bpp-phyl  2.4.0
bpp::AbstractTreeLikelihood Class Referenceabstract

Partial implementation of the TreeLikelihood interface. More...

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

+ Inheritance diagram for bpp::AbstractTreeLikelihood:
+ Collaboration diagram for bpp::AbstractTreeLikelihood:

Classes

class  ConstNoPartitionBranchModelDescription
 
class  ConstNoPartitionBranchModelIterator
 
class  ConstNoPartitionSiteModelDescription
 
class  SimpleBranchIterator
 A very simple branch iterator. More...
 
class  SimpleSiteIterator
 A very simple site iterator. More...
 

Public Member Functions

 AbstractTreeLikelihood ()
 
 AbstractTreeLikelihood (const AbstractTreeLikelihood &lik)
 
AbstractTreeLikelihoodoperator= (const AbstractTreeLikelihood &lik)
 
virtual ~AbstractTreeLikelihood ()
 Abstract class destructor. More...
 
TreeLikelihoodclone () const =0
 
virtual void setData (const SiteContainer &sites)=0
 Set the dataset for which the likelihood must be evaluated. More...
 
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 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 size_t getNumberOfStates () const =0
 
virtual int getAlphabetStateAsInt (size_t i) const =0
 
virtual std::string getAlphabetStateAsChar (size_t i) const =0
 
virtual const std::vector< int > & getAlphabetStates () const =0
 
virtual ParameterList getDerivableParameters () const =0
 All derivable parameters. More...
 
virtual ParameterList getNonDerivableParameters () const =0
 All non derivable parameters. More...
 
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 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
 
bool hasParameter (const std::string &name) const
 
const ParameterListgetParameters () const
 
const ParametergetParameter (const std::string &name) const
 
const std::shared_ptr< Parameter > & getSharedParameter (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
 
virtual void fireParameterChanged (const ParameterList &parameters)
 
virtual Clonableclone () const =0
 
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)
 
void enableSecondOrderDerivatives (bool yn)
 
bool enableFirstOrderDerivatives () const
 
bool enableSecondOrderDerivatives () const
 
bool isInitialized () const
 
void initialize ()
 Init the likelihood object. More...
 
Retrieve some particular parameters subsets.
virtual ParameterList getBranchLengthsParameters () const =0
 Get the branch lengths parameters. More...
 
virtual ParameterList getSubstitutionModelParameters () const =0
 Get the parameters associated to substitution model(s). More...
 
virtual const TransitionModelgetModelForSite (int nodeId, size_t siteIndex) const =0
 Get the substitution model associated to a given node and alignment column. More...
 
virtual TransitionModelgetModelForSite (int nodeId, size_t siteIndex)=0
 Get the substitution model associated to a given node and alignment column. More...
 
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 ConstBranchModelIteratorgetNewBranchModelIterator (int nodeId) const =0
 
virtual ConstSiteModelIteratorgetNewSiteModelIterator (size_t siteIndex) const =0
 
virtual size_t getSiteIndex (size_t site) const =0
 Get the index (used for inner computations) of a given site (original alignment column). More...
 
virtual const std::vector< double > & getRootFrequencies (size_t siteIndex) const =0
 Get the values of the frequencies for each state in the alphabet at the root node. More...
 

Protected Member Functions

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

const SiteContainerdata_
 
TreeTemplate< Node > * tree_
 
bool computeFirstOrderDerivatives_
 
bool computeSecondOrderDerivatives_
 
bool initialized_
 

Detailed Description

Partial implementation of the TreeLikelihood interface.

This class implements a few methods useful for most of likelihood computation methods.

It includes a tree_ and a data_ pointers. This objects are owned by the class, and hence hard copied when cloning, and destroyed by the destructor.

It also adds an abstract method for recursive computations.

Definition at line 69 of file AbstractTreeLikelihood.h.

Constructor & Destructor Documentation

bpp::AbstractTreeLikelihood::AbstractTreeLikelihood ( )
inline

Definition at line 236 of file AbstractTreeLikelihood.h.

bpp::AbstractTreeLikelihood::AbstractTreeLikelihood ( const AbstractTreeLikelihood lik)
inline

Definition at line 244 of file AbstractTreeLikelihood.h.

References bpp::SiteContainer::clone(), data_, and tree_.

virtual bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood ( )
inlinevirtual

Abstract class destructor.

This destructor is empty.

Definition at line 276 of file AbstractTreeLikelihood.h.

References data_, and tree_.

Member Function Documentation

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

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().

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

Implements bpp::DerivableSecondOrder.

Definition at line 297 of file AbstractTreeLikelihood.h.

bool bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( ) const
inlinevirtual

Implements bpp::DerivableSecondOrder.

Definition at line 299 of file AbstractTreeLikelihood.h.

References computeFirstOrderDerivatives_.

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

Implements bpp::DerivableSecondOrder.

Definition at line 298 of file AbstractTreeLikelihood.h.

bool bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( ) const
inlinevirtual

Implements bpp::DerivableSecondOrder.

Definition at line 300 of file AbstractTreeLikelihood.h.

References computeSecondOrderDerivatives_.

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

Get the alphabet associated to the dataset.

Returns
the alphabet associated to the dataset.

Implements bpp::TreeLikelihood.

Definition at line 289 of file AbstractTreeLikelihood.h.

References bpp::SiteContainer::getAlphabet(), getLikelihoodForEachSite(), getLikelihoodForEachSiteForEachState(), getLogLikelihoodForEachSite(), and getLogLikelihoodForEachSiteForEachState().

virtual std::string bpp::TreeLikelihood::getAlphabetStateAsChar ( size_t  i) const
pure virtualinherited
Returns
the alphabet state corresponding to the given model state.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

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

virtual int bpp::TreeLikelihood::getAlphabetStateAsInt ( size_t  i) const
pure virtualinherited
Returns
the alphabet state corresponding to the given model state.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

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

virtual const std::vector<int>& bpp::TreeLikelihood::getAlphabetStates ( ) const
pure virtualinherited
Returns
the alphabet states corresponding to all model states.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

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

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

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 data_.

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

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

Vdouble AbstractTreeLikelihood::getLikelihoodForEachSite ( ) const
virtual
VVdouble AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState ( ) const
virtual

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(), getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().

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

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

Vdouble AbstractTreeLikelihood::getLogLikelihoodForEachSite ( ) const
virtual

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 getNumberOfSites().

Referenced by getAlphabet().

VVdouble AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState ( ) const
virtual

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(), getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().

Referenced by getAlphabet().

virtual const TransitionModel* bpp::TreeLikelihood::getModelForSite ( int  nodeId,
size_t  siteIndex 
) const
pure virtualinherited

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.

Implemented in bpp::TwoTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, and bpp::HomogeneousTreeLikelihood.

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

virtual TransitionModel* bpp::TreeLikelihood::getModelForSite ( int  nodeId,
size_t  siteIndex 
)
pure virtualinherited

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).

Implemented in bpp::TwoTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, and bpp::HomogeneousTreeLikelihood.

virtual ConstSiteModelIterator* bpp::TreeLikelihood::getNewSiteModelIterator ( size_t  siteIndex) const
pure 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().

virtual const std::vector<double>& bpp::TreeLikelihood::getRootFrequencies ( size_t  siteIndex) const
pure virtualinherited

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;

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

Referenced by bpp::RewardMappingTools::computeRewardVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::TreeLikelihoodTools::getAncestralFrequencies(), and bpp::TreeLikelihood::~TreeLikelihood().

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 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().

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

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 tree_.

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

void bpp::AbstractTreeLikelihood::initialize ( )
inlinevirtual

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::RNonHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 302 of file AbstractTreeLikelihood.h.

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const
inlinevirtual

Member Data Documentation

bool bpp::AbstractTreeLikelihood::initialized_
protected
TreeTemplate<Node>* bpp::AbstractTreeLikelihood::tree_
mutableprotected

Definition at line 230 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), 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(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), 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=(), operator=(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), and ~AbstractTreeLikelihood().


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