bpp::DRHomogeneousTreeLikelihood Class Reference

This class implements the likelihood computation for a tree using the double-recursive algorithm. More...

#include <Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h>

Inheritance diagram for bpp::DRHomogeneousTreeLikelihood:

Collaboration diagram for bpp::DRHomogeneousTreeLikelihood:

Public Member Functions
	DRHomogeneousTreeLikelihood (const Tree &tree, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true) throw (Exception)
	Build a new DRHomogeneousTreeLikelihood object without data. More...
	DRHomogeneousTreeLikelihood (const Tree &tree, const SiteContainer &data, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true) throw (Exception)
	Build a new DRHomogeneousTreeLikelihood object and compute the corresponding likelihood. More...
	DRHomogeneousTreeLikelihood (const DRHomogeneousTreeLikelihood &lik)
	Copy constructor. More...
DRHomogeneousTreeLikelihood &	operator= (const DRHomogeneousTreeLikelihood &lik)
virtual	~DRHomogeneousTreeLikelihood ()
DRHomogeneousTreeLikelihood *	clone () const
void	computeTreeLikelihood ()
void	setParameters (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Implements the Function interface. More...
double	getValue () const throw (Exception)
	Function and NNISearchable interface. More...
DRASDRTreeLikelihoodData *	getLikelihoodData ()
const DRASDRTreeLikelihoodData *	getLikelihoodData () const
virtual void	computeLikelihoodAtNode (int nodeId, VVVdouble &likelihoodArray) const
	Compute the likelihood array at a given node. More...
virtual void	initParameters ()
	This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree. More...
virtual void	applyParameters () throw (Exception)
	All parameters are stored in a parameter list. This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths. More...
virtual void	initBranchLengthsParameters ()
virtual void	setMinimumBranchLength (double minimum) throw (Exception)
virtual void	setMaximumBranchLength (double maximum) throw (Exception)
virtual double	getMinimumBranchLength () const
virtual double	getMaximumBranchLength () const
virtual const SiteContainer *	getData () const =0
	Get the dataset for which the likelihood must be evaluated. More...
virtual bool	isInitialized () const =0
virtual double	getLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the likelihood for a site and for a state. More...
virtual double	getLogLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the logarithm of the likelihood for a site and for a state. More...
virtual Vdouble	getLikelihoodForEachSite () const =0
	Get the likelihood for each site. More...
virtual Vdouble	getLogLikelihoodForEachSite () const =0
	Get the logarithm of the likelihood for each site. More...
virtual VVdouble	getLikelihoodForEachSiteForEachState () const =0
	Get the likelihood for each site and for each state. More...
virtual VVdouble	getLogLikelihoodForEachSiteForEachState () const =0
	Get the logarithm of the likelihood for each site and for each state. More...
virtual const Tree &	getTree () const =0
	Get the tree (topology and branch lengths). More...
virtual size_t	getNumberOfSites () const =0
	Get the number of sites in the dataset. More...
virtual const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to the dataset. More...
virtual void	enableDerivatives (bool yn)=0
	Tell if derivatives must be computed. More...
virtual ParameterList	getDerivableParameters () const =0
	All derivable parameters. More...
virtual ParameterList	getNonDerivableParameters () const =0
	All non derivable parameters. More...
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
void	setData (const SiteContainer &sites) throw (Exception)
	Set the dataset for which the likelihood must be evaluated. More...
double	getLikelihood () const
	Get the likelihood for the whole dataset. More...
double	getLogLikelihood () const
	Get the logarithm of the likelihood for the whole dataset. More...
double	getLikelihoodForASite (size_t site) const
	Get the likelihood for a site. More...
double	getLogLikelihoodForASite (size_t site) const
	Get the logarithm of the likelihood for a site. More...
size_t	getSiteIndex (size_t site) const throw (IndexOutOfBoundsException)
	Get the index (used for inner computations) of a given site (original alignment column). More...
The DiscreteRatesAcrossSites interface implementation:
double	getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
	Get the likelihood for a site knowing its rate class. More...
double	getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
	Get the logarithm of the likelihood for a site knowing its rate class. More...
double	getLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const
	Get the likelihood for a site knowing its rate class and its ancestral state. More...
double	getLogLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const
	Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state. More...
DerivableFirstOrder interface.
double	getFirstOrderDerivative (const std::string &variable) const throw (Exception)
DerivableSecondOrder interface.
double	getSecondOrderDerivative (const std::string &variable) const throw (Exception)
double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const throw (Exception)
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
size_t	getNumberOfStates () const
const std::vector< int > &	getAlphabetStates () const
int	getAlphabetStateAsInt (size_t i) const
std::string	getAlphabetStateAsChar (size_t i) const
void	initialize () throw (Exception)
	Init the likelihood object. More...
ParameterList	getBranchLengthsParameters () const
	Get the branch lengths parameters. More...
ParameterList	getSubstitutionModelParameters () const
	Get the parameters associated to substitution model(s). More...
ParameterList	getRateDistributionParameters () const
	Get the parameters associated to the rate distirbution. More...
const std::vector< double > &	getRootFrequencies (size_t siteIndex) const
	Get the values of the frequencies for each state in the alphabet at the root node. More...
VVVdouble	getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const
	Retrieves all Pij(t) for a particular branch, defined by the upper node. More...
ConstBranchModelIterator *	getNewBranchModelIterator (int nodeId) const
ConstSiteModelIterator *	getNewSiteModelIterator (size_t siteIndex) const
The HomogeneousTreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
const SubstitutionModel *	getSubstitutionModel () const
const SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column. More...
SubstitutionModel *	getSubstitutionModel ()
SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column. More...
void	setSubstitutionModel (SubstitutionModel *model) throw (Exception)
The TreeLikelihood interface.
const SiteContainer *	getData () const
	Get the dataset for which the likelihood must be evaluated. More...
bool	isInitialized () const
Vdouble	getLikelihoodForEachSite () const
	Get the likelihood for each site. More...
Vdouble	getLogLikelihoodForEachSite () const
	Get the logarithm of the likelihood for each site. More...
VVdouble	getLikelihoodForEachSiteForEachState () const
	Get the likelihood for each site and for each state. More...
VVdouble	getLogLikelihoodForEachSiteForEachState () const
	Get the logarithm of the likelihood for each site and for each state. More...
const Tree &	getTree () const
	Get the tree (topology and branch lengths). More...
size_t	getNumberOfSites () const
	Get the number of sites in the dataset. More...
const Alphabet *	getAlphabet () const
	Get the alphabet associated to the dataset. More...
void	enableDerivatives (bool yn)
	Tell if derivatives must be computed. More...
void	enableFirstOrderDerivatives (bool yn)
bool	enableFirstOrderDerivatives () const
void	enableSecondOrderDerivatives (bool yn)
bool	enableSecondOrderDerivatives () const
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
double	getLikelihoodForASiteForAState (size_t site, int state) const
	Get the likelihood for a site and for a state. More...
double	getLogLikelihoodForASiteForAState (size_t site, int state) const
	Get the logarithm of the likelihood for a site and for a state. More...
VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const
	Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More...
ParameterList	getDerivableParameters () const
	All derivable parameters. More...
ParameterList	getNonDerivableParameters () const
	All non derivable parameters. More...
Retrieve some particular parameters subsets.
virtual VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const =0
	Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More...
The DiscreteRatesAcrossSites interface implementation:
const DiscreteDistribution *	getRateDistribution () const
	Get the rate distribution used for the computation. More...
DiscreteDistribution *	getRateDistribution ()
	Get the rate distribution used for the computation. More...
size_t	getNumberOfClasses () const
	Get the number of classes. More...
VVdouble	getLikelihoodForEachSiteForEachRateClass () const
	Get the likelihood for each site and each rate class. More...
VVdouble	getLogLikelihoodForEachSiteForEachRateClass () const
	Get the logarithm of the likelihood for each site and each rate class. More...
VVVdouble	getLikelihoodForEachSiteForEachRateClassForEachState () const
	Get the likelihood for each site and each rate class and each state. More...
VVVdouble	getLogLikelihoodForEachSiteForEachRateClassForEachState () const
	Get the logarithm of the likelihood for each site and each rate class and each state. More...
VVdouble	getPosteriorProbabilitiesOfEachRate () const
	Get the posterior probability for each site of belonging to a particular rate class. More...
Vdouble	getRateWithMaxPostProbOfEachSite () const
	Get the posterior rate (the one with maximum posterior probability) for each site. More...
std::vector< size_t >	getRateClassWithMaxPostProbOfEachSite () const
	Get the posterior rate class (the one with maximum posterior probability) for each site. More...
Vdouble	getPosteriorRateOfEachSite () const
	Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site. More...

Static Public Member Functions
Generic tools to deal with likelihood arrays
static void	resetLikelihoodArray (VVVdouble &likelihoodArray)
	Set all conditional likelihoods to 1. More...
static void	displayLikelihoodArray (const VVVdouble &likelihoodArray)
	Print the likelihood array to terminal (debugging tool). More...

Protected Member Functions
virtual void	computeLikelihoodAtNode_ (const Node *node, VVVdouble &likelihoodArray, const Node *sonNode=0) const
virtual void	computeSubtreeLikelihoodPostfix (const Node *node)
virtual void	computeSubtreeLikelihoodPrefix (const Node *node)
virtual void	computeRootLikelihood ()
virtual void	computeTreeDLikelihoodAtNode (const Node *node)
virtual void	computeTreeDLikelihoods ()
virtual void	computeTreeD2LikelihoodAtNode (const Node *node)
virtual void	computeTreeD2Likelihoods ()
virtual void	fireParameterChanged (const ParameterList &params)
virtual void	resetLikelihoodArrays (const Node *node)
virtual void	displayLikelihood (const Node *node)
	This method is mainly for debugging purpose. More...
virtual void	computeAllTransitionProbabilities ()
	Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes. More...
virtual void	computeTransitionProbabilitiesForNode (const Node *node)
	Fill the pxy_, dpxy_ and d2pxy_ arrays for one node. More...

Static Protected Member Functions
static void	computeLikelihoodFromArrays (const std::vector< const VVVdouble *> &iLik, const std::vector< const VVVdouble *> &tProb, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)
	Compute conditional likelihoods. More...
static void	computeLikelihoodFromArrays (const std::vector< const VVVdouble *> &iLik, const std::vector< const VVVdouble *> &tProb, const VVVdouble *iLikR, const VVVdouble *tProbR, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)
	Compute conditional likelihoods. More...

Protected Attributes
double	minusLogLik_
SubstitutionModel *	model_
ParameterList	brLenParameters_
std::map< int, VVVdouble >	pxy_
std::map< int, VVVdouble >	dpxy_
std::map< int, VVVdouble >	d2pxy_
std::vector< double >	rootFreqs_
std::vector< Node * >	nodes_
	Pointer toward all nodes in the tree. More...
size_t	nbSites_
size_t	nbDistinctSites_
size_t	nbClasses_
size_t	nbStates_
size_t	nbNodes_
bool	verbose_
double	minimumBrLen_
double	maximumBrLen_
std::auto_ptr< Constraint >	brLenConstraint_
DiscreteDistribution *	rateDistribution_
const SiteContainer *	data_
TreeTemplate< Node > *	tree_
bool	computeFirstOrderDerivatives_
bool	computeSecondOrderDerivatives_
bool	initialized_

Private Member Functions
void	init_ () throw (Exception)
	Method called by constructors. More...

Private Attributes
DRASDRTreeLikelihoodData *	likelihoodData_

Friends
class	DRHomogeneousMixedTreeLikelihood

Detailed Description

This class implements the likelihood computation for a tree using the double-recursive algorithm.

The substitution model is the same over the tree (homogeneous model). A non-uniform distribution of rates among the sites is allowed (ASRV models).

This class uses an instance of the DRASDRTreeLikelihoodData for conditionnal likelihood storage.

All nodes share the same site patterns.

Definition at line 64 of file DRHomogeneousTreeLikelihood.h.

Constructor & Destructor Documentation

DRHomogeneousTreeLikelihood() [1/3]

DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood	(	const Tree &	tree,
		SubstitutionModel *	model,
		DiscreteDistribution *	rDist,
		bool	checkRooted = true,
		bool	verbose = true
	)
throw	(	Exception
	)

Build a new DRHomogeneousTreeLikelihood object without data.

This constructor only initialize the parameters. To compute a likelihood, you will need to call the setData() and the computeTreeLikelihood() methods.

Parameters

tree	The tree to use.
model	The substitution model to use.
rDist	The rate across sites distribution to use.
checkRooted	Tell if we have to check for the tree to be unrooted. If true, any rooted tree will be unrooted before likelihood computation.
verbose	Should I display some info?

Exceptions

Exception

in an error occured.

Definition at line 60 of file DRHomogeneousTreeLikelihood.cpp.

Referenced by clone().

DRHomogeneousTreeLikelihood() [2/3]

DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood	(	const Tree &	tree,
		const SiteContainer &	data,
		SubstitutionModel *	model,
		DiscreteDistribution *	rDist,
		bool	checkRooted = true,
		bool	verbose = true
	)
throw	(	Exception
	)

Build a new DRHomogeneousTreeLikelihood object and compute the corresponding likelihood.

This constructor initializes all parameters, data, and likelihood arrays.

Parameters

tree	The tree to use.
data	Sequences to use.
model	The substitution model to use.
rDist	The rate across sites distribution to use.
checkRooted	Tell if we have to check for the tree to be unrooted. If true, any rooted tree will be unrooted before likelihood computation.
verbose	Should I display some info?

Exceptions

Exception

in an error occured.

Definition at line 76 of file DRHomogeneousTreeLikelihood.cpp.

DRHomogeneousTreeLikelihood() [3/3]

DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood

(

const DRHomogeneousTreeLikelihood &

lik

)

Copy constructor.

Definition at line 103 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRASDRTreeLikelihoodData::clone(), likelihoodData_, minusLogLik_, bpp::DRASDRTreeLikelihoodData::setTree(), and bpp::AbstractTreeLikelihood::tree_.

~DRHomogeneousTreeLikelihood()

DRHomogeneousTreeLikelihood::~DRHomogeneousTreeLikelihood ( )

virtual

Definition at line 128 of file DRHomogeneousTreeLikelihood.cpp.

References likelihoodData_.

Member Function Documentation

applyParameters()

void AbstractHomogeneousTreeLikelihood::applyParameters ( ) throw ( Exception )

virtualinherited

All parameters are stored in a parameter list. This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 286 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::SubstitutionModel::getFrequencies(), bpp::AbstractTreeLikelihood::initialized_, bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_.

Referenced by bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), and bpp::RHomogeneousTreeLikelihood::fireParameterChanged().

clone()

DRHomogeneousTreeLikelihood* bpp::DRHomogeneousTreeLikelihood::clone ( ) const

inlinevirtual

Implements bpp::DRTreeLikelihood.

Reimplemented in bpp::NNIHomogeneousTreeLikelihood.

Definition at line 129 of file DRHomogeneousTreeLikelihood.h.

References DRHomogeneousTreeLikelihood().

computeAllTransitionProbabilities()

void AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities ( )

protectedvirtualinherited

Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 340 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::SubstitutionModel::getFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, and bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_.

Referenced by fireParameterChanged(), and bpp::RHomogeneousTreeLikelihood::fireParameterChanged().

computeLikelihoodAtNode()

virtual void bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode ( int  nodeId, VVVdouble &  likelihoodArray  ) const

inlinevirtual

Compute the likelihood array at a given node.

Parameters

nodeId	The id of the node to consider.
likelihoodArray	The array where to store the results.

Implements bpp::DRTreeLikelihood.

Definition at line 209 of file DRHomogeneousTreeLikelihood.h.

References computeLikelihoodAtNode_(), and bpp::AbstractTreeLikelihood::tree_.

computeLikelihoodAtNode_()

void DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_ ( const Node *  node, VVVdouble &  likelihoodArray, const Node *  sonNode = 0  ) const

protectedvirtual

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 729 of file DRHomogeneousTreeLikelihood.cpp.

References computeLikelihoodFromArrays(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_.

Referenced by computeLikelihoodAtNode(), computeTreeD2LikelihoodAtNode(), and computeTreeDLikelihoodAtNode().

computeLikelihoodFromArrays() [1/2]

void DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays ( const std::vector< const VVVdouble *> &  iLik, const std::vector< const VVVdouble *> &  tProb, VVVdouble &  oLik, size_t  nbNodes, size_t  nbDistinctSites, size_t  nbClasses, size_t  nbStates, bool  reset = true  )

staticprotected

Compute conditional likelihoods.

This method is the "core" likelihood computation function, performing all the product uppon all nodes, the summation for each ancestral state and each rate class. It is designed for inner usage, and a maximum efficiency, so no checking is performed on the input parameters. Use with care!

Parameters

iLik	A vector of likelihood arrays, one for each conditional node.
tProb	A vector of transition probabilities, one for each node.
oLik	The likelihood array to store the computed likelihoods.
nbNodes	The number of nodes = the size of the input vectors.
nbDistinctSites	The number of distinct sites (the first dimension of the likelihood array).
nbClasses	The number of rate classes (the second dimension of the likelihood array).
nbStates	The number of states (the third dimension of the likelihood array).
reset	Tell if the output likelihood array must be initalized prior to computation. If true, the resetLikelihoodArray method will be called.

Definition at line 825 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

Referenced by computeLikelihoodAtNode_(), computeRootLikelihood(), computeSubtreeLikelihoodPostfix(), and computeSubtreeLikelihoodPrefix().

computeLikelihoodFromArrays() [2/2]

void DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays ( const std::vector< const VVVdouble *> &  iLik, const std::vector< const VVVdouble *> &  tProb, const VVVdouble *  iLikR, const VVVdouble *  tProbR, VVVdouble &  oLik, size_t  nbNodes, size_t  nbDistinctSites, size_t  nbClasses, size_t  nbStates, bool  reset = true  )

staticprotected

Compute conditional likelihoods.

This method is the "core" likelihood computation function, performing all the product uppon all nodes, the summation for each ancestral state and each rate class. This function is specific to non-reversible models: the subtree containing the root is specified separately. It is designed for inner usage, and a maximum efficiency, so no checking is performed on the input parameters. Use with care!

Parameters

iLik	A vector of likelihood arrays, one for each conditional node.
tProb	A vector of transition probabilities, one for each node.
iLikR	The likelihood array for the subtree containing the root of the tree.
tProbR	The transition probabilities for thr subtree containing the root of the tree.
oLik	The likelihood array to store the computed likelihoods.
nbNodes	The number of nodes = the size of the input vectors.
nbDistinctSites	The number of distinct sites (the first dimension of the likelihood array).
nbClasses	The number of rate classes (the second dimension of the likelihood array).
nbStates	The number of states (the third dimension of the likelihood array).
reset	Tell if the output likelihood array must be initalized prior to computation. If true, the resetLikelihoodArray method will be called.

Definition at line 874 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

computeRootLikelihood()

void DRHomogeneousTreeLikelihood::computeRootLikelihood ( )

protectedvirtual

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 659 of file DRHomogeneousTreeLikelihood.cpp.

References computeLikelihoodFromArrays(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays(), bpp::Node::getNumberOfSons(), bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray(), bpp::Node::getSon(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(), bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by computeTreeLikelihood().

computeSubtreeLikelihoodPostfix()

void DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix ( const Node *  node )

protectedvirtual

Initialize the arrays corresponding to each son node for the node passed as argument. The method is called for each son node and the result stored in the corresponding array.

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 489 of file DRHomogeneousTreeLikelihood.cpp.

References computeLikelihoodFromArrays(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and resetLikelihoodArrays().

Referenced by computeTreeLikelihood().

computeSubtreeLikelihoodPrefix()

void DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix ( const Node *  node )

protectedvirtual

This method initilize the remaining likelihood arrays, corresponding to father nodes. It must be called after the postfix method because it requires that the arrays for son nodes to be be computed.

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 549 of file DRHomogeneousTreeLikelihood.cpp.

References computeLikelihoodFromArrays(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(), and bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_.

Referenced by computeTreeLikelihood().

computeTransitionProbabilitiesForNode()

void AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode ( const Node *  node )

protectedvirtualinherited

Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 353 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::SubstitutionModel::getd2Pij_dt2(), bpp::Node::getDistanceToFather(), bpp::SubstitutionModel::getdPij_dt(), bpp::Node::getId(), bpp::SubstitutionModel::getPij_t(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), fireParameterChanged(), and bpp::RHomogeneousTreeLikelihood::fireParameterChanged().

computeTreeD2LikelihoodAtNode()

void DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode ( const Node *  node )

protectedvirtual

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 378 of file DRHomogeneousTreeLikelihood.cpp.

References computeLikelihoodAtNode_(), bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::DRASDRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by computeTreeD2Likelihoods().

computeTreeD2Likelihoods()

void DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods ( )

protectedvirtual

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 420 of file DRHomogeneousTreeLikelihood.cpp.

References computeTreeD2LikelihoodAtNode(), bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, and bpp::AbstractHomogeneousTreeLikelihood::nodes_.

Referenced by fireParameterChanged().

computeTreeDLikelihoodAtNode()

void DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode ( const Node *  node )

protectedvirtual

Definition at line 291 of file DRHomogeneousTreeLikelihood.cpp.

References computeLikelihoodAtNode_(), bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::DRASDRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by computeTreeDLikelihoods().

computeTreeDLikelihoods()

void DRHomogeneousTreeLikelihood::computeTreeDLikelihoods ( )

protectedvirtual

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 334 of file DRHomogeneousTreeLikelihood.cpp.

References computeTreeDLikelihoodAtNode(), bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, and bpp::AbstractHomogeneousTreeLikelihood::nodes_.

Referenced by fireParameterChanged().

computeTreeLikelihood()

void DRHomogeneousTreeLikelihood::computeTreeLikelihood

(

)

Definition at line 480 of file DRHomogeneousTreeLikelihood.cpp.

References computeRootLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), and bpp::AbstractTreeLikelihood::tree_.

Referenced by fireParameterChanged().

displayLikelihood()

void DRHomogeneousTreeLikelihood::displayLikelihood ( const Node *  node )

protectedvirtual

This method is mainly for debugging purpose.

Parameters

node	The node at which likelihood values must be displayed.

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 956 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), and likelihoodData_.

displayLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray ( const VVVdouble &  likelihoodArray )

staticinherited

Print the likelihood array to terminal (debugging tool).

Parameters

likelihoodArray

the likelihood array.

Definition at line 287 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

Referenced by displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), and bpp::RNonHomogeneousTreeLikelihood::displayLikelihood().

enableDerivatives() [1/2]

void bpp::AbstractTreeLikelihood::enableDerivatives ( bool  yn )

inlinevirtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

Implements bpp::TreeLikelihood.

Definition at line 292 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood(), and bpp::DistanceEstimation::computeMatrix().

enableDerivatives() [2/2]

virtual void bpp::TreeLikelihood::enableDerivatives ( bool  yn )

pure virtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

Implemented in bpp::AbstractTreeLikelihood.

enableFirstOrderDerivatives() [1/2]

void bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( bool  yn )

inlineinherited

Definition at line 293 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

enableFirstOrderDerivatives() [2/2]

bool bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( ) const

inlineinherited

Definition at line 295 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

enableSecondOrderDerivatives() [1/2]

void bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( bool  yn )

inlineinherited

Definition at line 294 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

enableSecondOrderDerivatives() [2/2]

bool bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( ) const

inlineinherited

Definition at line 296 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

fireParameterChanged()

void DRHomogeneousTreeLikelihood::fireParameterChanged ( const ParameterList &  params )

protectedvirtual

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 241 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihoods(), computeTreeDLikelihoods(), computeTreeLikelihood(), getLogLikelihood(), minusLogLik_, bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by bpp::NNIHomogeneousTreeLikelihood::topologyChangeTested().

getAlphabet() [1/2]

const Alphabet* bpp::AbstractTreeLikelihood::getAlphabet ( ) const

inlinevirtualinherited

Get the alphabet associated to the dataset.

Returns

the alphabet associated to the dataset.

Implements bpp::TreeLikelihood.

Definition at line 285 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

getAlphabet() [2/2]

virtual const Alphabet* bpp::TreeLikelihood::getAlphabet ( ) const

pure virtualinherited

Get the alphabet associated to the dataset.

Returns

the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

getAlphabetStateAsChar()

std::string bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar ( size_t  i ) const

inlinevirtualinherited

Returns

the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihood.

Definition at line 171 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::SubstitutionModel::getAlphabetStateAsChar(), and bpp::AbstractHomogeneousTreeLikelihood::model_.

getAlphabetStateAsInt()

int bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt ( size_t  i ) const

inlinevirtualinherited

Returns

the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihood.

Definition at line 169 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::SubstitutionModel::getAlphabetStateAsInt(), and bpp::AbstractHomogeneousTreeLikelihood::model_.

getAlphabetStates()

const std::vector<int>& bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates ( ) const

inlinevirtualinherited

Returns

the alphabet states corresponding to all model states.

Implements bpp::TreeLikelihood.

Definition at line 167 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::SubstitutionModel::getAlphabetStates(), and bpp::AbstractHomogeneousTreeLikelihood::model_.

getBranchLengthsParameters()

ParameterList AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters ( ) const

virtualinherited

Get the branch lengths parameters.

Returns

A ParameterList with all branch lengths.

Implements bpp::TreeLikelihood.

Definition at line 250 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, and bpp::AbstractTreeLikelihood::initialized_.

getData() [1/2]

virtual const SiteContainer* bpp::TreeLikelihood::getData ( ) const

pure virtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns

A pointer toward the site container where the sequences are stored.

Implemented in bpp::AbstractTreeLikelihood.

getData() [2/2]

const SiteContainer* bpp::AbstractTreeLikelihood::getData ( ) const

inlinevirtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns

A pointer toward the site container where the sequences are stored.

Implements bpp::TreeLikelihood.

Definition at line 284 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::init().

getDerivableParameters() [1/2]

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters ( ) const

virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns

A ParameterList.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 73 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getDerivableParameters() [2/2]

virtual ParameterList bpp::TreeLikelihood::getDerivableParameters ( ) const

pure virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns

A ParameterList.

Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

getFirstOrderDerivative()

double DRHomogeneousTreeLikelihood::getFirstOrderDerivative	(	const std::string &	variable	)	const
throw	(	Exception
	)

Definition at line 344 of file DRHomogeneousTreeLikelihood.cpp.

getLikelihood()

double DRHomogeneousTreeLikelihood::getLikelihood ( ) const

virtual

Get the likelihood for the whole dataset.

Returns

The likelihood of the dataset.

Implements bpp::TreeLikelihood.

Definition at line 158 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::AbstractTreeLikelihoodData::getWeights(), likelihoodData_, and bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_.

getLikelihoodData() [1/2]

DRASDRTreeLikelihoodData* bpp::DRHomogeneousTreeLikelihood::getLikelihoodData ( )

inlinevirtual

Returns

The underlying likelihood data structure.

Implements bpp::DRTreeLikelihood.

Definition at line 206 of file DRHomogeneousTreeLikelihood.h.

References likelihoodData_.

Referenced by bpp::NNIHomogeneousTreeLikelihood::setData(), and bpp::NNIHomogeneousTreeLikelihood::topologyChangeTested().

getLikelihoodData() [2/2]

const DRASDRTreeLikelihoodData* bpp::DRHomogeneousTreeLikelihood::getLikelihoodData ( ) const

inlinevirtual

Returns

The underlying likelihood data structure.

Implements bpp::DRTreeLikelihood.

Definition at line 207 of file DRHomogeneousTreeLikelihood.h.

References likelihoodData_.

getLikelihoodForASite()

double DRHomogeneousTreeLikelihood::getLikelihoodForASite ( size_t  site ) const

virtual

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns

The likelihood for site site.

Implements bpp::TreeLikelihood.

Definition at line 192 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), and likelihoodData_.

getLikelihoodForASiteForARateClass()

double DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass ( size_t  site, size_t  rateClass  ) const

virtual

Get the likelihood for a site knowing its rate class.

Parameters

site	The site index.
rateClass	The rate class index.

Returns

The likelihood for the specified site and rate class.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 205 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray(), and likelihoodData_.

getLikelihoodForASiteForARateClassForAState()

double DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState ( size_t  site, size_t  rateClass, int  state  ) const

virtual

Get the likelihood for a site knowing its rate class and its ancestral state.

Parameters

site	The site index.
rateClass	The rate class index.
state	The ancestral state.

Returns

The likelihood for the specified site and rate class and ancestral state.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 219 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray(), and likelihoodData_.

getLikelihoodForASiteForAState() [1/2]

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState ( size_t  site, int  state  ) const

virtualinherited

Get the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The likelihood for site site and state state.

Implements bpp::TreeLikelihood.

Definition at line 111 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLikelihoodForASiteForAState() [2/2]

virtual double bpp::TreeLikelihood::getLikelihoodForASiteForAState ( size_t  site, int  state  ) const

pure virtualinherited

Get the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState().

getLikelihoodForEachSite() [1/2]

virtual Vdouble bpp::TreeLikelihood::getLikelihoodForEachSite ( ) const

pure virtualinherited

Get the likelihood for each site.

Returns

A vector with all likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

getLikelihoodForEachSite() [2/2]

Vdouble AbstractTreeLikelihood::getLikelihoodForEachSite ( ) const

virtualinherited

Get the likelihood for each site.

Returns

A vector with all likelihoods for each site.

Implements bpp::TreeLikelihood.

Definition at line 46 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihood::getLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

getLikelihoodForEachSiteForEachRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClass ( ) const

virtualinherited

Get the likelihood for each site and each rate class.

Returns

A two-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 93 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLikelihoodForEachSiteForEachRateClassForEachState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClassForEachState ( ) const

virtualinherited

Get the likelihood for each site and each rate class and each state.

Returns

A three-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 156 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLikelihoodForEachSiteForEachState() [1/2]

virtual VVdouble bpp::TreeLikelihood::getLikelihoodForEachSiteForEachState ( ) const

pure virtualinherited

Get the likelihood for each site and for each state.

Returns

A 2d vector with all likelihoods for each site and for each state.

Implemented in bpp::AbstractTreeLikelihood.

getLikelihoodForEachSiteForEachState() [2/2]

VVdouble AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState ( ) const

virtualinherited

Get the likelihood for each site and for each state.

Returns

A 2d vector with all likelihoods for each site and for each state.

Implements bpp::TreeLikelihood.

Definition at line 64 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihood::getLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().

getLogLikelihood()

double DRHomogeneousTreeLikelihood::getLogLikelihood ( ) const

virtual

Get the logarithm of the likelihood for the whole dataset.

Returns

The logarithm of the likelihood of the dataset.

Implements bpp::TreeLikelihood.

Definition at line 172 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::AbstractTreeLikelihoodData::getWeights(), likelihoodData_, and bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_.

Referenced by fireParameterChanged().

getLogLikelihoodForASite()

double DRHomogeneousTreeLikelihood::getLogLikelihoodForASite ( size_t  site ) const

virtual

Get the logarithm of the likelihood for a site.

Parameters

site	The site index to analyse.

Returns

The logarithm of the likelihood for site site.

Implements bpp::TreeLikelihood.

Definition at line 199 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), and likelihoodData_.

getLogLikelihoodForASiteForARateClass()

double DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass ( size_t  site, size_t  rateClass  ) const

virtual

Get the logarithm of the likelihood for a site knowing its rate class.

Parameters

site	The site index.
rateClass	The rate class index.

Returns

The logarithm of the likelihood for the specified site and rate class.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 212 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray(), and likelihoodData_.

getLogLikelihoodForASiteForARateClassForAState()

double DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState ( size_t  site, size_t  rateClass, int  state  ) const

virtual

Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state.

Parameters

site	The site index.
rateClass	The rate class index.
state	The ancestral state.

Returns

The logarithm of the likelihood for the specified site and rate class and ancestral state..

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 226 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray(), and likelihoodData_.

getLogLikelihoodForASiteForAState() [1/2]

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState ( size_t  site, int  state  ) const

virtualinherited

Get the logarithm of the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The logarithm of the likelihood for site site and state state.

Implements bpp::TreeLikelihood.

Definition at line 124 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLogLikelihoodForASiteForAState() [2/2]

virtual double bpp::TreeLikelihood::getLogLikelihoodForASiteForAState ( size_t  site, int  state  ) const

pure virtualinherited

Get the logarithm of the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The logarithm of the likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState().

getLogLikelihoodForEachSite() [1/2]

virtual Vdouble bpp::TreeLikelihood::getLogLikelihoodForEachSite ( ) const

pure virtualinherited

Get the logarithm of the likelihood for each site.

Returns

A vector with all log likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

getLogLikelihoodForEachSite() [2/2]

Vdouble AbstractTreeLikelihood::getLogLikelihoodForEachSite ( ) const

virtualinherited

Get the logarithm of the likelihood for each site.

Returns

A vector with all log likelihoods for each site.

Implements bpp::TreeLikelihood.

Definition at line 55 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

getLogLikelihoodForEachSiteForEachRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClass ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and each rate class.

Returns

A two-dimension vector with all log likelihoods: V[i][j] = likelihood of site i and rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 138 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLogLikelihoodForEachSiteForEachRateClassForEachState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClassForEachState ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and each rate class and each state.

Returns

A three-dimension vector with all log likelihoods: V[i][j][k} = likelihood of site i and rate class j and state k.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 179 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLogLikelihoodForEachSiteForEachState() [1/2]

virtual VVdouble bpp::TreeLikelihood::getLogLikelihoodForEachSiteForEachState ( ) const

pure virtualinherited

Get the logarithm of the likelihood for each site and for each state.

Returns

A 2d vector with all log likelihoods for each site and for each state.

Implemented in bpp::AbstractTreeLikelihood.

getLogLikelihoodForEachSiteForEachState() [2/2]

VVdouble AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and for each state.

Returns

A 2d vector with all log likelihoods for each site and for each state.

Implements bpp::TreeLikelihood.

Definition at line 81 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihood::getLogLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().

getMaximumBranchLength()

virtual double bpp::AbstractHomogeneousTreeLikelihood::getMaximumBranchLength ( ) const

inlinevirtualinherited

Definition at line 254 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_.

getMinimumBranchLength()

virtual double bpp::AbstractHomogeneousTreeLikelihood::getMinimumBranchLength ( ) const

inlinevirtualinherited

Definition at line 253 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_.

getNewBranchModelIterator()

ConstBranchModelIterator* bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator ( int  nodeId ) const

inlinevirtualinherited

Implements bpp::TreeLikelihood.

Definition at line 188 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_.

getNewSiteModelIterator()

ConstSiteModelIterator* bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator ( size_t  siteIndex ) const

inlinevirtualinherited

Implements bpp::TreeLikelihood.

Definition at line 193 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractTreeLikelihood::tree_.

getNonDerivableParameters() [1/2]

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters ( ) const

virtualinherited

All non derivable parameters.

Usually, this contains all substitution model parameters and rate distribution.

Returns

A ParameterList.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 82 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getNonDerivableParameters() [2/2]

virtual ParameterList bpp::TreeLikelihood::getNonDerivableParameters ( ) const

pure virtualinherited

All non derivable parameters.

Usually, this contains all substitution model parameters and rate distribution.

Returns

A ParameterList.

Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

getNumberOfClasses()

size_t bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses ( ) const

inlinevirtualinherited

Get the number of classes.

Returns

The Number of classes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 108 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getNumberOfSites() [1/2]

size_t bpp::AbstractTreeLikelihood::getNumberOfSites ( ) const

inlinevirtualinherited

Get the number of sites in the dataset.

Returns

the number of sites in the dataset.

Implements bpp::TreeLikelihood.

Definition at line 290 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSite(), bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState(), bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSite(), and bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState().

getNumberOfSites() [2/2]

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

pure virtualinherited

Get the number of sites in the dataset.

Returns

the number of sites in the dataset.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::SubstitutionMappingTools::getNormalizationsPerBranch().

getNumberOfStates()

size_t bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates ( ) const

inlinevirtualinherited

Returns

the number of model states of the underlying Markov chain.

Implements bpp::TreeLikelihood.

Definition at line 165 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::SubstitutionModel::getNumberOfStates(), and bpp::AbstractHomogeneousTreeLikelihood::model_.

getPosteriorProbabilitiesOfEachRate()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate ( ) const

virtualinherited

Get the posterior probability for each site of belonging to a particular rate class.

Returns

A two-dimension vector with all posterior probabilities: V[i][j] = probablity for site i of belonging to rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 202 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getPosteriorRateOfEachSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRateOfEachSite ( ) const

virtualinherited

Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.

Returns

A vector with all rates.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 220 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getRateClassWithMaxPostProbOfEachSite()

vector< size_t > AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbOfEachSite ( ) const

virtualinherited

Get the posterior rate class (the one with maximum posterior probability) for each site.

Returns

A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 239 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getRateDistribution() [1/2]

const DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( ) const

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns

A const pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 106 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getRateDistribution() [2/2]

DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( )

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns

A pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 107 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getRateDistributionParameters()

ParameterList bpp::AbstractHomogeneousTreeLikelihood::getRateDistributionParameters ( ) const

inlinevirtualinherited

Get the parameters associated to the rate distirbution.

Returns

A ParameterList object with all rate distribution parameters.

Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 179 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters().

getRateWithMaxPostProbOfEachSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbOfEachSite ( ) const

virtualinherited

Get the posterior rate (the one with maximum posterior probability) for each site.

Returns

A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 253 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getRootFrequencies()

const std::vector<double>& bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies ( size_t  siteIndex ) const

inlinevirtualinherited

Get the values of the frequencies for each state in the alphabet at the root node.

For reversible models, these are the equilibrium frequencies. For non-reversible models, these usually are distinct parameters.

For models without site partitioning, the set of frequencies is the same for all positions. For partition models, the frequencies may differ from one site to another.

Parameters

siteIndex

The index of the alignment position.

See also

getSiteIndex

Returns

A vector with ancestral frequencies for each state in the alphabet;

Implements bpp::TreeLikelihood.

Definition at line 184 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::SubstitutionModel::getFrequencies(), and bpp::AbstractHomogeneousTreeLikelihood::model_.

getSecondOrderDerivative() [1/2]

double DRHomogeneousTreeLikelihood::getSecondOrderDerivative	(	const std::string &	variable	)	const
throw	(	Exception
	)

Definition at line 430 of file DRHomogeneousTreeLikelihood.cpp.

getSecondOrderDerivative() [2/2]

double bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative ( const std::string &  variable1, const std::string &  variable2  ) const throw ( Exception )

inline

Definition at line 201 of file DRHomogeneousTreeLikelihood.h.

getSiteIndex()

size_t bpp::DRHomogeneousTreeLikelihood::getSiteIndex ( size_t  site ) const throw ( IndexOutOfBoundsException )

inlinevirtual

Get the index (used for inner computations) of a given site (original alignment column).

Parameters

site	An alignment position.

Returns

The site index corresponding to the given input alignment position.

Implements bpp::TreeLikelihood.

Definition at line 152 of file DRHomogeneousTreeLikelihood.h.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), and likelihoodData_.

getSubstitutionModel() [1/4]

const SubstitutionModel* bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( ) const

inlinevirtualinherited

Returns

The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 207 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getSubstitutionModel() [2/4]

const SubstitutionModel* bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( int  nodeId, size_t  siteIndex  ) const throw ( NodeNotFoundException )

inlinevirtualinherited

Get the substitution model associated to a given node and alignment column.

Parameters

nodeId	The id of the request node.
siteIndex	The index of the alignment position.

See also

getSiteIndex

Returns

A pointer toward the corresponding model.

Exceptions

NodeNotFoundException

This exception may be thrown if the node is not found (depending on the implementation).

Implements bpp::TreeLikelihood.

Definition at line 208 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getSubstitutionModel() [3/4]

SubstitutionModel* bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( )

inlinevirtualinherited

Returns

The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 210 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getSubstitutionModel() [4/4]

SubstitutionModel* bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( int  nodeId, size_t  siteIndex  ) throw ( NodeNotFoundException )

inlinevirtualinherited

Get the substitution model associated to a given node and alignment column.

Parameters

nodeId	The id of the request node.
siteIndex	The index of the alignment position.

See also

getSiteIndex

Returns

A pointer toward the corresponding model.

Exceptions

NodeNotFoundException

This exception may be thrown if the node is not found (depending on the implementation).

Implements bpp::TreeLikelihood.

Definition at line 211 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getSubstitutionModelParameters()

ParameterList AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters ( ) const

virtualinherited

Get the parameters associated to substitution model(s).

Returns

A ParameterList.

Implements bpp::TreeLikelihood.

Definition at line 259 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractHomogeneousTreeLikelihood::model_.

getTransitionProbabilities() [1/2]

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities ( int  nodeId, size_t  siteIndex  ) const

virtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node and site.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The index of the alignment position.

See also

getSiteIndex

Returns

An array of dimension 2, where a[x][y] is the probability of substituting from x to y.

Implements bpp::TreeLikelihood.

Definition at line 311 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getTransitionProbabilities() [2/2]

virtual VVdouble bpp::TreeLikelihood::getTransitionProbabilities ( int  nodeId, size_t  siteIndex  ) const

pure virtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node and site.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The index of the alignment position.

See also

getSiteIndex

Returns

An array of dimension 2, where a[x][y] is the probability of substituting from x to y.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

getTransitionProbabilitiesPerRateClass()

VVVdouble bpp::AbstractHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass ( int  nodeId, size_t  siteIndex  ) const

inlinevirtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The position in the alignment.

Returns

An array of dimension 3, where a[c][x][y] is the probability of substituting from x to y while being in rate class c.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 186 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::pxy_.

getTree() [1/2]

const Tree& bpp::AbstractTreeLikelihood::getTree ( ) const

inlinevirtualinherited

Get the tree (topology and branch lengths).

Returns

The tree of this TreeLikelihood object.

Implements bpp::TreeLikelihood.

Definition at line 291 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::NNIHomogeneousTreeLikelihood::getTopology(), and bpp::RNonHomogeneousMixedTreeLikelihood::init().

getTree() [2/2]

virtual const Tree& bpp::TreeLikelihood::getTree ( ) const

pure virtualinherited

Get the tree (topology and branch lengths).

Returns

The tree of this TreeLikelihood object.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::GlobalClockTreeLikelihoodFunctionWrapper::fireParameterChanged(), bpp::SubstitutionMappingTools::getNormalizedCountsPerBranch(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_().

getValue()

double DRHomogeneousTreeLikelihood::getValue	(		)	const
throw	(	Exception
	)

Function and NNISearchable interface.

Definition at line 280 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::isInitialized(), and minusLogLik_.

Referenced by bpp::NNIHomogeneousTreeLikelihood::getTopologyValue().

init_()

void DRHomogeneousTreeLikelihood::init_ ( ) throw ( Exception )

private

Method called by constructors.

Definition at line 94 of file DRHomogeneousTreeLikelihood.cpp.

initBranchLengthsParameters()

void AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters ( )

virtualinherited

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 307 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, and bpp::AbstractHomogeneousTreeLikelihood::nodes_.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().

initialize()

void AbstractHomogeneousTreeLikelihood::initialize ( ) throw ( Exception )

virtualinherited

Init the likelihood object.

This method is used to initialize all parameters. It is typically called after the constructor and the setData method. It contains virtual methods that can't be called in the constructor.

Exceptions

Exception

if something bad happened, for instance if no data are associated to the likelihood function.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 237 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::data_, bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractHomogeneousTreeLikelihood::initParameters().

Referenced by bpp::OptimizationTools::buildDistanceTree(), bpp::RHomogeneousMixedTreeLikelihood::initialize(), and bpp::DRHomogeneousMixedTreeLikelihood::initialize().

initParameters()

void AbstractHomogeneousTreeLikelihood::initParameters ( )

virtualinherited

This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree.

Definition at line 268 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::initialize().

isInitialized() [1/2]

virtual bool bpp::TreeLikelihood::isInitialized ( ) const

pure virtualinherited

Returns

'true' is the likelihood function has been initialized.

Implemented in bpp::AbstractTreeLikelihood.

isInitialized() [2/2]

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const

inlinevirtualinherited

Returns

'true' is the likelihood function has been initialized.

Implements bpp::TreeLikelihood.

Definition at line 297 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::initialized_.

Referenced by getValue(), bpp::DRNonHomogeneousTreeLikelihood::getValue(), bpp::RHomogeneousTreeLikelihood::getValue(), and bpp::RNonHomogeneousTreeLikelihood::getValue().

operator=()

DRHomogeneousTreeLikelihood & DRHomogeneousTreeLikelihood::operator=

(

const DRHomogeneousTreeLikelihood &

lik

)

Definition at line 115 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRASDRTreeLikelihoodData::clone(), likelihoodData_, minusLogLik_, bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::DRASDRTreeLikelihoodData::setTree(), and bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::operator=(), and bpp::NNIHomogeneousTreeLikelihood::operator=().

resetLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray ( VVVdouble &  likelihoodArray )

staticinherited

Set all conditional likelihoods to 1.

Parameters

likelihoodArray

the likelihood array.

Definition at line 267 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

Referenced by computeLikelihoodFromArrays(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), resetLikelihoodArrays(), and bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays().

resetLikelihoodArrays()

void DRHomogeneousTreeLikelihood::resetLikelihoodArrays ( const Node *  node )

protectedvirtual

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 464 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), likelihoodData_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

Referenced by computeSubtreeLikelihoodPostfix().

setData()

void DRHomogeneousTreeLikelihood::setData ( const SiteContainer &  sites ) throw ( Exception )

virtual

Set the dataset for which the likelihood must be evaluated.

Parameters

sites

The data set to use.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::NNIHomogeneousTreeLikelihood.

Definition at line 135 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::PatternTools::getSequenceSubset().

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::setData(), and bpp::NNIHomogeneousTreeLikelihood::setData().

setMaximumBranchLength()

virtual void bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength ( double  maximum ) throw ( Exception )

inlinevirtualinherited

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 243 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, and bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_.

setMinimumBranchLength()

virtual void bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength ( double  minimum ) throw ( Exception )

inlinevirtualinherited

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 233 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, and bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_.

setParameters()

void DRHomogeneousTreeLikelihood::setParameters	(	const ParameterList &	parameters	)
throw	(	ParameterNotFoundException,
		ConstraintException
	)

Implements the Function interface.

Update the parameter list and call the fireParameterChanged() method.

If a subset of the whole parameter list is passed to the function, only these parameters are updated and the other remain constant (i.e. equal to their last value).

Parameters

parameters

The parameter list to pass to the function.

Definition at line 233 of file DRHomogeneousTreeLikelihood.cpp.

setSubstitutionModel()

void AbstractHomogeneousTreeLikelihood::setSubstitutionModel ( SubstitutionModel *  model ) throw ( Exception )

virtualinherited

Returns

Set the substitution model for this instance.

Exceptions

Exception

If the model could not be set (for instance, because of a wrong alphabet type).

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 172 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId().

Friends And Related Function Documentation

DRHomogeneousMixedTreeLikelihood

friend class DRHomogeneousMixedTreeLikelihood

friend

Definition at line 306 of file DRHomogeneousTreeLikelihood.h.

Member Data Documentation

brLenConstraint_

std::auto_ptr<Constraint> bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_

protectedinherited

Definition at line 118 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().

brLenParameters_

ParameterList bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_

protectedinherited

Definition at line 89 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

computeFirstOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_

protectedinherited

Definition at line 227 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().

computeSecondOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_

protectedinherited

Definition at line 228 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().

d2pxy_

std::map<int, VVVdouble> bpp::AbstractHomogeneousTreeLikelihood::d2pxy_

mutableprotectedinherited

Definition at line 95 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2LikelihoodAtNode(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

data_

const SiteContainer* bpp::AbstractTreeLikelihood::data_

protectedinherited

Definition at line 225 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::AbstractTreeLikelihood::getAlphabet(), bpp::AbstractTreeLikelihood::getData(), bpp::AbstractTreeLikelihood::getNumberOfSites(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::operator=(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().

dpxy_

std::map<int, VVVdouble> bpp::AbstractHomogeneousTreeLikelihood::dpxy_

mutableprotectedinherited

Definition at line 93 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoodAtNode(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

initialized_

bool bpp::AbstractTreeLikelihood::initialized_

protectedinherited

Definition at line 229 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::TwoTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::TwoTreeLikelihood::initialize(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::isInitialized(), and bpp::AbstractTreeLikelihood::operator=().

likelihoodData_

DRASDRTreeLikelihoodData* bpp::DRHomogeneousTreeLikelihood::likelihoodData_

mutableprivate

Definition at line 69 of file DRHomogeneousTreeLikelihood.h.

Referenced by computeLikelihoodAtNode_(), computeRootLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), computeTreeD2LikelihoodAtNode(), computeTreeDLikelihoodAtNode(), displayLikelihood(), DRHomogeneousTreeLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::getLikelihood(), getLikelihood(), getLikelihoodData(), getLikelihoodForASite(), getLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClassForAState(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood(), getLogLikelihood(), getLogLikelihoodForASite(), getLogLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClassForAState(), getSiteIndex(), operator=(), resetLikelihoodArrays(), and ~DRHomogeneousTreeLikelihood().

maximumBrLen_

double bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_

protectedinherited

Definition at line 117 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::getMaximumBranchLength(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().

minimumBrLen_

double bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_

protectedinherited

Definition at line 116 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::getMinimumBranchLength(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().

minusLogLik_

double bpp::DRHomogeneousTreeLikelihood::minusLogLik_

protected

Definition at line 72 of file DRHomogeneousTreeLikelihood.h.

Referenced by DRHomogeneousTreeLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), getValue(), and operator=().

model_

SubstitutionModel* bpp::AbstractHomogeneousTreeLikelihood::model_

protectedinherited

Definition at line 88 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates(), bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

nbClasses_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbClasses_

protectedinherited

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_(), computeLikelihoodAtNode_(), computeRootLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2LikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

nbDistinctSites_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_

protectedinherited

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_(), computeLikelihoodAtNode_(), computeRootLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), computeTreeD2LikelihoodAtNode(), computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousMixedTreeLikelihood::getLikelihood(), getLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood(), getLogLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

nbNodes_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbNodes_

protectedinherited

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), computeTreeD2Likelihoods(), computeTreeDLikelihoods(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

nbSites_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbSites_

protectedinherited

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihood(), bpp::RHomogeneousTreeLikelihood::getDLogLikelihood(), bpp::RHomogeneousTreeLikelihood::getLikelihood(), bpp::RHomogeneousTreeLikelihood::getLogLikelihood(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

nbStates_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbStates_

protectedinherited

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_(), computeLikelihoodAtNode_(), computeRootLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2LikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

nodes_

std::vector<Node*> bpp::AbstractHomogeneousTreeLikelihood::nodes_

protectedinherited

Pointer toward all nodes in the tree.

The position in the array is the number used in the parameter name. This may be different from the node id, unless you used the resetNodeId method on the input tree.

Definition at line 105 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2Likelihoods(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoods(), fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

pxy_

std::map<int, VVVdouble> bpp::AbstractHomogeneousTreeLikelihood::pxy_

mutableprotectedinherited

Definition at line 91 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), computeLikelihoodAtNode_(), computeRootLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

rateDistribution_

DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_

protectedinherited

Definition at line 61 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::applyParameters(), computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::TwoTreeLikelihood::initParameters(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=().

rootFreqs_

std::vector<double> bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_

protectedinherited

Definition at line 97 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), computeLikelihoodAtNode_(), computeRootLikelihood(), computeSubtreeLikelihoodPrefix(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

tree_

TreeTemplate<Node>* bpp::AbstractTreeLikelihood::tree_

mutableprotectedinherited

Definition at line 226 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), computeLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode(), computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), computeTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood(), DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractTreeLikelihood::getTree(), operator=(), bpp::DRNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::operator=(), bpp::RNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().

verbose_

bool bpp::AbstractHomogeneousTreeLikelihood::verbose_

protectedinherited

Definition at line 114 of file AbstractHomogeneousTreeLikelihood.h.

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

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

• Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h
• Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp