bpp-phyl
2.2.0
|
A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model. More...
#include <Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h>
Public Member Functions | |
DRHomogeneousMixedTreeLikelihood (const Tree &tree, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true, bool rootArray=false) throw (Exception) | |
Build a new DRHomogeneousMixedTreeLikelihood object without data. More... | |
DRHomogeneousMixedTreeLikelihood (const Tree &tree, const SiteContainer &data, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true, bool rootArray=false) throw (Exception) | |
Build a new DRHomogeneousMixedTreeLikelihood object with data. More... | |
DRHomogeneousMixedTreeLikelihood (const DRHomogeneousMixedTreeLikelihood &lik) | |
DRHomogeneousMixedTreeLikelihood & | operator= (const DRHomogeneousMixedTreeLikelihood &lik) |
virtual | ~DRHomogeneousMixedTreeLikelihood () |
DRHomogeneousMixedTreeLikelihood * | clone () const |
void | initialize () throw (Exception) |
Init the likelihood object. More... | |
void | fireParameterChanged (const ParameterList ¶ms) |
void | computeTreeLikelihood () |
virtual void | computeTreeDLikelihoods () |
void | setParameters (const ParameterList ¶meters) throw (ParameterNotFoundException, ConstraintException) |
Implements the Function interface. More... | |
double | getValue () const throw (Exception) |
Function and NNISearchable interface. More... | |
DRASDRTreeLikelihoodData * | getLikelihoodData () |
const DRASDRTreeLikelihoodData * | getLikelihoodData () const |
virtual void | computeLikelihoodAtNode (int nodeId, VVVdouble &likelihoodArray) const |
Compute the likelihood array at a given node. More... | |
virtual void | initParameters () |
This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree. More... | |
virtual void | applyParameters () 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... | |
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 |
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... | |
virtual ParameterList | getDerivableParameters () const =0 |
All derivable parameters. More... | |
virtual ParameterList | getNonDerivableParameters () const =0 |
All non derivable parameters. More... | |
The TreeLikelihood interface. | |
Other methods are implemented in the DRHomogeneousTreeLikelihood class. | |
double | getLikelihood () const |
Get the likelihood for the whole dataset. More... | |
double | getLogLikelihood () const |
Get the logarithm of the likelihood for the whole dataset. More... | |
void | setData (const SiteContainer &sites) throw (Exception) |
Set the dataset for which the likelihood must be evaluated. 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... | |
DerivableFirstOrder interface. | |
double | getFirstOrderDerivative (const std::string &variable) const throw (Exception) |
DerivableSecondOrder interface. | |
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 AbstractTreeLikelihood class. | |
size_t | getSiteIndex (size_t site) const throw (IndexOutOfBoundsException) |
Get the index (used for inner computations) of a given site (original alignment column). More... | |
The TreeLikelihood interface. | |
Other methods are implemented in the AbstractTreeLikelihood class. | |
size_t | getNumberOfStates () const |
const std::vector< int > & | getAlphabetStates () const |
int | getAlphabetStateAsInt (size_t i) const |
std::string | getAlphabetStateAsChar (size_t i) const |
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... | |
ParameterList | getDerivableParameters () const |
All derivable parameters. More... | |
ParameterList | getNonDerivableParameters () const |
All non derivable parameters. More... | |
Retrieve some particular parameters subsets. | |
virtual VVdouble | getTransitionProbabilities (int nodeId, size_t siteIndex) const =0 |
Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More... | |
The DiscreteRatesAcrossSites interface implementation: | |
const 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 | |
virtual void | computeLikelihoodAtNode_ (const Node *node, VVVdouble &likelihoodArray, const Node *sonNode=0) const |
virtual void | computeSubtreeLikelihoodPostfix (const Node *node) |
Compute the likelihood for a subtree defined by the Tree::Node node. More... | |
virtual void | computeSubtreeLikelihoodPrefix (const Node *node) |
virtual void | computeRootLikelihood () |
virtual void | computeTreeD2LikelihoodAtNode (const Node *) |
virtual void | computeTreeD2Likelihoods () |
void | resetLikelihoodArrays (const Node *node) |
virtual void | displayLikelihood (const Node *node) |
This method is mainly for debugging purpose. More... | |
virtual void | computeTreeDLikelihoodAtNode (const Node *node) |
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... | |
Static Protected Member Functions | |
static void | computeLikelihoodFromArrays (const std::vector< const VVVdouble *> &iLik, const std::vector< const VVVdouble *> &tProb, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true) |
Compute conditional likelihoods. More... | |
static void | computeLikelihoodFromArrays (const std::vector< const VVVdouble *> &iLik, const std::vector< const VVVdouble *> &tProb, const VVVdouble *iLikR, const VVVdouble *tProbR, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true) |
Compute conditional likelihoods. More... | |
Protected Attributes | |
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 Attributes | |
std::vector< DRHomogeneousTreeLikelihood * > | treeLikelihoodsContainer_ |
std::vector< double > | probas_ |
bool | rootArray_ |
A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model.
In all computations, the average of the likelihoods, probabilities are computed.
Definition at line 60 of file DRHomogeneousMixedTreeLikelihood.h.
DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood | ( | const Tree & | tree, |
SubstitutionModel * | model, | ||
DiscreteDistribution * | rDist, | ||
bool | checkRooted = true , |
||
bool | verbose = true , |
||
bool | rootArray = false |
||
) | |||
throw | ( | Exception | |
) |
Build a new DRHomogeneousMixedTreeLikelihood object without data.
This constructor only initialize the parameters. To compute a likelihood, you will need to call the setData() and the computeTreeLikelihood() methods.
tree | The tree to use. |
model | The mixed substitution model to use. |
rDist | The rate across sites distribution to use. |
checkRooted | Tell if we have to check for the tree to be unrooted. If true, any rooted tree will be unrooted before likelihood computation. |
verbose | Should I display some info? |
rootArray | is true if the array of the likelihoods at the root should be computed (useful for ancestral reconstruction). |
Exception | in an error occured. |
Definition at line 54 of file DRHomogeneousMixedTreeLikelihood.cpp.
References bpp::MixedSubstitutionModel::getNModel(), bpp::MixedSubstitutionModel::getNProbability(), and bpp::MixedSubstitutionModel::getNumberOfModels().
Referenced by clone().
DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood | ( | const Tree & | tree, |
const SiteContainer & | data, | ||
SubstitutionModel * | model, | ||
DiscreteDistribution * | rDist, | ||
bool | checkRooted = true , |
||
bool | verbose = true , |
||
bool | rootArray = false |
||
) | |||
throw | ( | Exception | |
) |
Build a new DRHomogeneousMixedTreeLikelihood object with data.
This constructor initializes all parameters, data, and likelihood arrays.
tree | The tree to use. |
data | Sequences to use. |
model | The mixed substitution model to use. |
rDist | The rate across sites distribution to use. |
checkRooted | Tell if we have to check for the tree to be unrooted. If true, any rooted tree will be unrooted before likelihood computation. |
verbose | Should I display some info? |
rootArray | is true if the array of the likelihoods at the root should be computed (useful for ancestral reconstruction). |
Exception | in an error occured. |
Definition at line 80 of file DRHomogeneousMixedTreeLikelihood.cpp.
References bpp::MixedSubstitutionModel::getNModel(), bpp::MixedSubstitutionModel::getNProbability(), and bpp::MixedSubstitutionModel::getNumberOfModels().
DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood | ( | const DRHomogeneousMixedTreeLikelihood & | lik | ) |
Definition at line 129 of file DRHomogeneousMixedTreeLikelihood.cpp.
References probas_, and treeLikelihoodsContainer_.
|
virtual |
Definition at line 142 of file DRHomogeneousMixedTreeLikelihood.cpp.
References treeLikelihoodsContainer_.
|
virtualinherited |
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 in bpp::RHomogeneousClockTreeLikelihood.
Definition at line 286 of file AbstractHomogeneousTreeLikelihood.cpp.
References bpp::SubstitutionModel::getFrequencies(), bpp::AbstractTreeLikelihood::initialized_, bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_.
Referenced by bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::RHomogeneousTreeLikelihood::fireParameterChanged().
|
inlinevirtual |
Implements bpp::DRTreeLikelihood.
Definition at line 132 of file DRHomogeneousMixedTreeLikelihood.h.
References DRHomogeneousMixedTreeLikelihood().
|
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().
|
inlinevirtualinherited |
Compute the likelihood array at a given node.
nodeId | The id of the node to consider. |
likelihoodArray | The array where to store the results. |
Implements bpp::DRTreeLikelihood.
Definition at line 209 of file DRHomogeneousTreeLikelihood.h.
References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), and bpp::AbstractTreeLikelihood::tree_.
|
protectedvirtual |
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 352 of file DRHomogeneousMixedTreeLikelihood.cpp.
References bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, probas_, and treeLikelihoodsContainer_.
|
staticprotectedinherited |
Compute conditional likelihoods.
This method is the "core" likelihood computation function, performing all the product uppon all nodes, the summation for each ancestral state and each rate class. It is designed for inner usage, and a maximum efficiency, so no checking is performed on the input parameters. Use with care!
iLik | A vector of likelihood arrays, one for each conditional node. |
tProb | A vector of transition probabilities, one for each node. |
oLik | The likelihood array to store the computed likelihoods. |
nbNodes | The number of nodes = the size of the input vectors. |
nbDistinctSites | The number of distinct sites (the first dimension of the likelihood array). |
nbClasses | The number of rate classes (the second dimension of the likelihood array). |
nbStates | The number of states (the third dimension of the likelihood array). |
reset | Tell if the output likelihood array must be initalized prior to computation. If true, the resetLikelihoodArray method will be called. |
Definition at line 825 of file DRHomogeneousTreeLikelihood.cpp.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().
Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), and bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix().
|
staticprotectedinherited |
Compute conditional likelihoods.
This method is the "core" likelihood computation function, performing all the product uppon all nodes, the summation for each ancestral state and each rate class. This function is specific to non-reversible models: the subtree containing the root is specified separately. It is designed for inner usage, and a maximum efficiency, so no checking is performed on the input parameters. Use with care!
iLik | A vector of likelihood arrays, one for each conditional node. |
tProb | A vector of transition probabilities, one for each node. |
iLikR | The likelihood array for the subtree containing the root of the tree. |
tProbR | The transition probabilities for thr subtree containing the root of the tree. |
oLik | The likelihood array to store the computed likelihoods. |
nbNodes | The number of nodes = the size of the input vectors. |
nbDistinctSites | The number of distinct sites (the first dimension of the likelihood array). |
nbClasses | The number of rate classes (the second dimension of the likelihood array). |
nbStates | The number of states (the third dimension of the likelihood array). |
reset | Tell if the output likelihood array must be initalized prior to computation. If true, the resetLikelihoodArray method will be called. |
Definition at line 874 of file DRHomogeneousTreeLikelihood.cpp.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().
|
protectedvirtual |
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 344 of file DRHomogeneousMixedTreeLikelihood.cpp.
References treeLikelihoodsContainer_.
Referenced by computeTreeLikelihood(), and initialize().
|
protectedvirtual |
Compute the likelihood for a subtree defined by the Tree::Node node.
node | The root of the subtree. |
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 328 of file DRHomogeneousMixedTreeLikelihood.cpp.
References treeLikelihoodsContainer_.
|
protectedvirtual |
This method initilize the remaining likelihood arrays, corresponding to father nodes. It must be called after the postfix method because it requires that the arrays for son nodes to be be computed.
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 336 of file DRHomogeneousMixedTreeLikelihood.cpp.
References treeLikelihoodsContainer_.
|
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().
|
protectedvirtual |
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 448 of file DRHomogeneousMixedTreeLikelihood.cpp.
References treeLikelihoodsContainer_.
|
protectedvirtual |
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 456 of file DRHomogeneousMixedTreeLikelihood.cpp.
References treeLikelihoodsContainer_.
|
protectedvirtualinherited |
Definition at line 291 of file DRHomogeneousTreeLikelihood.cpp.
References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::DRASDRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoods().
|
virtual |
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 392 of file DRHomogeneousMixedTreeLikelihood.cpp.
References treeLikelihoodsContainer_.
void DRHomogeneousMixedTreeLikelihood::computeTreeLikelihood | ( | ) |
Definition at line 203 of file DRHomogeneousMixedTreeLikelihood.cpp.
References computeRootLikelihood(), rootArray_, and treeLikelihoodsContainer_.
|
protectedvirtual |
This method is mainly for debugging purpose.
node | The node at which likelihood values must be displayed. |
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 515 of file DRHomogeneousMixedTreeLikelihood.cpp.
References treeLikelihoodsContainer_.
|
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_.
|
virtual |
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 173 of file DRHomogeneousMixedTreeLikelihood.cpp.
References bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), getLogLikelihood(), bpp::MixedSubstitutionModel::getNModel(), bpp::MixedSubstitutionModel::getNumberOfModels(), bpp::MixedSubstitutionModel::getProbabilities(), bpp::DRHomogeneousTreeLikelihood::minusLogLik_, bpp::AbstractHomogeneousTreeLikelihood::model_, probas_, and treeLikelihoodsContainer_.
|
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_.
|
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().
|
virtualinherited |
All derivable parameters.
Usually, this contains all branch lengths parameters.
Implements bpp::TreeLikelihood.
Reimplemented in bpp::RHomogeneousClockTreeLikelihood.
Definition at line 73 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
All derivable parameters.
Usually, this contains all branch lengths parameters.
Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
double DRHomogeneousMixedTreeLikelihood::getFirstOrderDerivative | ( | const std::string & | variable | ) | const |
throw | ( | Exception | |||
) |
Definition at line 400 of file DRHomogeneousMixedTreeLikelihood.cpp.
|
virtual |
Get the likelihood for the whole dataset.
Implements bpp::TreeLikelihood.
Definition at line 217 of file DRHomogeneousMixedTreeLikelihood.cpp.
References bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::AbstractTreeLikelihoodData::getWeights(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, probas_, and treeLikelihoodsContainer_.
|
inlinevirtualinherited |
Implements bpp::DRTreeLikelihood.
Definition at line 206 of file DRHomogeneousTreeLikelihood.h.
References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.
Referenced by bpp::NNIHomogeneousTreeLikelihood::setData(), and bpp::NNIHomogeneousTreeLikelihood::topologyChangeTested().
|
inlinevirtualinherited |
Implements bpp::DRTreeLikelihood.
Definition at line 207 of file DRHomogeneousTreeLikelihood.h.
References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.
|
virtual |
Get the likelihood for a site.
site | The site index to analyse. |
Implements bpp::TreeLikelihood.
Definition at line 272 of file DRHomogeneousMixedTreeLikelihood.cpp.
References probas_, and treeLikelihoodsContainer_.
Referenced by getLogLikelihoodForASite().
|
virtual |
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 290 of file DRHomogeneousMixedTreeLikelihood.cpp.
References probas_, and treeLikelihoodsContainer_.
Referenced by getLogLikelihoodForASiteForARateClass().
|
virtual |
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 308 of file DRHomogeneousMixedTreeLikelihood.cpp.
References probas_, and treeLikelihoodsContainer_.
Referenced by getLogLikelihoodForASiteForARateClassForAState().
|
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().
|
virtual |
Get the logarithm of the likelihood for the whole dataset.
Implements bpp::TreeLikelihood.
Definition at line 240 of file DRHomogeneousMixedTreeLikelihood.cpp.
References bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::AbstractTreeLikelihoodData::getWeights(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, probas_, and treeLikelihoodsContainer_.
Referenced by fireParameterChanged().
|
virtual |
Get the logarithm of the likelihood for a site.
site | The site index to analyse. |
Implements bpp::TreeLikelihood.
Definition at line 283 of file DRHomogeneousMixedTreeLikelihood.cpp.
References getLikelihoodForASite().
|
virtual |
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 301 of file DRHomogeneousMixedTreeLikelihood.cpp.
References getLikelihoodForASiteForARateClass().
|
virtual |
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 320 of file DRHomogeneousMixedTreeLikelihood.cpp.
References getLikelihoodForASiteForARateClassForAState().
|
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_.
|
virtualinherited |
All non derivable parameters.
Usually, this contains all substitution model parameters and rate distribution.
Implements bpp::TreeLikelihood.
Reimplemented in bpp::RHomogeneousClockTreeLikelihood.
Definition at line 82 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
All non derivable parameters.
Usually, this contains all substitution model parameters and rate distribution.
Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
|
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 DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative | ( | const std::string & | variable | ) | const |
throw | ( | Exception | |||
) |
Definition at line 464 of file DRHomogeneousMixedTreeLikelihood.cpp.
|
inline |
Definition at line 176 of file DRHomogeneousMixedTreeLikelihood.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 152 of file DRHomogeneousTreeLikelihood.h.
References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), and bpp::DRHomogeneousTreeLikelihood::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 |
Function and NNISearchable interface.
Definition at line 280 of file DRHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::isInitialized(), and bpp::DRHomogeneousTreeLikelihood::minusLogLik_.
Referenced by bpp::NNIHomogeneousTreeLikelihood::getTopologyValue().
|
virtualinherited |
Reimplemented in bpp::RHomogeneousClockTreeLikelihood.
Definition at line 307 of file AbstractHomogeneousTreeLikelihood.cpp.
References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, and bpp::AbstractHomogeneousTreeLikelihood::nodes_.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().
|
virtual |
Init the likelihood object.
This method is used to initialize all parameters. It is typically called after the constructor and the setData method. It contains virtual methods that can't be called in the constructor.
Exception | if something bad happened, for instance if no data are associated to the likelihood function. |
Reimplemented from bpp::AbstractHomogeneousTreeLikelihood.
Definition at line 151 of file DRHomogeneousMixedTreeLikelihood.cpp.
References computeRootLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), rootArray_, and treeLikelihoodsContainer_.
|
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().
DRHomogeneousMixedTreeLikelihood & DRHomogeneousMixedTreeLikelihood::operator= | ( | const DRHomogeneousMixedTreeLikelihood & | lik | ) |
Definition at line 111 of file DRHomogeneousMixedTreeLikelihood.cpp.
References bpp::DRHomogeneousTreeLikelihood::operator=(), probas_, rootArray_, and treeLikelihoodsContainer_.
|
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().
|
protectedvirtual |
Reimplemented from bpp::DRHomogeneousTreeLikelihood.
Definition at line 195 of file DRHomogeneousMixedTreeLikelihood.cpp.
References treeLikelihoodsContainer_.
|
virtual |
Set the dataset for which the likelihood must be evaluated.
sites | The data set to use. |
Implements bpp::TreeLikelihood.
Definition at line 162 of file DRHomogeneousMixedTreeLikelihood.cpp.
References bpp::DRHomogeneousTreeLikelihood::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 fireParameterChanged() method.
If a subset of the whole parameter list is passed to the function, only these parameters are updated and the other remain constant (i.e. equal to their last value).
parameters | The parameter list to pass to the function. |
Definition at line 233 of file DRHomogeneousTreeLikelihood.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 |
Definition at line 72 of file DRHomogeneousTreeLikelihood.h.
Referenced by bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::getValue(), and bpp::DRHomogeneousTreeLikelihood::operator=().
|
protectedinherited |
Definition at line 88 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), 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(), 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 computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihood(), 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(), 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=().
|
private |
Definition at line 65 of file DRHomogeneousMixedTreeLikelihood.h.
Referenced by computeLikelihoodAtNode_(), DRHomogeneousMixedTreeLikelihood(), fireParameterChanged(), getLikelihood(), getLikelihoodForASite(), getLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClassForAState(), getLogLikelihood(), and 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=().
|
private |
Definition at line 70 of file DRHomogeneousMixedTreeLikelihood.h.
Referenced by computeTreeLikelihood(), initialize(), and 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().
|
private |
Definition at line 64 of file DRHomogeneousMixedTreeLikelihood.h.
Referenced by computeLikelihoodAtNode_(), computeRootLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), computeTreeD2LikelihoodAtNode(), computeTreeD2Likelihoods(), computeTreeDLikelihoods(), computeTreeLikelihood(), displayLikelihood(), DRHomogeneousMixedTreeLikelihood(), fireParameterChanged(), getLikelihood(), getLikelihoodForASite(), getLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClassForAState(), getLogLikelihood(), initialize(), operator=(), resetLikelihoodArrays(), and ~DRHomogeneousMixedTreeLikelihood().
|
protectedinherited |
Definition at line 114 of file AbstractHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::operator=().