bpp-phyl  2.4.0
bpp::AbstractHomogeneousTreeLikelihood Class Referenceabstract

Partial implementation for homogeneous model of the TreeLikelihood interface. More...

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

+ Inheritance diagram for bpp::AbstractHomogeneousTreeLikelihood:
+ Collaboration diagram for bpp::AbstractHomogeneousTreeLikelihood:

Classes

class  ConstHomogeneousSiteModelIterator
 

Public Member Functions

 AbstractHomogeneousTreeLikelihood (const Tree &tree, TransitionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true)
 
 AbstractHomogeneousTreeLikelihood (const AbstractHomogeneousTreeLikelihood &lik)
 Copy constructor. More...
 
AbstractHomogeneousTreeLikelihoodoperator= (const AbstractHomogeneousTreeLikelihood &lik)
 Assignation operator. More...
 
virtual ~AbstractHomogeneousTreeLikelihood ()
 
virtual const SubstitutionModelgetSubstitutionModel () const
 Get a SubstitutionModel pointer toward the model associated to this instance, if possible. More...
 
virtual const SubstitutionModelgetSubstitutionModel (int nodeId, size_t siteIndex) const
 Get a SubstitutionModel pointer toward the model associated to this instance, if possible. 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 ()
 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 (bool verbose=true)
 
virtual void setMinimumBranchLength (double minimum)
 
virtual void setMaximumBranchLength (double maximum)
 
virtual double getMinimumBranchLength () const
 
virtual double getMaximumBranchLength () const
 
HomogeneousTreeLikelihoodclone () const =0
 
const TransitionModelgetModelForSite (int nodeId, size_t siteIndex) const
 Get the substitution model associated to a given node and alignment column. More...
 
TransitionModelgetModelForSite (int nodeId, size_t siteIndex)
 Get the substitution model associated to a given node and alignment column. More...
 
virtual void setData (const SiteContainer &sites)=0
 Set the dataset for which the likelihood must be evaluated. More...
 
virtual const SiteContainergetData () const =0
 Get the dataset for which the likelihood must be evaluated. More...
 
virtual bool isInitialized () const =0
 
virtual TreeLikelihoodDatagetLikelihoodData ()=0
 
virtual const TreeLikelihoodDatagetLikelihoodData () const =0
 
virtual double getLikelihoodForASite (size_t site) const =0
 Get the likelihood for a site. More...
 
virtual double getLogLikelihoodForASite (size_t site) const =0
 Get the logarithm of the likelihood for a site. More...
 
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 double getLikelihood () const =0
 Get the likelihood for the whole dataset. More...
 
virtual double getLogLikelihood () const =0
 Get the logarithm of the likelihood for the whole dataset. More...
 
virtual const TreegetTree () 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 AlphabetgetAlphabet () 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...
 
virtual void enableSecondOrderDerivatives (bool yn)=0
 
virtual bool enableSecondOrderDerivatives () const =0
 
virtual double getSecondOrderDerivative (const std::string &variable) const =0
 
virtual double getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const =0
 
virtual double d2f (const std::string &variable, const ParameterList &parameters)
 
virtual double d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters)
 
virtual void enableFirstOrderDerivatives (bool yn)=0
 
virtual bool enableFirstOrderDerivatives () const =0
 
virtual double getFirstOrderDerivative (const std::string &variable) const =0
 
virtual double df (const std::string &variable, const ParameterList &parameters)
 
virtual void setParameters (const ParameterList &parameters)=0
 
virtual double getValue () const =0
 
virtual double f (const ParameterList &parameters)
 
virtual bool hasParameter (const std::string &name) const =0
 
virtual const ParameterListgetParameters () const =0
 
virtual const ParametergetParameter (const std::string &name) const =0
 
virtual double getParameterValue (const std::string &name) const =0
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
virtual void setParameterValue (const std::string &name, double value)=0
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
virtual size_t getNumberOfParameters () const =0
 
virtual void setNamespace (const std::string &prefix)=0
 
virtual std::string getNamespace () const =0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
 
virtual Clonableclone () const =0
 
bool hasParameter (const std::string &name) const
 
const ParameterListgetParameters () const
 
const ParametergetParameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const
 
void setAllParametersValues (const ParameterList &parameters)
 
void setParameterValue (const std::string &name, double value)
 
void setParametersValues (const ParameterList &parameters)
 
bool matchParametersValues (const ParameterList &parameters)
 
size_t getNumberOfParameters () const
 
void setNamespace (const std::string &prefix)
 
std::string getNamespace () const
 
std::string getParameterNameWithoutNamespace (const std::string &name) const
 
const std::shared_ptr< Parameter > & getSharedParameter (const std::string &name) const
 
virtual void fireParameterChanged (const ParameterList &parameters)
 
virtual double getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
 Get the likelihood for a site knowing its rate class. More...
 
virtual double getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
 Get the logarithm of the likelihood for a site knowing its rate class. More...
 
virtual double getLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
 Get the likelihood for a site knowing its rate class and its ancestral state. More...
 
virtual double getLogLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
 Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state. More...
 
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 ()
 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...
 
ConstBranchModelIteratorgetNewBranchModelIterator (int nodeId) const
 
ConstSiteModelIteratorgetNewSiteModelIterator (size_t siteIndex) const
 
The HomogeneousTreeLikelihood interface.

Other methods are implemented in the AbstractTreeLikelihood class.

const TransitionModelgetModel () const
 
const TransitionModelgetModel (int nodeId, size_t siteIndex) const
 
TransitionModelgetModel ()
 
TransitionModelgetModel (int nodeId, size_t siteIndex)
 
void setModel (TransitionModel *model)
 
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...
 
virtual size_t getSiteIndex (size_t site) const =0
 Get the index (used for inner computations) of a given site (original alignment column). More...
 
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...
 
ParameterList getDerivableParameters () const
 All derivable parameters. More...
 
ParameterList getNonDerivableParameters () const
 All non derivable parameters. 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...
 
The DiscreteRatesAcrossSites interface implementation:
const DiscreteDistributiongetRateDistribution () const
 Get the rate distribution used for the computation. More...
 
DiscreteDistributiongetRateDistribution ()
 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...
 
The TreeLikelihood interface.
const SiteContainergetData () const
 Get the dataset for which the likelihood must be evaluated. More...
 
const AlphabetgetAlphabet () const
 Get the alphabet associated to the dataset. More...
 
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...
 
size_t getNumberOfSites () const
 Get the number of sites in the dataset. More...
 
const TreegetTree () const
 Get the tree (topology and branch lengths). 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
 
bool isInitialized () const
 

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 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...
 
const std::shared_ptr< Parameter > & getSharedParameter (size_t i) const
 
std::shared_ptr< Parameter > & getSharedParameter (size_t i)
 
virtual void addParameter_ (Parameter *parameter)
 
virtual void addParameters_ (const ParameterList &parameters)
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
virtual void includeParameters_ (const ParameterList &parameters)
 
virtual void deleteParameter_ (size_t index)
 
virtual void deleteParameter_ (std::string &name)
 
virtual void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
ParametergetParameter_ (const std::string &name)
 
ParametergetParameter_ (size_t index)
 
const ParametergetParameter_ (size_t index) const
 
ParametergetParameterWithNamespace_ (const std::string &name)
 
const ParametergetParameterWithNamespace_ (const std::string &name) const
 
ParameterListgetParameters_ ()
 

Protected Attributes

TransitionModelmodel_
 
ParameterList brLenParameters_
 
std::map< int, VVVdoublepxy_
 
std::map< int, VVVdoubledpxy_
 
std::map< int, VVVdoubled2pxy_
 
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::unique_ptr< ConstraintbrLenConstraint_
 
DiscreteDistributionrateDistribution_
 
const SiteContainerdata_
 
TreeTemplate< Node > * tree_
 
bool computeFirstOrderDerivatives_
 
bool computeSecondOrderDerivatives_
 
bool initialized_
 

Private Member Functions

void init_ (const Tree &tree, TransitionModel *model, DiscreteDistribution *rDist, bool checkRooted, bool verbose)
 Method called by constructor. More...
 

Detailed Description

Partial implementation for homogeneous model of the TreeLikelihood interface.

This class provides a pointer toward a single substitution model + several utilitary variables.

Definition at line 56 of file AbstractHomogeneousTreeLikelihood.h.

Constructor & Destructor Documentation

AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood ( const Tree tree,
TransitionModel model,
DiscreteDistribution rDist,
bool  checkRooted = true,
bool  verbose = true 
)

Definition at line 59 of file AbstractHomogeneousTreeLikelihood.cpp.

References init_().

AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood ( const AbstractHomogeneousTreeLikelihood lik)

Copy constructor.

This constructor is to be called by the derived class copy constructor.

Definition at line 88 of file AbstractHomogeneousTreeLikelihood.cpp.

References nodes_, and bpp::AbstractTreeLikelihood::tree_.

virtual bpp::AbstractHomogeneousTreeLikelihood::~AbstractHomogeneousTreeLikelihood ( )
inlinevirtual

Definition at line 140 of file AbstractHomogeneousTreeLikelihood.h.

References init_().

Member Function Documentation

void AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities ( )
protectedvirtual
void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray ( const VVVdouble likelihoodArray)
staticinherited
void bpp::AbstractTreeLikelihood::enableDerivatives ( bool  yn)
inlinevirtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters
ynYes or no.

Implements bpp::TreeLikelihood.

Definition at line 296 of file AbstractTreeLikelihood.h.

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

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

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters
ynYes or no.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::TreeLikelihood::~TreeLikelihood().

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

Implements bpp::DerivableSecondOrder.

Definition at line 297 of file AbstractTreeLikelihood.h.

bool bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( ) const
inlinevirtualinherited
void bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( bool  yn)
inlinevirtualinherited

Implements bpp::DerivableSecondOrder.

Definition at line 298 of file AbstractTreeLikelihood.h.

bool bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( ) const
inlinevirtualinherited
const Alphabet* bpp::AbstractTreeLikelihood::getAlphabet ( ) const
inlinevirtualinherited
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.

Referenced by bpp::TreeLikelihood::~TreeLikelihood().

std::string bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar ( size_t  i) const
inlinevirtual
Returns
the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihood.

Definition at line 166 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::TransitionModel::getAlphabetStateAsChar(), getBranchLengthsParameters(), getSubstitutionModelParameters(), and initialize().

int bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt ( size_t  i) const
inlinevirtual
Returns
the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihood.

Definition at line 164 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::TransitionModel::getAlphabetStateAsInt().

const std::vector<int>& bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates ( ) const
inlinevirtual
Returns
the alphabet states corresponding to all model states.

Implements bpp::TreeLikelihood.

Definition at line 162 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::TransitionModel::getAlphabetStates().

ParameterList AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters ( ) const
virtual
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 288 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

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

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters ( ) const
virtualinherited
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.

Referenced by bpp::TreeLikelihood::~TreeLikelihood().

virtual double bpp::TreeLikelihood::getLikelihood ( ) const
pure virtualinherited
virtual const TreeLikelihoodData* bpp::TreeLikelihood::getLikelihoodData ( ) const
pure virtualinherited
virtual double bpp::TreeLikelihood::getLikelihoodForASite ( size_t  site) const
pure virtualinherited
virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClass ( size_t  site,
size_t  rateClass 
) const
pure virtualinherited
virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClassForAState ( size_t  site,
size_t  rateClass,
int  state 
) const
pure virtualinherited
double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState ( size_t  site,
int  state 
) const
virtualinherited
virtual double bpp::TreeLikelihood::getLikelihoodForASiteForAState ( size_t  site,
int  state 
) const
pure virtualinherited

Get the likelihood for a site and for a state.

Parameters
siteThe site index to analyse.
stateThe state to consider.
Returns
The likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState(), and bpp::TreeLikelihood::~TreeLikelihood().

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.

Referenced by bpp::TreeLikelihood::~TreeLikelihood().

Vdouble AbstractTreeLikelihood::getLikelihoodForEachSite ( ) const
virtualinherited
VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClassForEachState ( ) const
virtualinherited
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.

Referenced by bpp::TreeLikelihood::~TreeLikelihood().

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().

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

virtual double bpp::TreeLikelihood::getLogLikelihood ( ) const
pure virtualinherited
virtual double bpp::TreeLikelihood::getLogLikelihoodForASite ( size_t  site) const
pure virtualinherited

Get the logarithm of the likelihood for a site.

Parameters
siteThe site index to analyse.
Returns
The logarithm of the likelihood for site site.

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSite(), and bpp::TreeLikelihood::~TreeLikelihood().

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClass ( size_t  site,
size_t  rateClass 
) const
pure virtualinherited
virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState ( size_t  site,
size_t  rateClass,
int  state 
) const
pure virtualinherited

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

Parameters
siteThe site index.
rateClassThe rate class index.
stateThe ancestral state.
Returns
The logarithm of the likelihood for the specified site and rate class and ancestral state..

Implemented in bpp::TwoTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClassForEachState(), and bpp::DiscreteRatesAcrossSitesTreeLikelihood::~DiscreteRatesAcrossSitesTreeLikelihood().

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState ( size_t  site,
int  state 
) const
virtualinherited
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
siteThe site index to analyse.
stateThe state to consider.
Returns
The logarithm of the likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState(), and bpp::TreeLikelihood::~TreeLikelihood().

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.

Referenced by bpp::PairedSiteLikelihoods::appendModel(), and bpp::TreeLikelihood::~TreeLikelihood().

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().

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

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 137 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses().

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 178 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses().

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.

Referenced by bpp::TreeLikelihood::~TreeLikelihood().

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().

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

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

Definition at line 268 of file AbstractHomogeneousTreeLikelihood.h.

References minimumBrLen_.

const TransitionModel* bpp::AbstractHomogeneousTreeLikelihood::getModel ( ) const
inlinevirtual
Returns
The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 202 of file AbstractHomogeneousTreeLikelihood.h.

References model_.

const TransitionModel* bpp::AbstractHomogeneousTreeLikelihood::getModel ( int  nodeId,
size_t  siteIndex 
) const
inline

Definition at line 203 of file AbstractHomogeneousTreeLikelihood.h.

References model_.

TransitionModel* bpp::AbstractHomogeneousTreeLikelihood::getModel ( )
inlinevirtual
Returns
The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 205 of file AbstractHomogeneousTreeLikelihood.h.

References model_.

TransitionModel* bpp::AbstractHomogeneousTreeLikelihood::getModel ( int  nodeId,
size_t  siteIndex 
)
inline

Definition at line 206 of file AbstractHomogeneousTreeLikelihood.h.

References model_, and setModel().

const TransitionModel* bpp::HomogeneousTreeLikelihood::getModelForSite ( int  nodeId,
size_t  siteIndex 
) const
inlinevirtualinherited

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

Parameters
nodeIdThe id of the request node.
siteIndexThe index of the alignment position.
See also
getSiteIndex
Returns
A pointer toward the corresponding model.

Implements bpp::TreeLikelihood.

Definition at line 66 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getModel().

TransitionModel* bpp::HomogeneousTreeLikelihood::getModelForSite ( int  nodeId,
size_t  siteIndex 
)
inlinevirtualinherited

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

Parameters
nodeIdThe id of the request node.
siteIndexThe index of the alignment position.
See also
getSiteIndex
Returns
A pointer toward the corresponding model.
Exceptions
NodeNotFoundExceptionThis exception may be thrown if the node is not found (depending on the implementation).

Implements bpp::TreeLikelihood.

Definition at line 70 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getModel(), bpp::HomogeneousTreeLikelihood::getSubstitutionModel(), and bpp::HomogeneousTreeLikelihood::setModel().

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

Implements bpp::TreeLikelihood.

Definition at line 183 of file AbstractHomogeneousTreeLikelihood.h.

ConstSiteModelIterator* bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator ( size_t  siteIndex) const
inlinevirtual
ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters ( ) const
virtualinherited
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.

Referenced by bpp::OptimizationTools::optimizeNumericalParameters2(), and bpp::TreeLikelihood::~TreeLikelihood().

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::displayLikelihoodArray(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClassForEachState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClassForEachState(), bpp::DiscreteDistribution::getNumberOfCategories(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRateOfEachSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbOfEachSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbOfEachSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClassForEachState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClassForEachState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRateOfEachSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities().

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(), and bpp::TreeLikelihood::~TreeLikelihood().

size_t bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates ( ) const
inlinevirtual
Returns
the number of model states of the underlying Markov chain.

Implements bpp::TreeLikelihood.

Definition at line 160 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::TransitionModel::getNumberOfStates().

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate ( ) const
virtualinherited
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 238 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClass(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses().

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_.

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_.

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbOfEachSite ( ) const
virtualinherited
const std::vector<double>& bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies ( size_t  siteIndex) const
inlinevirtual

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
siteIndexThe 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 179 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::TransitionModel::getFrequencies().

virtual size_t bpp::TreeLikelihood::getSiteIndex ( size_t  site) const
pure virtualinherited

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

Parameters
siteAn alignment position.
Returns
The site index corresponding to the given input alignment position.

Implemented in bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousTreeLikelihood.

Referenced by bpp::TreeLikelihoodTools::getAncestralFrequencies(), and bpp::TreeLikelihood::~TreeLikelihood().

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

Get a SubstitutionModel pointer toward the model associated to this instance, if possible.

Performs a cast operation on the pointer. Return NULL if cast failed.

Returns
A SubstitutionModel pointer toward the model associated to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 217 of file AbstractHomogeneousTreeLikelihood.h.

References model_.

virtual const SubstitutionModel* bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( int  nodeId,
size_t  siteIndex 
) const
inlinevirtual

Get a SubstitutionModel pointer toward the model associated to this instance, if possible.

Performs a cast operation on the pointer. Return NULL if cast failed.

Returns
A SubstitutionModel pointer toward the model associated to this instance.
Parameters
nodeIdId of the node
siteIndexPosition of the site

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 228 of file AbstractHomogeneousTreeLikelihood.h.

References applyParameters(), initBranchLengthsParameters(), initParameters(), and model_.

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
nodeIdThe node defining the branch of interest.
siteIndexThe 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 310 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::TreeLikelihood::getNumberOfStates(), bpp::DiscreteDistribution::getProbabilities(), bpp::DiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilitiesPerRateClass(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::~AbstractDiscreteRatesAcrossSitesTreeLikelihood().

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
nodeIdThe node defining the branch of interest.
siteIndexThe 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.

Referenced by bpp::TreeLikelihoodTools::getAncestralFrequencies_(), and bpp::TreeLikelihood::~TreeLikelihood().

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

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

These intermediate results may be used by other methods.

Parameters
nodeIdThe node defining the branch of interest.
siteIndexThe 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 181 of file AbstractHomogeneousTreeLikelihood.h.

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 295 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::tree_.

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

void AbstractHomogeneousTreeLikelihood::initialize ( )
virtual

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
Exceptionif 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::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, and initParameters().

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

void AbstractHomogeneousTreeLikelihood::initParameters ( )
virtual
bool bpp::AbstractTreeLikelihood::isInitialized ( ) const
inlinevirtualinherited
virtual void bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength ( double  maximum)
inlinevirtual
virtual void bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength ( double  minimum)
inlinevirtual
void AbstractHomogeneousTreeLikelihood::setModel ( TransitionModel model)
virtual
Returns
Set the substitution model for this instance.
Exceptions
ExceptionIf 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 d2pxy_, bpp::AbstractTreeLikelihood::data_, dpxy_, bpp::SiteContainer::getAlphabet(), bpp::TransitionModel::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::Node::getId(), bpp::TransitionModel::getNumberOfStates(), model_, nbClasses_, nbNodes_, nbStates_, nodes_, pxy_, and bpp::TreeLikelihood::setData().

Referenced by getModel(), and init_().

Member Data Documentation

std::unique_ptr<Constraint> bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_
protected
double bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_
protected
DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_
protectedinherited

Definition at line 61 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

Referenced by bpp::RHomogeneousClockTreeLikelihood::applyParameters(), applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::applyParameters(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRateOfEachSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbOfEachSite(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::DRHomogeneousTreeLikelihood::init_(), bpp::DRNonHomogeneousTreeLikelihood::init_(), init_(), bpp::RHomogeneousTreeLikelihood::init_(), bpp::RNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::TwoTreeLikelihood::initParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), and bpp::TwoTreeLikelihood::TwoTreeLikelihood().

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

Definition at line 230 of file AbstractTreeLikelihood.h.

Referenced by AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::RHomogeneousClockTreeLikelihood::applyParameters(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::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(), getNewSiteModelIterator(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractTreeLikelihood::getTree(), bpp::RHomogeneousClockTreeLikelihood::init_(), bpp::DRHomogeneousTreeLikelihood::init_(), bpp::DRNonHomogeneousTreeLikelihood::init_(), init_(), bpp::RHomogeneousTreeLikelihood::init_(), bpp::RNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(), bpp::DRHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::operator=(), operator=(), bpp::RHomogeneousTreeLikelihood::operator=(), bpp::RNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().

bool bpp::AbstractHomogeneousTreeLikelihood::verbose_
protected

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