Parameters

length	The length of the branch.
mat	A matrix to store all rewards for each initial and final states.

Implemented in bpp::DecompositionReward.

Member Data Documentation

◆ alphIndex_

std::shared_ptr<const AlphabetIndex1> bpp::AbstractReward::alphIndex_

protected

Definition at line 126 of file Reward.h.

Referenced by alphabetIndex(), bpp::DecompositionReward::alphabetIndexHasChanged(), bpp::DecompositionReward::DecompositionReward(), getAlphabetIndex(), hasAlphabetIndex(), operator=(), setAlphabetIndex(), and bpp::DecompositionReward::setSubstitutionModel().

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

Bpp/Phyl/Mapping/Reward.h

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractReward() [1/2]

◆ AbstractReward() [2/2]

◆ ~AbstractReward()

Member Function Documentation

◆ alphabetIndex()

◆ alphabetIndexHasChanged()

◆ clone()

◆ getAllRewards()

◆ getAlphabet()

◆ getAlphabetIndex()

◆ getNumberOfStates()

◆ getReward()

◆ hasAlphabetIndex()

◆ operator=()

◆ setAlphabetIndex()

◆ setSubstitutionModel()

◆ storeAllRewards()

Member Data Documentation

◆ alphIndex_