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// File: RHomogeneousMixedTreeLikelihood.h
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// Created by: Davud Fournier, Laurent Gueguen
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Copyright or � or Copr. CNRS, (November 16, 2004)
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This software is a computer program whose purpose is to provide classes
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for phylogenetic data analysis.
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This software is governed by the CeCILL license under French law and
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abiding by the rules of distribution of free software. You can use,
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modify and/ or redistribute the software under the terms of the CeCILL
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license as circulated by CEA, CNRS and INRIA at the following URL
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"http://www.cecill.info".
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As a counterpart to the access to the source code and rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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economic rights, and the successive licensors have only limited
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In this respect, the user's attention is drawn to the risks associated
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with loading, using, modifying and/or developing or reproducing the
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software by the user in light of its specific status of free software,
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that may mean that it is complicated to manipulate, and that also
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therefore means that it is reserved for developers and experienced
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professionals having in-depth computer knowledge. Users are therefore
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encouraged to load and test the software's suitability as regards their
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requirements in conditions enabling the security of their systems and/or
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data to be ensured and, more generally, to use and operate it in the
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same conditions as regards security.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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#ifndef _RHOMOGENEOUSMIXEDTREELIKELIHOOD_H_
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#define _RHOMOGENEOUSMIXEDTREELIKELIHOOD_H_
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#include "RHomogeneousTreeLikelihood.h"
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#include "../Model/SubstitutionModel.h"
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#include "../Model/MixedSubstitutionModel.h"
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#include <Bpp/Numeric/VectorTools.h>
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#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
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*@ brief A class to compute the average of several
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*RHomogeneousTreeLikelihood defined from a Mixed Substitution
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* In all the calculs, the average of the likelihoods, probabilities
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class RHomogeneousMixedTreeLikelihood :
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public RHomogeneousTreeLikelihood
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std::vector<RHomogeneousTreeLikelihood*> treeLikelihoodsContainer_;
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std::vector<double> probas_;
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* @brief Build a new RHomogeneousMixedTreeLikelihood object without
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* This constructor only initialize the parameters. To compute a
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* likelihood, you will need to call the setData() and the
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* computeTreeLikelihood() methods.
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* @param tree The tree to use.
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* @param model The mixed substitution model to use.
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* @param rDist The rate across sites distribution to use.
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* @param checkRooted Tell if we have to check for the tree to be unrooted.
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* If true, any rooted tree will be unrooted before likelihood computation.
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* @param verbose Should I display some info?
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* @param usePatterns Tell if recursive site compression should be performed.
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* @throw Exception in an error occured.
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RHomogeneousMixedTreeLikelihood(
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SubstitutionModel* model,
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DiscreteDistribution* rDist,
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bool checkRooted = true,
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bool usePatterns = true)
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* @brief Build a new RHomogeneousMixedTreeLikelihood object with data.
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* This constructor initializes all parameters, data, and likelihood arrays.
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* @param tree The tree to use.
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* @param data Sequences to use.
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* @param model The mixed substitution model to use.
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* @param rDist The rate across sites distribution to use.
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* @param checkRooted Tell if we have to check for the tree to be unrooted.
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* If true, any rooted tree will be unrooted before likelihood computation.
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* @param verbose Should I display some info?
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* @param usePatterns Tell if recursive site compression should be performed.
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* @throw Exception in an error occured.
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RHomogeneousMixedTreeLikelihood(
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const SiteContainer& data,
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SubstitutionModel* model,
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DiscreteDistribution* rDist,
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bool checkRooted = true,
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bool usePatterns = true)
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RHomogeneousMixedTreeLikelihood(const RHomogeneousMixedTreeLikelihood& lik);
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RHomogeneousMixedTreeLikelihood& operator=(const RHomogeneousMixedTreeLikelihood& lik);
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virtual ~RHomogeneousMixedTreeLikelihood();
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RHomogeneousMixedTreeLikelihood* clone() const { return new RHomogeneousMixedTreeLikelihood(*this); }
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* @name The TreeLikelihood interface.
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* Other methods are implemented in the RHomogeneousTreeLikelihood class.
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void setData(const SiteContainer& sites) throw (Exception);
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* @name The DiscreteRatesAcrossSites interface implementation:
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double getLikelihoodForASiteForARateClass(unsigned int site, unsigned int rateClass) const;
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double getLogLikelihoodForASiteForARateClass(unsigned int site, unsigned int rateClass) const;
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double getLikelihoodForASiteForARateClassForAState(unsigned int site, unsigned int rateClass, int state) const;
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double getLogLikelihoodForASiteForARateClassForAState(unsigned int site, unsigned int rateClass, int state) const;
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void initialize() throw (Exception);
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void fireParameterChanged(const ParameterList& params);
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void computeTreeLikelihood();
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virtual double getDLikelihoodForASiteForARateClass(unsigned int site, unsigned int rateClass) const;
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virtual void computeTreeDLikelihood(const std::string& variable);
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virtual double getD2LikelihoodForASiteForARateClass(unsigned int site, unsigned int rateClass) const;
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virtual void computeTreeD2Likelihood(const std::string& variable);
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* @brief Compute the likelihood for a subtree defined by the Tree::Node <i>node</i>.
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* @param node The root of the subtree.
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virtual void computeSubtreeLikelihood(const Node* node); // Recursive method.
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virtual void computeDownSubtreeDLikelihood(const Node*);
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virtual void computeDownSubtreeD2Likelihood(const Node*);
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* @brief This method is used by fireParameterChanged method.
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void computeAllTransitionProbabilities();
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* @brief This method is used by fireParameterChanged method.
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void computeTransitionProbabilitiesForNode(const Node* node);
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* @brief This method is mainly for debugging purpose.
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* @param node The node at which likelihood values must be displayed.
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virtual void displayLikelihood(const Node* node);
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} // end of namespace bpp.
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#endif // _RHOMOGENEOUSMIXEDTREELIKELIHOOD_H_
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src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h
