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 (AlphabetIndex1 *alphIndex)

	AbstractReward (const AbstractReward &ar)

AbstractReward &	operator= (const AbstractReward &ar)

	~AbstractReward ()

bool	hasAlphabetIndex () const

void	setAlphabetIndex (AlphabetIndex1 *alphIndex)

const AlphabetIndex1 *	getAlphabetIndex () const

AlphabetIndex1 *	getAlphabetIndex ()

virtual Reward *	clone () const =0

virtual 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	setSubstitutionModel (const SubstitutionModel *model)=0
	Set the substitution model associated with this reward, if relevant. More...

Protected Member Functions
virtual void	alphabetIndexHasChanged ()=0

Protected Attributes
AlphabetIndex1 *	alphIndex_

Detailed Description

Basic implementation of the the Reward interface.

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

Definition at line 151 of file Reward.h.

Constructor & Destructor Documentation

◆ AbstractReward() [1/2]

bpp::AbstractReward::AbstractReward ( AlphabetIndex1 * alphIndex )

inline

Definition at line 158 of file Reward.h.

◆ AbstractReward() [2/2]

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

inline

Definition at line 162 of file Reward.h.

◆ ~AbstractReward()

bpp::AbstractReward::~AbstractReward ( )

inline

Definition at line 173 of file Reward.h.

Member Function Documentation

◆ alphabetIndexHasChanged()

virtual void bpp::AbstractReward::alphabetIndexHasChanged ( )

protectedpure virtual

Implemented in bpp::DecompositionReward.

Referenced by setAlphabetIndex().

◆ clone()

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

pure virtualinherited

Implemented in bpp::DecompositionReward.

◆ 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 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 108 of file Reward.h.

References bpp::Reward::getAlphabetIndex().

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

◆ getAlphabetIndex() [1/2]

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 194 of file Reward.h.

References alphIndex_.

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

◆ getAlphabetIndex() [2/2]

AlphabetIndex1* bpp::AbstractReward::getAlphabetIndex ( )

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 196 of file Reward.h.

References alphIndex_.

◆ 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 115 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 179 of file Reward.h.

References alphIndex_.

◆ operator=()

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

inline

Definition at line 166 of file Reward.h.

References alphIndex_.

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

◆ setAlphabetIndex()

void bpp::AbstractReward::setAlphabetIndex ( AlphabetIndex1 * alphind )

inlinevirtual

Parameters

alphind The new AlphabetIndex1 object to be associated to this instance.

Implements bpp::Reward.

Definition at line 188 of file Reward.h.

References alphabetIndexHasChanged(), and alphIndex_.

◆ setSubstitutionModel()

virtual void bpp::Reward::setSubstitutionModel ( const SubstitutionModel * 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.

Member Data Documentation

◆ alphIndex_

AlphabetIndex1* bpp::AbstractReward::alphIndex_

protected

Definition at line 155 of file Reward.h.

Referenced by 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

◆ alphabetIndexHasChanged()

◆ clone()

◆ getAllRewards()

◆ getAlphabet()

◆ getAlphabetIndex() [1/2]

◆ getAlphabetIndex() [2/2]

◆ getNumberOfStates()

◆ getReward()

◆ hasAlphabetIndex()

◆ operator=()

◆ setAlphabetIndex()

◆ setSubstitutionModel()

Member Data Documentation

◆ alphIndex_