bpp-phyl
2.2.0
|
Likelihood computation with a global clock. More...
#include <Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h>
Public Member Functions | |
RHomogeneousClockTreeLikelihood (const Tree &tree, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true) throw (Exception) | |
Build a new HomogeneousClockTreeLikelihood object. More... | |
RHomogeneousClockTreeLikelihood (const Tree &tree, const SiteContainer &data, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true) throw (Exception) | |
Build a new RHomogeneousClockTreeLikelihood object. More... | |
RHomogeneousClockTreeLikelihood * | clone () const |
virtual | ~RHomogeneousClockTreeLikelihood () |
void | setParameters (const ParameterList ¶meters) throw (ParameterNotFoundException, ConstraintException) |
Implements the Function interface. More... | |
double | getValue () const throw (Exception) |
size_t | getSiteIndex (size_t site) const throw (IndexOutOfBoundsException) |
Get the index (used for inner computations) of a given site (original alignment column). More... | |
DRASRTreeLikelihoodData * | getLikelihoodData () |
const DRASRTreeLikelihoodData * | getLikelihoodData () const |
void | computeTreeLikelihood () |
virtual double | getDLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const |
virtual double | getDLikelihoodForASite (size_t site) const |
virtual double | getDLogLikelihoodForASite (size_t site) const |
virtual double | getDLogLikelihood () const |
virtual void | computeTreeDLikelihood (const std::string &variable) |
virtual double | getD2LikelihoodForASiteForARateClass (size_t site, size_t rateClass) const |
virtual double | getD2LikelihoodForASite (size_t site) const |
virtual double | getD2LogLikelihoodForASite (size_t site) const |
virtual double | getD2LogLikelihood () const |
virtual void | computeTreeD2Likelihood (const std::string &variable) |
virtual void | initParameters () |
This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree. More... | |
virtual void | setMinimumBranchLength (double minimum) throw (Exception) |
virtual void | setMaximumBranchLength (double maximum) throw (Exception) |
virtual double | getMinimumBranchLength () const |
virtual double | getMaximumBranchLength () const |
virtual const SiteContainer * | getData () const =0 |
Get the dataset for which the likelihood must be evaluated. More... | |
virtual bool | isInitialized () const =0 |
virtual double | getLikelihoodForASiteForAState (size_t site, int state) const =0 |
Get the likelihood for a site and for a state. More... | |
virtual double | getLogLikelihoodForASiteForAState (size_t site, int state) const =0 |
Get the logarithm of the likelihood for a site and for a state. More... | |
virtual Vdouble | getLikelihoodForEachSite () const =0 |
Get the likelihood for each site. More... | |
virtual Vdouble | getLogLikelihoodForEachSite () const =0 |
Get the logarithm of the likelihood for each site. More... | |
virtual VVdouble | getLikelihoodForEachSiteForEachState () const =0 |
Get the likelihood for each site and for each state. More... | |
virtual VVdouble | getLogLikelihoodForEachSiteForEachState () const =0 |
Get the logarithm of the likelihood for each site and for each state. More... | |
virtual const Tree & | getTree () const =0 |
Get the tree (topology and branch lengths). More... | |
virtual size_t | getNumberOfSites () const =0 |
Get the number of sites in the dataset. More... | |
virtual const Alphabet * | getAlphabet () const =0 |
Get the alphabet associated to the dataset. More... | |
virtual void | enableDerivatives (bool yn)=0 |
Tell if derivatives must be computed. More... | |
Re-implementation from the RHomogeneousTreeLikelihood class: | |
void | applyParameters () throw (Exception) |
All parameters are stored in a parameter list. This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths. More... | |
void | fireParameterChanged (const ParameterList ¶ms) |
void | initBranchLengthsParameters () |
ParameterList | getDerivableParameters () const throw (Exception) |
All derivable parameters. More... | |
ParameterList | getNonDerivableParameters () const throw (Exception) |
All non derivable parameters. More... | |
double | getFirstOrderDerivative (const std::string &variable) const throw (Exception) |
double | getSecondOrderDerivative (const std::string &variable) const throw (Exception) |
double | getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const throw (Exception) |
The TreeLikelihood interface. | |
Other methods are implemented in the AbstractHomogeneousTreeLikelihood class. | |
void | setData (const SiteContainer &sites) throw (Exception) |
Set the dataset for which the likelihood must be evaluated. More... | |
double | getLikelihood () const |
Get the likelihood for the whole dataset. More... | |
double | getLogLikelihood () const |
Get the logarithm of the likelihood for the whole dataset. More... | |
double | getLikelihoodForASite (size_t site) const |
Get the likelihood for a site. More... | |
double | getLogLikelihoodForASite (size_t site) const |
Get the logarithm of the likelihood for a site. More... | |
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... | |
The TreeLikelihood interface. | |
Other methods are implemented in the AbstractTreeLikelihood class. | |
size_t | getNumberOfStates () const |
const std::vector< int > & | getAlphabetStates () const |
int | getAlphabetStateAsInt (size_t i) const |
std::string | getAlphabetStateAsChar (size_t i) const |
void | initialize () throw (Exception) |
Init the likelihood object. More... | |
ParameterList | getBranchLengthsParameters () const |
Get the branch lengths parameters. More... | |
ParameterList | getSubstitutionModelParameters () const |
Get the parameters associated to substitution model(s). More... | |
ParameterList | getRateDistributionParameters () const |
Get the parameters associated to the rate distirbution. More... | |
const std::vector< double > & | getRootFrequencies (size_t siteIndex) const |
Get the values of the frequencies for each state in the alphabet at the root node. More... | |
VVVdouble | getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const |
Retrieves all Pij(t) for a particular branch, defined by the upper node. More... | |
ConstBranchModelIterator * | getNewBranchModelIterator (int nodeId) const |
ConstSiteModelIterator * | getNewSiteModelIterator (size_t siteIndex) const |
The HomogeneousTreeLikelihood interface. | |
Other methods are implemented in the AbstractTreeLikelihood class. | |
const SubstitutionModel * | getSubstitutionModel () const |
const SubstitutionModel * | getSubstitutionModel (int nodeId, size_t siteIndex) const throw (NodeNotFoundException) |
Get the substitution model associated to a given node and alignment column. More... | |
SubstitutionModel * | getSubstitutionModel () |
SubstitutionModel * | getSubstitutionModel (int nodeId, size_t siteIndex) throw (NodeNotFoundException) |
Get the substitution model associated to a given node and alignment column. More... | |
void | setSubstitutionModel (SubstitutionModel *model) throw (Exception) |
The TreeLikelihood interface. | |
const SiteContainer * | getData () const |
Get the dataset for which the likelihood must be evaluated. More... | |
bool | isInitialized () const |
Vdouble | getLikelihoodForEachSite () const |
Get the likelihood for each site. More... | |
Vdouble | getLogLikelihoodForEachSite () const |
Get the logarithm of the likelihood for each site. More... | |
VVdouble | getLikelihoodForEachSiteForEachState () const |
Get the likelihood for each site and for each state. More... | |
VVdouble | getLogLikelihoodForEachSiteForEachState () const |
Get the logarithm of the likelihood for each site and for each state. More... | |
const Tree & | getTree () const |
Get the tree (topology and branch lengths). More... | |
size_t | getNumberOfSites () const |
Get the number of sites in the dataset. More... | |
const Alphabet * | getAlphabet () const |
Get the alphabet associated to the dataset. More... | |
void | enableDerivatives (bool yn) |
Tell if derivatives must be computed. More... | |
void | enableFirstOrderDerivatives (bool yn) |
bool | enableFirstOrderDerivatives () const |
void | enableSecondOrderDerivatives (bool yn) |
bool | enableSecondOrderDerivatives () const |
The TreeLikelihood interface. | |
Other methods are implemented in the AbstractTreeLikelihood class. | |
double | getLikelihoodForASiteForAState (size_t site, int state) const |
Get the likelihood for a site and for a state. More... | |
double | getLogLikelihoodForASiteForAState (size_t site, int state) const |
Get the logarithm of the likelihood for a site and for a state. More... | |
VVdouble | getTransitionProbabilities (int nodeId, size_t siteIndex) const |
Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More... | |
Retrieve some particular parameters subsets. | |
virtual VVdouble | getTransitionProbabilities (int nodeId, size_t siteIndex) const =0 |
Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More... | |
The DiscreteRatesAcrossSites interface implementation: | |
const DiscreteDistribution * | getRateDistribution () const |
Get the rate distribution used for the computation. More... | |
DiscreteDistribution * | getRateDistribution () |
Get the rate distribution used for the computation. More... | |
size_t | getNumberOfClasses () const |
Get the number of classes. More... | |
VVdouble | getLikelihoodForEachSiteForEachRateClass () const |
Get the likelihood for each site and each rate class. More... | |
VVdouble | getLogLikelihoodForEachSiteForEachRateClass () const |
Get the logarithm of the likelihood for each site and each rate class. More... | |
VVVdouble | getLikelihoodForEachSiteForEachRateClassForEachState () const |
Get the likelihood for each site and each rate class and each state. More... | |
VVVdouble | getLogLikelihoodForEachSiteForEachRateClassForEachState () const |
Get the logarithm of the likelihood for each site and each rate class and each state. More... | |
VVdouble | getPosteriorProbabilitiesOfEachRate () const |
Get the posterior probability for each site of belonging to a particular rate class. More... | |
Vdouble | getRateWithMaxPostProbOfEachSite () const |
Get the posterior rate (the one with maximum posterior probability) for each site. More... | |
std::vector< size_t > | getRateClassWithMaxPostProbOfEachSite () const |
Get the posterior rate class (the one with maximum posterior probability) for each site. More... | |
Vdouble | getPosteriorRateOfEachSite () const |
Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site. More... | |
Static Public Member Functions | |
Generic tools to deal with likelihood arrays | |
static void | resetLikelihoodArray (VVVdouble &likelihoodArray) |
Set all conditional likelihoods to 1. More... | |
static void | displayLikelihoodArray (const VVVdouble &likelihoodArray) |
Print the likelihood array to terminal (debugging tool). More... | |
Protected Member Functions | |
void | computeBranchLengthsFromHeights (Node *node, double height) throw (Exception) |
Update all lengths according to parameter values. More... | |
virtual void | computeSubtreeLikelihood (const Node *node) |
Compute the likelihood for a subtree defined by the Tree::Node node. More... | |
virtual void | computeDownSubtreeDLikelihood (const Node *) |
virtual void | computeDownSubtreeD2Likelihood (const 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... | |
Protected Attributes | |
double | minusLogLik_ |
SubstitutionModel * | model_ |
ParameterList | brLenParameters_ |
std::map< int, VVVdouble > | pxy_ |
std::map< int, VVVdouble > | dpxy_ |
std::map< int, VVVdouble > | d2pxy_ |
std::vector< double > | rootFreqs_ |
std::vector< Node * > | nodes_ |
Pointer toward all nodes in the tree. More... | |
size_t | nbSites_ |
size_t | nbDistinctSites_ |
size_t | nbClasses_ |
size_t | nbStates_ |
size_t | nbNodes_ |
bool | verbose_ |
double | minimumBrLen_ |
double | maximumBrLen_ |
std::auto_ptr< Constraint > | brLenConstraint_ |
DiscreteDistribution * | rateDistribution_ |
const SiteContainer * | data_ |
TreeTemplate< Node > * | tree_ |
bool | computeFirstOrderDerivatives_ |
bool | computeSecondOrderDerivatives_ |
bool | initialized_ |
Private Member Functions | |
void | init_ () |
Method called by constructor. More... | |
Likelihood computation with a global clock.
This class overrides the HomogeneousTreeLikelihood class, and change the branch length parameters which are the heights of the ancestral nodes. Heights are coded as percentage (HeightP) of the height of their father + the total height of the tree (TotalHeight). This parametrization resolve the linear constraint between heights, but has the limitation that the first and second order derivatives for HeightP parameters are not (easilly) computable analytically, and one may wish to use numerical derivatives instead. The tree must be rooted and fully resolved (no multifurcation).
Constraint on parameters HeightP are of class IncludingInterval, initially set to [0,1].
Definition at line 68 of file RHomogeneousClockTreeLikelihood.h.
RHomogeneousClockTreeLikelihood::RHomogeneousClockTreeLikelihood | ( | const Tree & | tree, |
SubstitutionModel * | model, | ||
DiscreteDistribution * | rDist, | ||
bool | checkRooted = true , |
||
bool | verbose = true |
||
) | |||
throw | ( | Exception | |
) |
Build a new HomogeneousClockTreeLikelihood object.
tree | The tree to use. |
model | The substitution model to use. |
rDist | The rate across sites distribution to use. |
checkRooted | Tell if we have to check for the tree to be rooted. If true, any unrooted tree will throw an exception. If set to false, the tree will be considered rooted, and any basal multifurcation will be considered as a true multifurcation. In the current version of this class however, multifurcation are not supported, so this option is mainly for forward compatibility! |
verbose | Should I display some info? |
Exception | in an error occured. |
Definition at line 54 of file RHomogeneousClockTreeLikelihood.cpp.
Referenced by clone().
RHomogeneousClockTreeLikelihood::RHomogeneousClockTreeLikelihood | ( | const Tree & | tree, |
const SiteContainer & | data, | ||
SubstitutionModel * | model, | ||
DiscreteDistribution * | rDist, | ||
bool | checkRooted = true , |
||
bool | verbose = true |
||
) | |||
throw | ( | Exception | |
) |
Build a new RHomogeneousClockTreeLikelihood object.
tree | The tree to use. |
data | Sequences to use. |
model | The substitution model to use. |
rDist | The rate across sites distribution to use. |
checkRooted | Tell if we have to check for the tree to be rooted. If true, any unrooted tree will throw an exception. If set to false, the tree will be considered rooted, and any basal multifurcation will be considered as a true multifurcation. In the current version of this class however, multifurcation are not supported, so this option is mainly for forward compatibility! |
verbose | Should I display some info? |
Exception | in an error occured. |
Definition at line 68 of file RHomogeneousClockTreeLikelihood.cpp.
|
inlinevirtual |
Definition at line 123 of file RHomogeneousClockTreeLikelihood.h.
|
virtual |
All parameters are stored in a parameter list. This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths.
Reimplemented from bpp::AbstractHomogeneousTreeLikelihood.
Definition at line 93 of file RHomogeneousClockTreeLikelihood.cpp.
|
inlinevirtual |
Implements bpp::DiscreteRatesAcrossSitesClockTreeLikelihood.
Definition at line 121 of file RHomogeneousClockTreeLikelihood.h.
References RHomogeneousClockTreeLikelihood().
|
protectedvirtualinherited |
Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 340 of file AbstractHomogeneousTreeLikelihood.cpp.
References bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::SubstitutionModel::getFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, and bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_.
Referenced by bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::RHomogeneousTreeLikelihood::fireParameterChanged().
|
protected |
Update all lengths according to parameter values.
Conflicting heights will be resolved arbitrarily.
NB: This is a recursive method.
node | the current node. |
height | the current height. |
Exception | If something unexpected happened. |
Definition at line 161 of file RHomogeneousClockTreeLikelihood.cpp.
References bpp::Node::getId(), bpp::Node::getSon(), bpp::Node::isLeaf(), and bpp::Node::setDistanceToFather().
|
protectedvirtualinherited |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 711 of file RHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.
Referenced by bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood().
|
protectedvirtualinherited |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 460 of file RHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.
Referenced by bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood().
|
protectedvirtualinherited |
Compute the likelihood for a subtree defined by the Tree::Node node.
node | The root of the subtree. |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 808 of file RHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::isLeaf(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.
Referenced by bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood().
|
protectedvirtualinherited |
Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 353 of file AbstractHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::SubstitutionModel::getd2Pij_dt2(), bpp::Node::getDistanceToFather(), bpp::SubstitutionModel::getdPij_dt(), bpp::Node::getId(), bpp::SubstitutionModel::getPij_t(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::RHomogeneousTreeLikelihood::fireParameterChanged().
|
virtualinherited |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 621 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.
|
virtualinherited |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 370 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.
|
inherited |
Definition at line 801 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), and bpp::AbstractTreeLikelihood::tree_.
Referenced by bpp::RHomogeneousTreeLikelihood::fireParameterChanged().
|
protectedvirtualinherited |
This method is mainly for debugging purpose.
node | The node at which likelihood values must be displayed. |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 874 of file RHomogeneousTreeLikelihood.cpp.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getName(), and bpp::RHomogeneousTreeLikelihood::likelihoodData_.
|
staticinherited |
Print the likelihood array to terminal (debugging tool).
likelihoodArray | the likelihood array. |
Definition at line 287 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
Referenced by bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), and bpp::RNonHomogeneousTreeLikelihood::displayLikelihood().
|
inlinevirtualinherited |
Tell if derivatives must be computed.
This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.
yn | Yes or no. |
Implements bpp::TreeLikelihood.
Definition at line 292 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.
Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood(), and bpp::DistanceEstimation::computeMatrix().
|
pure virtualinherited |
Tell if derivatives must be computed.
This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.
yn | Yes or no. |
Implemented in bpp::AbstractTreeLikelihood.
|
inlineinherited |
Definition at line 293 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.
|
inlineinherited |
Definition at line 295 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.
|
inlineinherited |
Definition at line 294 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.
|
inlineinherited |
Definition at line 296 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.
void RHomogeneousClockTreeLikelihood::fireParameterChanged | ( | const ParameterList & | params | ) |
Definition at line 108 of file RHomogeneousClockTreeLikelihood.cpp.
|
inlinevirtualinherited |
Get the alphabet associated to the dataset.
Implements bpp::TreeLikelihood.
Definition at line 285 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::data_.
|
pure virtualinherited |
Get the alphabet associated to the dataset.
Implemented in bpp::AbstractTreeLikelihood.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 171 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModel::getAlphabetStateAsChar(), and bpp::AbstractHomogeneousTreeLikelihood::model_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 169 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModel::getAlphabetStateAsInt(), and bpp::AbstractHomogeneousTreeLikelihood::model_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 167 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModel::getAlphabetStates(), and bpp::AbstractHomogeneousTreeLikelihood::model_.
|
virtualinherited |
Get the branch lengths parameters.
Implements bpp::TreeLikelihood.
Definition at line 250 of file AbstractHomogeneousTreeLikelihood.cpp.
References bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, and bpp::AbstractTreeLikelihood::initialized_.
|
virtualinherited |
Definition at line 567 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite().
|
virtualinherited |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 552 of file RHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
Referenced by bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite().
|
virtualinherited |
Definition at line 588 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.
|
virtualinherited |
Definition at line 580 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), and bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite().
Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihood().
|
pure virtualinherited |
Get the dataset for which the likelihood must be evaluated.
Implemented in bpp::AbstractTreeLikelihood.
|
inlinevirtualinherited |
Get the dataset for which the likelihood must be evaluated.
Implements bpp::TreeLikelihood.
Definition at line 284 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::data_.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::init().
|
virtual |
All derivable parameters.
Usually, this contains all branch lengths parameters.
Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 183 of file RHomogeneousClockTreeLikelihood.cpp.
|
virtualinherited |
Definition at line 316 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), and bpp::RHomogeneousTreeLikelihood::getDLogLikelihoodForASite().
|
virtualinherited |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 301 of file RHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
Referenced by bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite().
|
virtualinherited |
Definition at line 337 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getDLogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.
|
virtualinherited |
Definition at line 329 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), and bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite().
Referenced by bpp::RHomogeneousTreeLikelihood::getDLogLikelihood().
double RHomogeneousClockTreeLikelihood::getFirstOrderDerivative | ( | const std::string & | variable | ) | const |
throw | ( | Exception | |||
) |
Definition at line 201 of file RHomogeneousClockTreeLikelihood.cpp.
|
virtualinherited |
Get the likelihood for the whole dataset.
Implements bpp::TreeLikelihood.
Definition at line 152 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 222 of file RHomogeneousTreeLikelihood.h.
References bpp::RHomogeneousTreeLikelihood::likelihoodData_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 223 of file RHomogeneousTreeLikelihood.h.
References bpp::RHomogeneousTreeLikelihood::likelihoodData_.
|
virtualinherited |
Get the likelihood for a site.
site | The site index to analyse. |
Implements bpp::TreeLikelihood.
Definition at line 182 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLogLikelihoodForASite(), and bpp::RHomogeneousTreeLikelihood::getLikelihood().
|
virtualinherited |
Get the likelihood for a site knowing its rate class.
site | The site index. |
rateClass | The rate class index. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 207 of file RHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
Referenced by bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), and bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite().
|
virtualinherited |
Get the likelihood for a site knowing its rate class and its ancestral state.
site | The site index. |
rateClass | The rate class index. |
state | The ancestral state. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 236 of file RHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, and bpp::AbstractTreeLikelihood::tree_.
|
virtualinherited |
Get the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implements bpp::TreeLikelihood.
Definition at line 111 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
Get the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState().
|
pure virtualinherited |
Get the likelihood for each site.
Implemented in bpp::AbstractTreeLikelihood.
|
virtualinherited |
Get the likelihood for each site.
Implements bpp::TreeLikelihood.
Definition at line 46 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().
|
virtualinherited |
Get the likelihood for each site and each rate class.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 93 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
virtualinherited |
Get the likelihood for each site and each rate class and each state.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 156 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
Get the likelihood for each site and for each state.
Implemented in bpp::AbstractTreeLikelihood.
|
virtualinherited |
Get the likelihood 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().
|
virtualinherited |
Get the logarithm of the likelihood for the whole dataset.
Implements bpp::TreeLikelihood.
Definition at line 164 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.
Referenced by bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), and bpp::RHomogeneousTreeLikelihood::fireParameterChanged().
|
virtualinherited |
Get the logarithm of the likelihood for a site.
site | The site index to analyse. |
Implements bpp::TreeLikelihood.
Definition at line 194 of file RHomogeneousTreeLikelihood.cpp.
References bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::RHomogeneousTreeLikelihood::getLogLikelihood().
|
virtualinherited |
Get the logarithm of the likelihood for a site knowing its rate class.
site | The site index. |
rateClass | The rate class index. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 222 of file RHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
|
virtualinherited |
Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state.
site | The site index. |
rateClass | The rate class index. |
state | The ancestral state. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 243 of file RHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::RHomogeneousTreeLikelihood::likelihoodData_, and bpp::AbstractTreeLikelihood::tree_.
|
virtualinherited |
Get the logarithm of the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implements bpp::TreeLikelihood.
Definition at line 124 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
Get the logarithm of the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Referenced by bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState().
|
pure virtualinherited |
Get the logarithm of the likelihood for each site.
Implemented in bpp::AbstractTreeLikelihood.
|
virtualinherited |
Get the logarithm of the likelihood for each site.
Implements bpp::TreeLikelihood.
Definition at line 55 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().
|
virtualinherited |
Get the logarithm of the likelihood for each site and each rate class.
V[i][j] =
likelihood of site i and rate class j. Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 138 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
virtualinherited |
Get the logarithm of the likelihood for each site and each rate class and each state.
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.
|
pure virtualinherited |
Get the logarithm of the likelihood for each site and for each state.
Implemented in bpp::AbstractTreeLikelihood.
|
virtualinherited |
Get the logarithm of the likelihood 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().
|
inlinevirtualinherited |
Definition at line 254 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_.
|
inlinevirtualinherited |
Definition at line 253 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 188 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 193 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractTreeLikelihood::tree_.
|
virtual |
All non derivable parameters.
Usually, this contains all substitution model parameters and rate distribution.
Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 191 of file RHomogeneousClockTreeLikelihood.cpp.
|
inlinevirtualinherited |
Get the number of classes.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 108 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
|
inlinevirtualinherited |
Get the number of sites in the dataset.
Implements bpp::TreeLikelihood.
Definition at line 290 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::data_.
Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSite(), bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState(), bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSite(), and bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState().
|
pure virtualinherited |
Get the number of sites in the dataset.
Implemented in bpp::AbstractTreeLikelihood.
Referenced by bpp::SubstitutionMappingTools::getNormalizationsPerBranch().
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 165 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModel::getNumberOfStates(), and bpp::AbstractHomogeneousTreeLikelihood::model_.
|
virtualinherited |
Get the posterior probability for each site of belonging to a particular rate class.
V[i][j] =
probablity for site i of belonging to rate class j. Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 202 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
virtualinherited |
Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 220 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
virtualinherited |
Get the posterior rate class (the one with maximum posterior probability) for each site.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 239 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
inlinevirtualinherited |
Get the rate distribution used for the computation.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 106 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
|
inlinevirtualinherited |
Get the rate distribution used for the computation.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 107 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
|
inlinevirtualinherited |
Get the parameters associated to the rate distirbution.
Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 179 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters().
|
virtualinherited |
Get the posterior rate (the one with maximum posterior probability) for each site.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 253 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
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.
siteIndex | The index of the alignment position. |
Implements bpp::TreeLikelihood.
Definition at line 184 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModel::getFrequencies(), and bpp::AbstractHomogeneousTreeLikelihood::model_.
double RHomogeneousClockTreeLikelihood::getSecondOrderDerivative | ( | const std::string & | variable | ) | const |
throw | ( | Exception | |||
) |
Definition at line 211 of file RHomogeneousClockTreeLikelihood.cpp.
|
inline |
Definition at line 146 of file RHomogeneousClockTreeLikelihood.h.
|
inlinevirtualinherited |
Get the index (used for inner computations) of a given site (original alignment column).
site | An alignment position. |
Implements bpp::TreeLikelihood.
Definition at line 201 of file RHomogeneousTreeLikelihood.h.
References bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), and bpp::RHomogeneousTreeLikelihood::likelihoodData_.
|
inlinevirtualinherited |
Implements bpp::HomogeneousTreeLikelihood.
Definition at line 207 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::model_.
|
inlinevirtualinherited |
Get the substitution model associated to a given node and alignment column.
nodeId | The id of the request node. |
siteIndex | The index of the alignment position. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implements bpp::TreeLikelihood.
Definition at line 208 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::model_.
|
inlinevirtualinherited |
Implements bpp::HomogeneousTreeLikelihood.
Definition at line 210 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::model_.
|
inlinevirtualinherited |
Get the substitution model associated to a given node and alignment column.
nodeId | The id of the request node. |
siteIndex | The index of the alignment position. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implements bpp::TreeLikelihood.
Definition at line 211 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::model_.
|
virtualinherited |
Get the parameters associated to substitution model(s).
Implements bpp::TreeLikelihood.
Definition at line 259 of file AbstractHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractHomogeneousTreeLikelihood::model_.
|
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.
nodeId | The node defining the branch of interest. |
siteIndex | The index of the alignment position. |
Implements bpp::TreeLikelihood.
Definition at line 311 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
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.
nodeId | The node defining the branch of interest. |
siteIndex | The index of the alignment position. |
Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
|
inlinevirtualinherited |
Retrieves all Pij(t) for a particular branch, defined by the upper node.
These intermediate results may be used by other methods.
nodeId | The node defining the branch of interest. |
siteIndex | The position in the alignment. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 186 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::pxy_.
|
inlinevirtualinherited |
Get the tree (topology and branch lengths).
Implements bpp::TreeLikelihood.
Definition at line 291 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::tree_.
Referenced by bpp::NNIHomogeneousTreeLikelihood::getTopology(), and bpp::RNonHomogeneousMixedTreeLikelihood::init().
|
pure virtualinherited |
Get the tree (topology and branch lengths).
Implemented in bpp::AbstractTreeLikelihood.
Referenced by bpp::GlobalClockTreeLikelihoodFunctionWrapper::fireParameterChanged(), bpp::SubstitutionMappingTools::getNormalizedCountsPerBranch(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_().
|
inherited |
Definition at line 290 of file RHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::isInitialized(), and bpp::RHomogeneousTreeLikelihood::minusLogLik_.
|
private |
Method called by constructor.
Definition at line 83 of file RHomogeneousClockTreeLikelihood.cpp.
|
virtual |
Reimplemented from bpp::AbstractHomogeneousTreeLikelihood.
Definition at line 121 of file RHomogeneousClockTreeLikelihood.cpp.
|
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.
Exception | if something bad happened, for instance if no data are associated to the likelihood function. |
Implements bpp::TreeLikelihood.
Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 237 of file AbstractHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::data_, bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractHomogeneousTreeLikelihood::initParameters().
Referenced by bpp::OptimizationTools::buildDistanceTree(), bpp::RHomogeneousMixedTreeLikelihood::initialize(), and bpp::DRHomogeneousMixedTreeLikelihood::initialize().
|
virtualinherited |
This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree.
Definition at line 268 of file AbstractHomogeneousTreeLikelihood.cpp.
References bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::initialize().
|
pure virtualinherited |
Implemented in bpp::AbstractTreeLikelihood.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 297 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::initialized_.
Referenced by bpp::DRHomogeneousTreeLikelihood::getValue(), bpp::DRNonHomogeneousTreeLikelihood::getValue(), bpp::RHomogeneousTreeLikelihood::getValue(), and bpp::RNonHomogeneousTreeLikelihood::getValue().
|
staticinherited |
Set all conditional likelihoods to 1.
likelihoodArray | the likelihood array. |
Definition at line 267 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), and bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays().
|
virtualinherited |
Set the dataset for which the likelihood must be evaluated.
sites | The data set to use. |
Implements bpp::TreeLikelihood.
Definition at line 133 of file RHomogeneousTreeLikelihood.cpp.
References bpp::PatternTools::getSequenceSubset().
Referenced by bpp::RHomogeneousMixedTreeLikelihood::setData().
|
inlinevirtualinherited |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 243 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, and bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_.
|
inlinevirtualinherited |
Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 233 of file AbstractHomogeneousTreeLikelihood.h.
References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, and bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_.
|
inherited |
Implements the Function interface.
Update the parameter list and call the applyParameters() method. Then compute the likelihoods at each node (computeLikelihood() method) and call the getLogLikelihood() 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 | The parameter list to pass to the function. |
Definition at line 250 of file RHomogeneousTreeLikelihood.cpp.
|
virtualinherited |
Exception | If the model could not be set (for instance, because of a wrong alphabet type). |
Implements bpp::HomogeneousTreeLikelihood.
Definition at line 172 of file AbstractHomogeneousTreeLikelihood.cpp.
References bpp::Node::getId().
|
protectedinherited |
Definition at line 118 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().
|
protectedinherited |
Definition at line 89 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 227 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 228 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().
|
mutableprotectedinherited |
Definition at line 95 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 225 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::AbstractTreeLikelihood::getAlphabet(), bpp::AbstractTreeLikelihood::getData(), bpp::AbstractTreeLikelihood::getNumberOfSites(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::operator=(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().
|
mutableprotectedinherited |
Definition at line 93 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 229 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::TwoTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::TwoTreeLikelihood::initialize(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::isInitialized(), and bpp::AbstractTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 117 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::getMaximumBranchLength(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().
|
protectedinherited |
Definition at line 116 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::getMinimumBranchLength(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().
|
protectedinherited |
|
protectedinherited |
Definition at line 88 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates(), bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousMixedTreeLikelihood::getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihood(), bpp::RHomogeneousTreeLikelihood::getDLogLikelihood(), bpp::RHomogeneousTreeLikelihood::getLikelihood(), bpp::RHomogeneousTreeLikelihood::getLogLikelihood(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Pointer toward all nodes in the tree.
The position in the array is the number used in the parameter name. This may be different from the node id, unless you used the resetNodeId method on the input tree.
Definition at line 105 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
mutableprotectedinherited |
Definition at line 91 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 61 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.
Referenced by 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::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::TwoTreeLikelihood::initParameters(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 97 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().
|
mutableprotectedinherited |
Definition at line 226 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::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(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractTreeLikelihood::getTree(), 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(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().
|
protectedinherited |
Definition at line 114 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::operator=().