bpp-phyl
2.2.0
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This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions. More...
#include <Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h>
Public Member Functions | |
DRNonHomogeneousTreeLikelihood (const Tree &tree, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose=true, bool reparametrizeRoot=false) throw (Exception) | |
Build a new DRNonHomogeneousTreeLikelihood object without data. More... | |
DRNonHomogeneousTreeLikelihood (const Tree &tree, const SiteContainer &data, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose=true, bool reparametrizeRoot=false) throw (Exception) | |
Build a new DRNonHomogeneousTreeLikelihood object and compute the corresponding likelihood. More... | |
DRNonHomogeneousTreeLikelihood (const DRNonHomogeneousTreeLikelihood &lik) | |
Copy constructor. More... | |
DRNonHomogeneousTreeLikelihood & | operator= (const DRNonHomogeneousTreeLikelihood &lik) |
virtual | ~DRNonHomogeneousTreeLikelihood () |
DRNonHomogeneousTreeLikelihood * | clone () const |
void | computeTreeLikelihood () |
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 |
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 (int nodeId, size_t siteIndex) throw (NodeNotFoundException) |
Get the substitution model associated to a given node and alignment column. More... | |
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 AbstractTreeLikelihood 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... | |
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 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 | 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 SubstitutionModel * | getSubstitutionModelForNode (int nodeId) const throw (NodeNotFoundException) |
Get the substitution model associated to a given node. More... | |
SubstitutionModel * | getSubstitutionModelForNode (int nodeId) throw (NodeNotFoundException) |
Get the substitution model associated to a given node. 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 NonHomogeneousTreeLikelihood interface. | |
Other methods are implemented in the AbstractTreeLikelihood class. | |
const SubstitutionModelSet * | getSubstitutionModelSet () const |
SubstitutionModelSet * | getSubstitutionModelSet () |
void | setSubstitutionModelSet (SubstitutionModelSet *modelSet) throw (Exception) |
ParameterList | getRootFrequenciesParameters () const |
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 |
virtual void | computeSubtreeLikelihoodPostfix (const Node *node) |
virtual void | computeSubtreeLikelihoodPrefix (const Node *node) |
virtual void | computeRootLikelihood () |
virtual void | computeTreeDLikelihoodAtNode (const Node *node) |
virtual void | computeTreeDLikelihoods () |
virtual void | computeTreeD2LikelihoodAtNode (const Node *node) |
virtual void | computeTreeD2Likelihoods () |
void | fireParameterChanged (const ParameterList ¶ms) |
void | resetLikelihoodArrays (const Node *node) |
virtual void | displayLikelihood (const Node *node) |
This method is mainly for debugging purpose. More... | |
virtual void | computeAllTransitionProbabilities () |
Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes. More... | |
virtual void | computeTransitionProbabilitiesForNode (const Node *node) |
Fill the pxy_, dpxy_ and d2pxy_ arrays for one node. More... | |
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 | |
DRASDRTreeLikelihoodData * | likelihoodData_ |
double | minusLogLik_ |
SubstitutionModelSet * | modelSet_ |
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... | |
std::map< int, const Node * > | idToNode_ |
An index linking nodes to their id, for faster access than the getNode() method. 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_ |
bool | reparametrizeRoot_ |
int | root1_ |
int | root2_ |
DiscreteDistribution * | rateDistribution_ |
const SiteContainer * | data_ |
TreeTemplate< Node > * | tree_ |
bool | computeFirstOrderDerivatives_ |
bool | computeSecondOrderDerivatives_ |
bool | initialized_ |
Private Member Functions | |
void | init_ () throw (Exception) |
Method called by constructors. More... | |
Friends | |
class | DRNonHomogeneousMixedTreeLikelihood |
This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions.
The substitution model is the same over the tree (homogeneous model). A non-uniform distribution of rates among the sites is allowed (ASRV models).
This class uses an instance of the DRASDRTreeLikelihoodData for conditionnal likelihood storage.
All nodes share the same site patterns.
Important note: The input tree will be considered as rooted, since the likelihood of non-stationary models depends on the position of the root. If the input tree is not rooted, it will be considered as a rotted tree with a root multifurcation.
Definition at line 68 of file DRNonHomogeneousTreeLikelihood.h.
DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood | ( | const Tree & | tree, |
SubstitutionModelSet * | modelSet, | ||
DiscreteDistribution * | rDist, | ||
bool | verbose = true , |
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bool | reparametrizeRoot = false |
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throw | ( | Exception | |
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Build a new DRNonHomogeneousTreeLikelihood 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. |
modelSet | The set of substitution models to use. |
rDist | The rate across sites distribution to use. If true, any rooted tree will be unrooted before likelihood computation. |
verbose | Should I display some info? |
reparametrizeRoot | Should we reparametrize the branch lengths at root? |
Exception | in an error occured. |
Definition at line 60 of file DRNonHomogeneousTreeLikelihood.cpp.
Referenced by clone().
DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood | ( | const Tree & | tree, |
const SiteContainer & | data, | ||
SubstitutionModelSet * | modelSet, | ||
DiscreteDistribution * | rDist, | ||
bool | verbose = true , |
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bool | reparametrizeRoot = false |
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throw | ( | Exception | |
) |
Build a new DRNonHomogeneousTreeLikelihood object and compute the corresponding likelihood.
This constructor initializes all parameters, data, and likelihood arrays.
tree | The tree to use. |
data | Sequences to use. |
modelSet | The set of substitution models to use. |
rDist | The rate across sites distribution to use. If true, any rooted tree will be unrooted before likelihood computation. |
verbose | Should I display some info? |
reparametrizeRoot | Should we reparametrize the branch lengths at root? |
Exception | in an error occured. |
Definition at line 78 of file DRNonHomogeneousTreeLikelihood.cpp.
DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood | ( | const DRNonHomogeneousTreeLikelihood & | lik | ) |
Copy constructor.
Definition at line 107 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASDRTreeLikelihoodData::clone(), likelihoodData_, bpp::DRASDRTreeLikelihoodData::setTree(), and bpp::AbstractTreeLikelihood::tree_.
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virtual |
Definition at line 131 of file DRNonHomogeneousTreeLikelihood.cpp.
References likelihoodData_.
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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.
Definition at line 314 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::initialized_, bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractNonHomogeneousTreeLikelihood::reparametrizeRoot_, bpp::AbstractNonHomogeneousTreeLikelihood::root1_, and bpp::AbstractNonHomogeneousTreeLikelihood::root2_.
Referenced by fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged().
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inlinevirtual |
Implements bpp::DRTreeLikelihood.
Definition at line 131 of file DRNonHomogeneousTreeLikelihood.h.
References DRNonHomogeneousTreeLikelihood().
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protectedvirtualinherited |
Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.
Definition at line 393 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::SubstitutionModelSet::getRootFrequencies(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, and bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.
Referenced by fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), and bpp::AbstractNonHomogeneousTreeLikelihood::initialize().
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inlinevirtual |
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 211 of file DRNonHomogeneousTreeLikelihood.h.
References computeLikelihoodAtNode_(), and bpp::AbstractTreeLikelihood::tree_.
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protectedvirtual |
Definition at line 1101 of file DRNonHomogeneousTreeLikelihood.cpp.
References computeLikelihoodFromArrays(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, and bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.
Referenced by computeLikelihoodAtNode(), computeTreeD2LikelihoodAtNode(), and computeTreeDLikelihoodAtNode().
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staticprotected |
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 1186 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().
Referenced by computeLikelihoodAtNode_(), computeRootLikelihood(), computeSubtreeLikelihoodPostfix(), and computeSubtreeLikelihoodPrefix().
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staticprotected |
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 1235 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().
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protectedvirtual |
Definition at line 1031 of file DRNonHomogeneousTreeLikelihood.cpp.
References computeLikelihoodFromArrays(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays(), bpp::Node::getNumberOfSons(), bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray(), bpp::Node::getSon(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(), bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
Referenced by computeTreeLikelihood().
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protectedvirtual |
Initialize the arrays corresponding to each son node for the node passed as argument. The method is called for each son node and the result stored in the corresponding array.
Definition at line 861 of file DRNonHomogeneousTreeLikelihood.cpp.
References computeLikelihoodFromArrays(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, and resetLikelihoodArrays().
Referenced by computeTreeLikelihood().
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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.
Definition at line 921 of file DRNonHomogeneousTreeLikelihood.cpp.
References computeLikelihoodFromArrays(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(), and bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.
Referenced by computeTreeLikelihood().
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protectedvirtualinherited |
Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.
Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.
Definition at line 406 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractNonHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::SubstitutionModel::getd2Pij_dt2(), bpp::Node::getDistanceToFather(), bpp::SubstitutionModel::getdPij_dt(), bpp::Node::getId(), bpp::SubstitutionModelSet::getModelForNode(), bpp::SubstitutionModel::getPij_t(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), fireParameterChanged(), and bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged().
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protectedvirtual |
Definition at line 444 of file DRNonHomogeneousTreeLikelihood.cpp.
References computeLikelihoodAtNode_(), bpp::AbstractNonHomogeneousTreeLikelihood::d2pxy_, bpp::DRASDRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by computeTreeD2Likelihoods().
|
protectedvirtual |
Definition at line 492 of file DRNonHomogeneousTreeLikelihood.cpp.
References computeTreeD2LikelihoodAtNode(), bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, and bpp::AbstractNonHomogeneousTreeLikelihood::nodes_.
Referenced by fireParameterChanged().
|
protectedvirtual |
Definition at line 316 of file DRNonHomogeneousTreeLikelihood.cpp.
References computeLikelihoodAtNode_(), bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::DRASDRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by computeTreeDLikelihoods().
|
protectedvirtual |
Definition at line 363 of file DRNonHomogeneousTreeLikelihood.cpp.
References computeTreeDLikelihoodAtNode(), bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, and bpp::AbstractNonHomogeneousTreeLikelihood::nodes_.
Referenced by fireParameterChanged().
void DRNonHomogeneousTreeLikelihood::computeTreeLikelihood | ( | ) |
Definition at line 852 of file DRNonHomogeneousTreeLikelihood.cpp.
References computeRootLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), and bpp::AbstractTreeLikelihood::tree_.
Referenced by fireParameterChanged().
|
protectedvirtual |
This method is mainly for debugging purpose.
node | The node at which likelihood values must be displayed. |
Definition at line 1317 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), and 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(), 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_.
|
protected |
Definition at line 245 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihoods(), computeTreeDLikelihoods(), computeTreeLikelihood(), bpp::SubstitutionModelSet::getNodeParameters(), bpp::SubstitutionModelSet::getNodesWithParameter(), bpp::SubstitutionModelSet::getRootFrequencies(), bpp::AbstractNonHomogeneousTreeLikelihood::idToNode_, bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
|
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 183 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getAlphabetStateAsChar(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 181 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getAlphabetStateAsInt(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 179 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getAlphabetStates(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
virtualinherited |
Get the branch lengths parameters.
Implements bpp::TreeLikelihood.
Definition at line 280 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::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 DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative | ( | const std::string & | variable | ) | const |
throw | ( | Exception | |||
) |
Definition at line 373 of file DRNonHomogeneousTreeLikelihood.cpp.
|
virtual |
Get the likelihood for the whole dataset.
Implements bpp::TreeLikelihood.
Definition at line 162 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::AbstractTreeLikelihoodData::getWeights(), likelihoodData_, and bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_.
|
inlinevirtual |
Implements bpp::DRTreeLikelihood.
Definition at line 208 of file DRNonHomogeneousTreeLikelihood.h.
References likelihoodData_.
|
inlinevirtual |
Implements bpp::DRTreeLikelihood.
Definition at line 209 of file DRNonHomogeneousTreeLikelihood.h.
References likelihoodData_.
|
virtual |
Get the likelihood for a site.
site | The site index to analyse. |
Implements bpp::TreeLikelihood.
Definition at line 196 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), and likelihoodData_.
|
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 209 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray(), and likelihoodData_.
|
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 223 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray(), and likelihoodData_.
|
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 176 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::AbstractTreeLikelihoodData::getWeights(), likelihoodData_, and bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_.
Referenced by getValue().
|
virtual |
Get the logarithm of the likelihood for a site.
site | The site index to analyse. |
Implements bpp::TreeLikelihood.
Definition at line 203 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), and likelihoodData_.
|
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 216 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray(), and likelihoodData_.
|
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 230 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray(), and likelihoodData_.
|
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 279 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_.
|
inlinevirtualinherited |
Definition at line 278 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 210 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getModelForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, and bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 215 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
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 177 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getNumberOfStates(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
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 191 of file AbstractNonHomogeneousTreeLikelihood.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 206 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.
|
inlinevirtualinherited |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 235 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getRootFrequenciesParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
double DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative | ( | const std::string & | variable | ) | const |
throw | ( | Exception | |||
) |
Definition at line 502 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::Node::getId(), bpp::Node::getNumberOfSons(), and bpp::Node::getSon().
|
inline |
Definition at line 203 of file DRNonHomogeneousTreeLikelihood.h.
|
inlinevirtual |
Get the index (used for inner computations) of a given site (original alignment column).
site | An alignment position. |
Implements bpp::TreeLikelihood.
Definition at line 154 of file DRNonHomogeneousTreeLikelihood.h.
References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), and likelihoodData_.
|
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 69 of file NonHomogeneousTreeLikelihood.h.
References bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelForNode().
|
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 74 of file NonHomogeneousTreeLikelihood.h.
References bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelForNode().
|
inlinevirtualinherited |
Get the substitution model associated to a given node.
nodeId | The id of the request node. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 196 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getModelForNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Get the substitution model associated to a given node.
nodeId | The id of the request node. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 201 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getModelForNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
virtualinherited |
Get the parameters associated to substitution model(s).
Implements bpp::TreeLikelihood.
Definition at line 288 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 229 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 231 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
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 208 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::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_().
double DRNonHomogeneousTreeLikelihood::getValue | ( | ) | const | |
throw | ( | Exception | ||
) |
Function and NNISearchable interface.
Definition at line 305 of file DRNonHomogeneousTreeLikelihood.cpp.
References getLogLikelihood(), and bpp::AbstractTreeLikelihood::isInitialized().
|
private |
Method called by constructors.
Definition at line 98 of file DRNonHomogeneousTreeLikelihood.cpp.
|
virtualinherited |
Definition at line 348 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractNonHomogeneousTreeLikelihood::reparametrizeRoot_, bpp::AbstractNonHomogeneousTreeLikelihood::root1_, and bpp::AbstractNonHomogeneousTreeLikelihood::root2_.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().
|
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::RNonHomogeneousMixedTreeLikelihood.
Definition at line 268 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractTreeLikelihood::data_, bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractNonHomogeneousTreeLikelihood::initParameters().
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::initialize().
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virtualinherited |
This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree.
Definition at line 296 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), and bpp::RNonHomogeneousMixedTreeLikelihood::initialize().
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pure virtualinherited |
Implemented in bpp::AbstractTreeLikelihood.
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inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 297 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::initialized_.
Referenced by bpp::DRHomogeneousTreeLikelihood::getValue(), getValue(), bpp::RHomogeneousTreeLikelihood::getValue(), and bpp::RNonHomogeneousTreeLikelihood::getValue().
DRNonHomogeneousTreeLikelihood & DRNonHomogeneousTreeLikelihood::operator= | ( | const DRNonHomogeneousTreeLikelihood & | lik | ) |
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staticinherited |
Set all conditional likelihoods to 1.
likelihoodArray | the likelihood array. |
Definition at line 267 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), computeLikelihoodFromArrays(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), and resetLikelihoodArrays().
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Definition at line 836 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), likelihoodData_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().
Referenced by computeSubtreeLikelihoodPostfix().
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virtual |
Set the dataset for which the likelihood must be evaluated.
sites | The data set to use. |
Implements bpp::TreeLikelihood.
Definition at line 138 of file DRNonHomogeneousTreeLikelihood.cpp.
References bpp::PatternTools::getSequenceSubset().
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inlinevirtualinherited |
Definition at line 268 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_, and bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_.
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Definition at line 258 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_, and bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_.
void DRNonHomogeneousTreeLikelihood::setParameters | ( | const ParameterList & | parameters | ) | |
throw | ( | ParameterNotFoundException, | |||
ConstraintException | |||||
) |
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 237 of file DRNonHomogeneousTreeLikelihood.cpp.
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virtualinherited |
Exception | If the model could not be set (for instance, because of a wrong alphabet type). |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 195 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::Node::getId().
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friend |
Definition at line 309 of file DRNonHomogeneousTreeLikelihood.h.
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Definition at line 127 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().
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Definition at line 93 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::RNonHomogeneousMixedTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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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(), fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().
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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(), fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().
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Definition at line 99 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2LikelihoodAtNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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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().
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mutableprotectedinherited |
Definition at line 97 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoodAtNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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mutableprotectedinherited |
An index linking nodes to their id, for faster access than the getNode() method.
Definition at line 114 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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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=().
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mutableprotected |
Definition at line 73 of file DRNonHomogeneousTreeLikelihood.h.
Referenced by computeLikelihoodAtNode_(), computeRootLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), computeTreeD2LikelihoodAtNode(), computeTreeDLikelihoodAtNode(), displayLikelihood(), DRNonHomogeneousTreeLikelihood(), getLikelihood(), getLikelihoodData(), getLikelihoodForASite(), getLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClassForAState(), getLogLikelihood(), getLogLikelihoodForASite(), getLogLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClassForAState(), getSiteIndex(), operator=(), resetLikelihoodArrays(), and ~DRNonHomogeneousTreeLikelihood().
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Definition at line 126 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getMaximumBranchLength(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().
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Definition at line 125 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getMinimumBranchLength(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().
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Definition at line 74 of file DRNonHomogeneousTreeLikelihood.h.
Referenced by operator=().
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Definition at line 92 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStates(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewBranchModelIterator(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractNonHomogeneousTreeLikelihood::getNumberOfStates(), bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequenciesParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelSet(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), computeLikelihoodAtNode_(), computeRootLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2LikelihoodAtNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoodAtNode(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by computeLikelihoodAtNode_(), computeRootLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), computeTreeD2LikelihoodAtNode(), computeTreeDLikelihoodAtNode(), getLikelihood(), getLogLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewBranchModelIterator(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), computeTreeD2Likelihoods(), computeTreeDLikelihoods(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::RNonHomogeneousTreeLikelihood::getD2LogLikelihood(), bpp::RNonHomogeneousTreeLikelihood::getDLogLikelihood(), bpp::RNonHomogeneousTreeLikelihood::getLikelihood(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihood(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), computeLikelihoodAtNode_(), computeRootLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2LikelihoodAtNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoodAtNode(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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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 109 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2Likelihoods(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoods(), fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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mutableprotectedinherited |
Definition at line 95 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), computeLikelihoodAtNode_(), computeRootLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), computeSubtreeLikelihoodPostfix(), computeSubtreeLikelihoodPrefix(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2LikelihoodAtNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihoodAtNode(), bpp::AbstractNonHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 61 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::applyParameters(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), computeRootLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), computeTreeD2LikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), computeTreeDLikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), 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=().
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Definition at line 129 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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Definition at line 130 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 130 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 101 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), computeLikelihoodAtNode_(), computeRootLikelihood(), computeSubtreeLikelihoodPrefix(), fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequencies(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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mutableprotectedinherited |
Definition at line 226 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), computeRootLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeLikelihood(), computeTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), 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=(), 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().
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protectedinherited |
Definition at line 123 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::operator=().