bpp-phyl  2.1.0
bpp::AbstractHomogeneousTreeLikelihood Class Reference

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

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

+ Inheritance diagram for bpp::AbstractHomogeneousTreeLikelihood:
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List of all members.

Classes

class  ConstHomogeneousSiteModelIterator

Public Member Functions

 AbstractHomogeneousTreeLikelihood (const Tree &tree, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true) throw (Exception)
 AbstractHomogeneousTreeLikelihood (const AbstractHomogeneousTreeLikelihood &lik)
 Copy constructor.
AbstractHomogeneousTreeLikelihoodoperator= (const AbstractHomogeneousTreeLikelihood &lik)
 Assignation operator.
virtual ~AbstractHomogeneousTreeLikelihood ()
virtual void initParameters ()
 This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree.
virtual void applyParameters () throw (Exception)
 All parameters are stored in a parameter list. This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths.
virtual void initBranchLengthsParameters ()
virtual void setMinimumBranchLength (double minimum) throw (Exception)
virtual void setMaximumBranchLength (double maximum) throw (Exception)
virtual double getMinimumBranchLength () const
virtual double getMaximumBranchLength () const
HomogeneousTreeLikelihoodclone () const =0
const SubstitutionModelgetSubstitutionModel (int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
 Get the substitution model associated to a given node and alignment column.
SubstitutionModelgetSubstitutionModel (int nodeId, size_t siteIndex) throw (NodeNotFoundException)
 Get the substitution model associated to a given node and alignment column.
virtual void setData (const SiteContainer &sites)=0
 Set the dataset for which the likelihood must be evaluated.
virtual const SiteContainergetData () const =0
 Get the dataset for which the likelihood must be evaluated.
virtual bool isInitialized () const =0
virtual TreeLikelihoodDatagetLikelihoodData ()=0
virtual const TreeLikelihoodDatagetLikelihoodData () const =0
virtual double getLikelihoodForASite (size_t site) const =0
 Get the likelihood for a site.
virtual double getLogLikelihoodForASite (size_t site) const =0
 Get the logarithm of the likelihood for a site.
virtual double getLikelihoodForASiteForAState (size_t site, int state) const =0
 Get the likelihood for a site and for a state.
virtual double getLogLikelihoodForASiteForAState (size_t site, int state) const =0
 Get the logarithm of the likelihood for a site and for a state.
virtual Vdouble getLikelihoodForEachSite () const =0
 Get the likelihood for each site.
virtual Vdouble getLogLikelihoodForEachSite () const =0
 Get the logarithm of the likelihood for each site.
virtual VVdouble getLikelihoodForEachSiteForEachState () const =0
 Get the likelihood for each site and for each state.
virtual VVdouble getLogLikelihoodForEachSiteForEachState () const =0
 Get the logarithm of the likelihood for each site and for each state.
virtual double getLikelihood () const =0
 Get the likelihood for the whole dataset.
virtual double getLogLikelihood () const =0
 Get the logarithm of the likelihood for the whole dataset.
virtual const TreegetTree () const =0
 Get the tree (topology and branch lengths).
virtual size_t getNumberOfSites () const =0
 Get the number of sites in the dataset.
virtual size_t getNumberOfStates () const =0
 Get the number of states in the alphabet associated to the dataset.
virtual const AlphabetgetAlphabet () const =0
 Get the alphabet associated to the dataset.
virtual void enableDerivatives (bool yn)=0
 Tell if derivatives must be computed.
virtual ParameterList getDerivableParameters () const =0
 All derivable parameters.
virtual ParameterList getNonDerivableParameters () const =0
 All non derivable parameters.
virtual void enableSecondOrderDerivatives (bool yn)=0
virtual bool enableSecondOrderDerivatives () const =0
virtual double getSecondOrderDerivative (const std::string &variable) const =0
virtual double getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const =0
virtual double d2f (const std::string &variable, const ParameterList &parameters)
virtual double d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters)
virtual void enableFirstOrderDerivatives (bool yn)=0
virtual bool enableFirstOrderDerivatives () const =0
virtual double getFirstOrderDerivative (const std::string &variable) const =0
virtual double df (const std::string &variable, const ParameterList &parameters)
virtual void setParameters (const ParameterList &parameters)=0
virtual double getValue () const =0
virtual double f (const ParameterList &parameters)
virtual bool hasParameter (const std::string &name) const =0
virtual const ParameterListgetParameters () const =0
virtual const ParametergetParameter (const std::string &name) const =0
virtual double getParameterValue (const std::string &name) const =0
virtual void setAllParametersValues (const ParameterList &parameters)=0
virtual void setParameterValue (const std::string &name, double value)=0
virtual void setParametersValues (const ParameterList &parameters)=0
virtual bool matchParametersValues (const ParameterList &parameters)=0
virtual size_t getNumberOfParameters () const =0
virtual void setNamespace (const std::string &prefix)=0
virtual std::string getNamespace () const =0
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
virtual Clonableclone () const =0
bool hasParameter (const std::string &name) const
const ParameterListgetParameters () const
const ParametergetParameter (const std::string &name) const
double getParameterValue (const std::string &name) const
void setAllParametersValues (const ParameterList &parameters)
void setParameterValue (const std::string &name, double value)
void setParametersValues (const ParameterList &parameters)
bool matchParametersValues (const ParameterList &parameters)
size_t getNumberOfParameters () const
void setNamespace (const std::string &prefix)
std::string getNamespace () const
std::string getParameterNameWithoutNamespace (const std::string &name) const
virtual void fireParameterChanged (const ParameterList &parameters)=0
virtual double getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
 Get the likelihood for a site knowing its rate class.
virtual double getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
 Get the logarithm of the likelihood for a site knowing its rate class.
virtual double getLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
 Get the likelihood for a site knowing its rate class and its ancestral state.
virtual double getLogLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
 Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state.
The TreeLikelihood interface.

Other methods are implemented in the AbstractTreeLikelihood class.

void initialize () throw (Exception)
 Init the likelihood object.
ParameterList getBranchLengthsParameters () const
 Get the branch lengths parameters.
ParameterList getSubstitutionModelParameters () const
 Get the parameters associated to substitution model(s).
ParameterList getRateDistributionParameters () const
 Get the parameters associated to the rate distirbution.
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.
VVVdouble getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const
 Retrieves all Pij(t) for a particular branch, defined by the upper node.
ConstBranchModelIteratorgetNewBranchModelIterator (int nodeId) const
ConstSiteModelIteratorgetNewSiteModelIterator (size_t siteIndex) const
The HomogeneousTreeLikelihood interface.

Other methods are implemented in the AbstractTreeLikelihood class.

const SubstitutionModelgetSubstitutionModel () const
SubstitutionModelgetSubstitutionModel ()
void setSubstitutionModel (SubstitutionModel *model) throw (Exception)
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.
virtual size_t getSiteIndex (size_t site) const =0 throw (IndexOutOfBoundsException)
 Get the index (used for inner computations) of a given site (original alignment column).
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.
double getLogLikelihoodForASiteForAState (size_t site, int state) const
 Get the logarithm of the likelihood for a site and for a state.
ParameterList getDerivableParameters () const
 All derivable parameters.
ParameterList getNonDerivableParameters () const
 All non derivable parameters.
VVdouble getTransitionProbabilities (int nodeId, size_t siteIndex) const
 Retrieves all Pij(t) for a particular branch, defined by the upper node and site.
The DiscreteRatesAcrossSites interface implementation:
const DiscreteDistributiongetRateDistribution () const
 Get the rate distribution used for the computation.
DiscreteDistributiongetRateDistribution ()
 Get the rate distribution used for the computation.
size_t getNumberOfClasses () const
 Get the number of classes.
VVdouble getLikelihoodForEachSiteForEachRateClass () const
 Get the likelihood for each site and each rate class.
VVdouble getLogLikelihoodForEachSiteForEachRateClass () const
 Get the logarithm of the likelihood for each site and each rate class.
VVVdouble getLikelihoodForEachSiteForEachRateClassForEachState () const
 Get the likelihood for each site and each rate class and each state.
VVVdouble getLogLikelihoodForEachSiteForEachRateClassForEachState () const
 Get the logarithm of the likelihood for each site and each rate class and each state.
VVdouble getPosteriorProbabilitiesOfEachRate () const
 Get the posterior probability for each site of belonging to a particular rate class.
Vdouble getRateWithMaxPostProbOfEachSite () const
 Get the posterior rate (the one with maximum posterior probability) for each site.
std::vector< size_t > getRateClassWithMaxPostProbOfEachSite () const
 Get the posterior rate class (the one with maximum posterior probability) for each site.
Vdouble getPosteriorRateOfEachSite () const
 Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.
The TreeLikelihood interface.
const SiteContainergetData () const
 Get the dataset for which the likelihood must be evaluated.
const AlphabetgetAlphabet () const
 Get the alphabet associated to the dataset.
Vdouble getLikelihoodForEachSite () const
 Get the likelihood for each site.
Vdouble getLogLikelihoodForEachSite () const
 Get the logarithm of the likelihood for each site.
VVdouble getLikelihoodForEachSiteForEachState () const
 Get the likelihood for each site and for each state.
VVdouble getLogLikelihoodForEachSiteForEachState () const
 Get the logarithm of the likelihood for each site and for each state.
size_t getNumberOfSites () const
 Get the number of sites in the dataset.
size_t getNumberOfStates () const
 Get the number of states in the alphabet associated to the dataset.
const TreegetTree () const
 Get the tree (topology and branch lengths).
void enableDerivatives (bool yn)
 Tell if derivatives must be computed.
void enableFirstOrderDerivatives (bool yn)
bool enableFirstOrderDerivatives () const
void enableSecondOrderDerivatives (bool yn)
bool enableSecondOrderDerivatives () const
bool isInitialized () const

Static Public Member Functions

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

Protected Member Functions

virtual void computeAllTransitionProbabilities ()
 Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.
virtual void computeTransitionProbabilitiesForNode (const Node *node)
 Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.
void addParameter_ (Parameter *parameter)
void addParameters_ (const ParameterList &parameters)
void deleteParameter_ (size_t index)
void deleteParameter_ (std::string &name)
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

SubstitutionModelmodel_
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.
size_t nbSites_
size_t nbDistinctSites_
size_t nbClasses_
size_t nbStates_
size_t nbNodes_
bool verbose_
double minimumBrLen_
double maximumBrLen_
std::auto_ptr< ConstraintbrLenConstraint_
DiscreteDistributionrateDistribution_
const SiteContainerdata_
TreeTemplate< Node > * tree_
bool computeFirstOrderDerivatives_
bool computeSecondOrderDerivatives_
bool initialized_

Private Member Functions

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

Detailed Description

Partial implementation for homogeneous model of the TreeLikelihood interface.

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

Definition at line 57 of file AbstractHomogeneousTreeLikelihood.h.


Constructor & Destructor Documentation

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

Definition at line 59 of file AbstractHomogeneousTreeLikelihood.cpp.

Copy constructor.

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

Definition at line 89 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::TreeTemplate< N >::getNodes(), nodes_, and bpp::AbstractTreeLikelihood::tree_.


Member Function Documentation

void bpp::AbstractTreeLikelihood::enableDerivatives ( bool  yn) [inline, virtual, inherited]

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters:
ynYes or no.

Implements bpp::TreeLikelihood.

Definition at line 293 of file AbstractTreeLikelihood.h.

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

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

virtual void bpp::TreeLikelihood::enableDerivatives ( bool  yn) [pure virtual, inherited]

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters:
ynYes or no.

Implemented in bpp::AbstractTreeLikelihood.

const Alphabet* bpp::AbstractTreeLikelihood::getAlphabet ( ) const [inline, virtual, inherited]

Get the alphabet associated to the dataset.

Returns:
the alphabet associated to the dataset.

Implements bpp::TreeLikelihood.

Definition at line 285 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_, and bpp::SiteContainer::getAlphabet().

virtual const Alphabet* bpp::TreeLikelihood::getAlphabet ( ) const [pure virtual, inherited]

Get the alphabet associated to the dataset.

Returns:
the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

virtual const SiteContainer* bpp::TreeLikelihood::getData ( ) const [pure virtual, inherited]

Get the dataset for which the likelihood must be evaluated.

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

Implemented in bpp::AbstractTreeLikelihood.

const SiteContainer* bpp::AbstractTreeLikelihood::getData ( ) const [inline, virtual, inherited]

Get the dataset for which the likelihood must be evaluated.

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

Implements bpp::TreeLikelihood.

Definition at line 284 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

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

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns:
A ParameterList.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 73 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

virtual ParameterList bpp::TreeLikelihood::getDerivableParameters ( ) const [pure virtual, inherited]

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns:
A ParameterList.

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

virtual double bpp::TreeLikelihood::getLikelihood ( ) const [pure virtual, inherited]
virtual double bpp::TreeLikelihood::getLikelihoodForASite ( size_t  site) const [pure virtual, inherited]

Get the likelihood for a site.

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

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

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClass ( size_t  site,
size_t  rateClass 
) const [pure virtual, inherited]

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.

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClassForAState ( size_t  site,
size_t  rateClass,
int  state 
) const [pure virtual, inherited]

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.

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

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState ( size_t  site,
int  state 
) const [virtual, inherited]

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.

Implements bpp::TreeLikelihood.

Definition at line 111 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

virtual double bpp::TreeLikelihood::getLikelihoodForASiteForAState ( size_t  site,
int  state 
) const [pure virtual, inherited]

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().

virtual Vdouble bpp::TreeLikelihood::getLikelihoodForEachSite ( ) const [pure virtual, inherited]

Get the likelihood for each site.

Returns:
A vector with all likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

Get the likelihood for each site.

Returns:
A vector with all likelihoods for each site.

Implements bpp::TreeLikelihood.

Definition at line 46 of file AbstractTreeLikelihood.cpp.

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

Get the likelihood for each site and each rate class.

Returns:
A two-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 93 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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

Returns:
A three-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 156 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

virtual VVdouble bpp::TreeLikelihood::getLikelihoodForEachSiteForEachState ( ) const [pure virtual, inherited]

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.

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::AbstractTreeLikelihood::getNumberOfStates().

virtual double bpp::TreeLikelihood::getLogLikelihood ( ) const [pure virtual, inherited]

Get the logarithm of the likelihood for the whole dataset.

Returns:
The logarithm of the likelihood of the dataset.

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

virtual double bpp::TreeLikelihood::getLogLikelihoodForASite ( size_t  site) const [pure virtual, inherited]

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::DRNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, and bpp::DRHomogeneousTreeLikelihood.

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClass ( size_t  site,
size_t  rateClass 
) const [pure virtual, inherited]

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.

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState ( size_t  site,
size_t  rateClass,
int  state 
) const [pure virtual, inherited]

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

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

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

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState ( size_t  site,
int  state 
) const [virtual, inherited]

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.

Implements bpp::TreeLikelihood.

Definition at line 124 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

virtual double bpp::TreeLikelihood::getLogLikelihoodForASiteForAState ( size_t  site,
int  state 
) const [pure virtual, inherited]

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().

virtual Vdouble bpp::TreeLikelihood::getLogLikelihoodForEachSite ( ) const [pure virtual, inherited]

Get the logarithm of the likelihood for each site.

Returns:
A vector with all log likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

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().

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

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

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 138 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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

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

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 179 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

virtual VVdouble bpp::TreeLikelihood::getLogLikelihoodForEachSiteForEachState ( ) const [pure virtual, inherited]

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.

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::AbstractTreeLikelihood::getNumberOfStates().

virtual double bpp::AbstractHomogeneousTreeLikelihood::getMaximumBranchLength ( ) const [inline, virtual]

Definition at line 244 of file AbstractHomogeneousTreeLikelihood.h.

References maximumBrLen_.

virtual double bpp::AbstractHomogeneousTreeLikelihood::getMinimumBranchLength ( ) const [inline, virtual]

Definition at line 243 of file AbstractHomogeneousTreeLikelihood.h.

References minimumBrLen_.

All non derivable parameters.

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

Returns:
A ParameterList.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 82 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::ParameterList::addParameters().

virtual ParameterList bpp::TreeLikelihood::getNonDerivableParameters ( ) const [pure virtual, inherited]

All non derivable parameters.

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

Returns:
A ParameterList.

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

virtual size_t bpp::TreeLikelihood::getNumberOfSites ( ) const [pure virtual, inherited]

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().

size_t bpp::AbstractTreeLikelihood::getNumberOfStates ( ) const [inline, virtual, inherited]

Get the number of states in the alphabet associated to the dataset.

Returns:
the number of states in the alphabet associated to the dataset.

Implements bpp::TreeLikelihood.

Definition at line 291 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_, bpp::SiteContainer::getAlphabet(), and bpp::Alphabet::getSize().

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

virtual size_t bpp::TreeLikelihood::getNumberOfStates ( ) const [pure virtual, inherited]

Get the number of states in the alphabet associated to the dataset.

Returns:
the number of states in the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().

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

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

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 202 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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

Returns:
A vector with all rates.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 220 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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

Returns:
A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 239 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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_.

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_.

Get the parameters associated to the rate distirbution.

Returns:
A ParameterList object with all rate distribution parameters.

Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 171 of file AbstractHomogeneousTreeLikelihood.h.

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

Returns:
A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 253 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

const std::vector<double>& bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies ( size_t  siteIndex) const [inline, virtual]

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 176 of file AbstractHomogeneousTreeLikelihood.h.

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

virtual size_t bpp::TreeLikelihood::getSiteIndex ( size_t  site) const throw (IndexOutOfBoundsException) [pure virtual, inherited]

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::RNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousTreeLikelihood.

const SubstitutionModel* bpp::HomogeneousTreeLikelihood::getSubstitutionModel ( int  nodeId,
size_t  siteIndex 
) const throw (NodeNotFoundException) [inline, virtual, inherited]

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 67 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getSubstitutionModel().

SubstitutionModel* bpp::HomogeneousTreeLikelihood::getSubstitutionModel ( int  nodeId,
size_t  siteIndex 
) throw (NodeNotFoundException) [inline, virtual, inherited]

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 72 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getSubstitutionModel().

Returns:
The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 199 of file AbstractHomogeneousTreeLikelihood.h.

References model_.

Returns:
The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 201 of file AbstractHomogeneousTreeLikelihood.h.

References model_.

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities ( int  nodeId,
size_t  siteIndex 
) const [virtual, inherited]

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 311 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

virtual VVdouble bpp::TreeLikelihood::getTransitionProbabilities ( int  nodeId,
size_t  siteIndex 
) const [pure virtual, inherited]

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.

VVVdouble bpp::AbstractHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass ( int  nodeId,
size_t  siteIndex 
) const [inline, virtual]

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 178 of file AbstractHomogeneousTreeLikelihood.h.

References pxy_.

const Tree& bpp::AbstractTreeLikelihood::getTree ( ) const [inline, virtual, inherited]

Get the tree (topology and branch lengths).

Returns:
The tree of this TreeLikelihood object.

Implements bpp::TreeLikelihood.

Definition at line 292 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::tree_.

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

void AbstractHomogeneousTreeLikelihood::init_ ( const Tree tree,
SubstitutionModel model,
DiscreteDistribution rDist,
bool  checkRooted,
bool  verbose 
) throw (Exception) [private]

Method called by constructor.

Definition at line 142 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::TreeTools::checkIds(), and bpp::ApplicationTools::displayWarning().

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.

Reimplemented from bpp::AbstractTreeLikelihood.

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

Definition at line 237 of file AbstractHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::OptimizationTools::buildDistanceTree().

virtual bool bpp::TreeLikelihood::isInitialized ( ) const [pure virtual, inherited]
Returns:
'true' is the likelihood function has been initialized.

Implemented in bpp::AbstractTreeLikelihood.

AbstractHomogeneousTreeLikelihood & AbstractHomogeneousTreeLikelihood::operator= ( const AbstractHomogeneousTreeLikelihood lik)
Returns:
Set the substitution model for this instance.
Exceptions:
ExceptionIf the model could not be set (for instance, because of a wrong alphabet type).

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 172 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId().


Member Data Documentation

Definition at line 61 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

Referenced by applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::applyParameters(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::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::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::TwoTreeLikelihood::initParameters(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=().

TreeTemplate<Node>* bpp::AbstractTreeLikelihood::tree_ [mutable, protected, inherited]

Definition at line 226 of file AbstractTreeLikelihood.h.

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

Definition at line 114 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by operator=().


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