bpp-phyl  2.4.0
bpp::NNIHomogeneousTreeLikelihood Class Referenceabstract

This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class. More...

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

+ Inheritance diagram for bpp::NNIHomogeneousTreeLikelihood:
+ Collaboration diagram for bpp::NNIHomogeneousTreeLikelihood:

Public Member Functions

 NNIHomogeneousTreeLikelihood (const Tree &tree, TransitionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true)
 Build a new NNIHomogeneousTreeLikelihood object. More...
 
 NNIHomogeneousTreeLikelihood (const Tree &tree, const SiteContainer &data, TransitionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true)
 Build a new NNIHomogeneousTreeLikelihood object. More...
 
 NNIHomogeneousTreeLikelihood (const NNIHomogeneousTreeLikelihood &lik)
 Copy constructor. More...
 
NNIHomogeneousTreeLikelihoodoperator= (const NNIHomogeneousTreeLikelihood &lik)
 
virtual ~NNIHomogeneousTreeLikelihood ()
 
NNIHomogeneousTreeLikelihoodclone () const
 
void setData (const SiteContainer &sites)
 Set the dataset for which the likelihood must be evaluated. More...
 
void computeTreeLikelihood ()
 
void setParameters (const ParameterList &parameters)
 Implements the Function interface. More...
 
double getValue () const
 Function and NNISearchable interface. More...
 
DRASDRTreeLikelihoodDatagetLikelihoodData ()
 
const DRASDRTreeLikelihoodDatagetLikelihoodData () const
 
virtual void computeLikelihoodAtNode (int nodeId, VVVdouble &likelihoodArray) const
 Compute the likelihood array at a given node. More...
 
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
 
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 const SiteContainergetData () 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 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 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 df (const std::string &variable, const ParameterList &parameters)
 
virtual double f (const ParameterList &parameters)
 
virtual bool hasParameter (const std::string &name) const =0
 
bool hasParameter (const std::string &name) const
 
virtual const ParameterListgetParameters () const =0
 
const ParameterListgetParameters () const
 
virtual const ParametergetParameter (const std::string &name) const =0
 
const ParametergetParameter (const std::string &name) const
 
virtual double getParameterValue (const std::string &name) const =0
 
double getParameterValue (const std::string &name) const
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
void setAllParametersValues (const ParameterList &parameters)
 
virtual void setParameterValue (const std::string &name, double value)=0
 
void setParameterValue (const std::string &name, double value)
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
void setParametersValues (const ParameterList &parameters)
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
bool matchParametersValues (const ParameterList &parameters)
 
virtual size_t getNumberOfParameters () const =0
 
size_t getNumberOfParameters () const
 
virtual void setNamespace (const std::string &prefix)=0
 
void setNamespace (const std::string &prefix)
 
virtual std::string getNamespace () const =0
 
std::string getNamespace () const
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
 
std::string getParameterNameWithoutNamespace (const std::string &name) const
 
const std::shared_ptr< Parameter > & getSharedParameter (const std::string &name) const
 
virtual void topologyChangePerformed (const TopologyChangeEvent &event)
 Notify a topology change event. More...
 
The NNISearchable interface.

Current implementation: When testing a particular NNI, only the branch length of the parent node is optimized (and roughly). All other parameters (substitution model, rate distribution and other branch length are kept at there current value. When performing a NNI, only the topology change is performed. This is up to the user to re-initialize the underlying likelihood data to match the new topology. Usually, this is achieved by calling the topologyChangePerformed() method, which call the reInit() method of the LikelihoodData object.

const TreegetTopology () const
 Get the tree associated to this NNISearchable object. More...
 
double getTopologyValue () const
 Get the current score of this NNISearchable object. More...
 
double testNNI (int nodeId) const
 Send the score of a NNI movement, without performing it. More...
 
void doNNI (int nodeId)
 Perform a NNI movement. More...
 
void topologyChangeTested (const TopologyChangeEvent &event)
 Notify a topology change event. More...
 
void topologyChangeSuccessful (const TopologyChangeEvent &event)
 Tell that a topology change is definitive. More...
 
The TreeLikelihood interface.

Other methods are implemented in the AbstractTreeLikelihood class.

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
 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
 
DerivableSecondOrder interface.
double getSecondOrderDerivative (const std::string &variable) const
 
double getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const
 
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)
 
The TreeLikelihood interface.
const SiteContainergetData () 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 TreegetTree () const
 Get the tree (topology and branch lengths). More...
 
size_t getNumberOfSites () const
 Get the number of sites in the dataset. More...
 
const AlphabetgetAlphabet () const
 Get the alphabet associated to the dataset. More...
 
void enableDerivatives (bool yn)
 Tell if derivatives must be computed. More...
 
void enableSecondOrderDerivatives (bool yn)
 
bool enableSecondOrderDerivatives () const
 
void enableFirstOrderDerivatives (bool yn)
 
bool enableFirstOrderDerivatives () 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 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...
 

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...
 
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_ ()
 

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

BranchLikelihoodbrLikFunction_
 
BrentOneDimensionbrentOptimizer_
 Optimizer used for testing NNI. More...
 
std::map< int, double > brLenNNIValues_
 Hash used for backing up branch lengths when testing NNIs. More...
 
ParameterList brLenNNIParams_
 
double minusLogLik_
 
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_
 

Detailed Description

This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class.

Definition at line 164 of file NNIHomogeneousTreeLikelihood.h.

Constructor & Destructor Documentation

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

Build a new NNIHomogeneousTreeLikelihood object.

Parameters
treeThe tree to use.
modelThe substitution model to use.
rDistThe rate across sites distribution to use.
checkRootedTell if we have to check for the tree to be unrooted. If true, any rooted tree will be unrooted before likelihood computation.
verboseShould I display some info?
Exceptions
Exceptionin an error occured.

Definition at line 124 of file NNIHomogeneousTreeLikelihood.cpp.

References brentOptimizer_, bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::BrentOneDimension::setConstraintPolicy(), bpp::BrentOneDimension::setMessageHandler(), bpp::BrentOneDimension::setProfiler(), and bpp::BrentOneDimension::setVerbose().

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

Build a new NNIHomogeneousTreeLikelihood object.

Parameters
treeThe tree to use.
dataSequences to use.
modelThe substitution model to use.
rDistThe rate across sites distribution to use.
checkRootedTell if we have to check for the tree to be unrooted. If true, any rooted tree will be unrooted before likelihood computation.
verboseShould I display some info?
Exceptions
Exceptionin an error occured.

Definition at line 145 of file NNIHomogeneousTreeLikelihood.cpp.

References brentOptimizer_, brLikFunction_, bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::DRHomogeneousTreeLikelihood::getLikelihoodData(), bpp::BrentOneDimension::setConstraintPolicy(), bpp::BrentOneDimension::setMessageHandler(), bpp::BrentOneDimension::setProfiler(), and bpp::BrentOneDimension::setVerbose().

NNIHomogeneousTreeLikelihood::NNIHomogeneousTreeLikelihood ( const NNIHomogeneousTreeLikelihood lik)
NNIHomogeneousTreeLikelihood::~NNIHomogeneousTreeLikelihood ( )
virtual

Definition at line 198 of file NNIHomogeneousTreeLikelihood.cpp.

References brentOptimizer_, and brLikFunction_.

Member Function Documentation

NNIHomogeneousTreeLikelihood* bpp::NNIHomogeneousTreeLikelihood::clone ( ) const
inlinevirtual

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 230 of file NNIHomogeneousTreeLikelihood.h.

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 
)
staticprotectedinherited

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
iLikA vector of likelihood arrays, one for each conditional node.
tProbA vector of transition probabilities, one for each node.
oLikThe likelihood array to store the computed likelihoods.
nbNodesThe number of nodes = the size of the input vectors.
nbDistinctSitesThe number of distinct sites (the first dimension of the likelihood array).
nbClassesThe number of rate classes (the second dimension of the likelihood array).
nbStatesThe number of states (the third dimension of the likelihood array).
resetTell if the output likelihood array must be initalized prior to computation. If true, the resetLikelihoodArray method will be called.

Definition at line 819 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), and testNNI().

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 
)
staticprotectedinherited

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
iLikA vector of likelihood arrays, one for each conditional node.
tProbA vector of transition probabilities, one for each node.
iLikRThe likelihood array for the subtree containing the root of the tree.
tProbRThe transition probabilities for thr subtree containing the root of the tree.
oLikThe likelihood array to store the computed likelihoods.
nbNodesThe number of nodes = the size of the input vectors.
nbDistinctSitesThe number of distinct sites (the first dimension of the likelihood array).
nbClassesThe number of rate classes (the second dimension of the likelihood array).
nbStatesThe number of states (the third dimension of the likelihood array).
resetTell if the output likelihood array must be initalized prior to computation. If true, the resetLikelihoodArray method will be called.

Definition at line 868 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

void DRHomogeneousTreeLikelihood::displayLikelihood ( const Node node)
protectedvirtualinherited
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
inlinevirtualinherited
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 164 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::TransitionModel::getAlphabetStateAsInt().

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

double DRHomogeneousTreeLikelihood::getLikelihood ( ) const
virtualinherited
DRASDRTreeLikelihoodData* bpp::DRHomogeneousTreeLikelihood::getLikelihoodData ( )
inlinevirtualinherited
Returns
The underlying likelihood data structure.

Implements bpp::DRTreeLikelihood.

Definition at line 204 of file DRHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

Referenced by NNIHomogeneousTreeLikelihood(), and testNNI().

const DRASDRTreeLikelihoodData* bpp::DRHomogeneousTreeLikelihood::getLikelihoodData ( ) const
inlinevirtualinherited
Returns
The underlying likelihood data structure.

Implements bpp::DRTreeLikelihood.

Definition at line 205 of file DRHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

double DRHomogeneousTreeLikelihood::getLikelihoodForASite ( size_t  site) const
virtualinherited

Get the likelihood for a site.

Parameters
siteThe site index to analyse.
Returns
The likelihood for site site.

Implements bpp::TreeLikelihood.

Definition at line 190 of file DRHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::DRHomogeneousTreeLikelihood::clone().

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

Get the likelihood for a site knowing its rate class.

Parameters
siteThe site index.
rateClassThe rate class index.
Returns
The likelihood for the specified site and rate class.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 203 of file DRHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::DRHomogeneousTreeLikelihood::getSiteIndex().

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

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

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 217 of file DRHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::DRHomogeneousTreeLikelihood::getSiteIndex().

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().

double DRHomogeneousTreeLikelihood::getLogLikelihood ( ) const
virtualinherited
double DRHomogeneousTreeLikelihood::getLogLikelihoodForASite ( size_t  site) const
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.

Implements bpp::TreeLikelihood.

Definition at line 197 of file DRHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::DRHomogeneousTreeLikelihood::clone().

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

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

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

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 210 of file DRHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::DRHomogeneousTreeLikelihood::getSiteIndex().

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

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 224 of file DRHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::DRHomogeneousTreeLikelihood::getSiteIndex().

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

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 202 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

const TransitionModel* bpp::AbstractHomogeneousTreeLikelihood::getModel ( int  nodeId,
size_t  siteIndex 
) const
inlineinherited
TransitionModel* bpp::AbstractHomogeneousTreeLikelihood::getModel ( )
inlinevirtualinherited
Returns
The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 205 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

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

Implements bpp::TreeLikelihood.

Definition at line 183 of file AbstractHomogeneousTreeLikelihood.h.

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

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

Implements bpp::DerivableSecondOrder.

Definition at line 199 of file DRHomogeneousTreeLikelihood.h.

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

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 bpp::AbstractHomogeneousTreeLikelihood::model_.

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

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 bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractHomogeneousTreeLikelihood::model_.

const Tree& bpp::NNIHomogeneousTreeLikelihood::getTopology ( ) const
inlinevirtual

Get the tree associated to this NNISearchable object.

Returns
The tree associated to this instance.

Implements bpp::NNISearchable.

Definition at line 251 of file NNIHomogeneousTreeLikelihood.h.

double bpp::NNIHomogeneousTreeLikelihood::getTopologyValue ( ) const
inlinevirtual

Get the current score of this NNISearchable object.

Returns
The current score of this instance.

Implements bpp::NNISearchable.

Definition at line 253 of file NNIHomogeneousTreeLikelihood.h.

References bpp::BranchLikelihood::getValue().

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
inlinevirtualinherited

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().

double DRHomogeneousTreeLikelihood::getValue ( ) const
virtualinherited
void AbstractHomogeneousTreeLikelihood::initialize ( )
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
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 bpp::AbstractHomogeneousTreeLikelihood::initParameters().

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

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const
inlinevirtualinherited
void bpp::NNIHomogeneousTreeLikelihood::setData ( const SiteContainer sites)
inlinevirtual

Set the dataset for which the likelihood must be evaluated.

Parameters
sitesThe data set to use.

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 233 of file NNIHomogeneousTreeLikelihood.h.

References bpp::BranchLikelihood::BranchLikelihood(), and bpp::DRHomogeneousTreeLikelihood::setData().

virtual void bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength ( double  maximum)
inlinevirtualinherited
virtual void bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength ( double  minimum)
inlinevirtualinherited
void DRHomogeneousTreeLikelihood::setParameters ( const ParameterList parameters)
virtualinherited

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
parametersThe parameter list to pass to the function.

Implements bpp::DerivableSecondOrder.

Definition at line 231 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::setParametersValues().

Referenced by bpp::DRHomogeneousTreeLikelihood::getSiteIndex().

double NNIHomogeneousTreeLikelihood::testNNI ( int  nodeId) const
virtual

Send the score of a NNI movement, without performing it.

This methods sends the score variation. This variation must be negative if the new point is better, i.e. the object is to be used with a minimizing optimization (for consistence with Optimizer objects).

Parameters
nodeIdThe id of the node defining the NNI movement.
Returns
The score variation of the NNI.
Exceptions
NodeExceptionIf the node does not define a valid NNI.

Implements bpp::NNISearchable.

Definition at line 205 of file NNIHomogeneousTreeLikelihood.cpp.

References bpp::ParameterList::addParameter(), brentOptimizer_, brLenNNIValues_, brLikFunction_, bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrayForNeighbor(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodData(), bpp::DRASDRTreeLikelihoodData::getNodeData(), bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::getParameter(), bpp::BrentOneDimension::getParameters(), bpp::TreeTemplateTools::getRemainingNeighbors(), bpp::Node::getSon(), bpp::Node::getSonPosition(), bpp::BrentOneDimension::getStopCondition(), bpp::Parameter::getValue(), bpp::BranchLikelihood::getValue(), bpp::DRHomogeneousTreeLikelihood::getValue(), bpp::Node::hasFather(), bpp::BrentOneDimension::init(), bpp::BranchLikelihood::initLikelihoods(), bpp::BranchLikelihood::initModel(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::BrentOneDimension::optimize(), bpp::AbstractHomogeneousTreeLikelihood::pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(), bpp::BranchLikelihood::resetLikelihoods(), bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, bpp::BrentOneDimension::setFunction(), bpp::BrentOneDimension::setInitialInterval(), bpp::Parameter::setName(), bpp::BranchLikelihood::setParameters(), bpp::OptimizationStopCondition::setTolerance(), bpp::TextTools::toString(), and bpp::AbstractTreeLikelihood::tree_.

virtual void bpp::TopologyListener::topologyChangePerformed ( const TopologyChangeEvent event)
inlinevirtualinherited

Notify a topology change event.

This method is to be invoked after one or several NNI are performed. It allows appropriate recomputations.

In most case, this is the same as topologyChangeTested() + topologyChangeSuccessful().

Parameters
eventThe topology change event.

Definition at line 103 of file TopologySearch.h.

void bpp::NNIHomogeneousTreeLikelihood::topologyChangeSuccessful ( const TopologyChangeEvent event)
inlinevirtual

Tell that a topology change is definitive.

This method is called after the topologyChangeTested() method.

Parameters
eventThe topology change event.

Implements bpp::TopologyListener.

Definition at line 267 of file NNIHomogeneousTreeLikelihood.h.

void bpp::NNIHomogeneousTreeLikelihood::topologyChangeTested ( const TopologyChangeEvent event)
inlinevirtual

Notify a topology change event.

Parameters
eventThe topology change event.

Implements bpp::TopologyListener.

Definition at line 259 of file NNIHomogeneousTreeLikelihood.h.

References bpp::BranchLikelihood::fireParameterChanged(), and bpp::ParameterList::reset().

Member Data Documentation

BrentOneDimension* bpp::NNIHomogeneousTreeLikelihood::brentOptimizer_
protected
ParameterList bpp::NNIHomogeneousTreeLikelihood::brLenNNIParams_
protected

Definition at line 180 of file NNIHomogeneousTreeLikelihood.h.

Referenced by doNNI(), NNIHomogeneousTreeLikelihood(), and operator=().

std::map<int, double> bpp::NNIHomogeneousTreeLikelihood::brLenNNIValues_
mutableprotected

Hash used for backing up branch lengths when testing NNIs.

Definition at line 178 of file NNIHomogeneousTreeLikelihood.h.

Referenced by doNNI(), NNIHomogeneousTreeLikelihood(), operator=(), and testNNI().

BranchLikelihood* bpp::NNIHomogeneousTreeLikelihood::brLikFunction_
protected
bool bpp::AbstractTreeLikelihood::initialized_
protectedinherited

Definition at line 233 of file AbstractTreeLikelihood.h.

Referenced by bpp::RHomogeneousClockTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters(), bpp::RHomogeneousClockTreeLikelihood::getDerivableParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters(), bpp::RHomogeneousClockTreeLikelihood::getNonDerivableParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::TwoTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::TwoTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::isInitialized(), bpp::AbstractTreeLikelihood::operator=(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

size_t bpp::AbstractHomogeneousTreeLikelihood::nbStates_
protectedinherited
std::vector<Node*> bpp::AbstractHomogeneousTreeLikelihood::nodes_
protectedinherited
DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_
protectedinherited

Definition at line 61 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

Referenced by bpp::RHomogeneousClockTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::applyParameters(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::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_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousTreeLikelihood::init_(), bpp::RNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::TwoTreeLikelihood::initParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(), testNNI(), and bpp::TwoTreeLikelihood::TwoTreeLikelihood().

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

Definition at line 230 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::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(), 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(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractTreeLikelihood::getTree(), bpp::RHomogeneousClockTreeLikelihood::init_(), bpp::DRHomogeneousTreeLikelihood::init_(), bpp::DRNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousTreeLikelihood::init_(), bpp::RNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousClockTreeLikelihood::initBranchLengthsParameters(), bpp::DRHomogeneousTreeLikelihood::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(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), testNNI(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().


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