bpp-phyl  2.4.0
DiscreteRatesAcrossSitesTreeLikelihood.h
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1 //
2 // File: DiscreteRateAcrossSitesTreeLikelihood.h
3 // Created by: Julien Dutheil
4 // Created on: 2005
5 //
6 
7 /*
8  Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
9 
10  This software is a computer program whose purpose is to provide classes
11  for phylogenetic data analysis.
12 
13  This software is governed by the CeCILL license under French law and
14  abiding by the rules of distribution of free software. You can use,
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17  "http://www.cecill.info".
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39 
40 #ifndef _DISCRETE_RATES_ACROSS_SITESTREELIKELIHOOD_H_
41 #define _DISCRETE_RATES_ACROSS_SITESTREELIKELIHOOD_H_
42 
43 #include "TreeLikelihood.h"
44 
47 
48 namespace bpp
49 {
50 
57  public virtual TreeLikelihood
58  {
59  public:
62 
63  public:
64 
70  virtual const DiscreteDistribution* getRateDistribution() const = 0;
71 
78 
86  virtual double getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const = 0;
87 
95  virtual double getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const = 0;
96 
105  virtual double getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const = 0;
106 
115  virtual double getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const = 0;
116 
123 
131 
138 
146 
154  virtual VVdouble getPosteriorProbabilitiesOfEachRate() const = 0;
155 
162  virtual std::vector<size_t> getRateClassWithMaxPostProbOfEachSite() const = 0;
163 
170  virtual Vdouble getRateWithMaxPostProbOfEachSite() const = 0;
171 
178  virtual Vdouble getPosteriorRateOfEachSite() const = 0;
179 
185  virtual ParameterList getRateDistributionParameters() const = 0;
186 
192  virtual size_t getNumberOfClasses() const = 0;
193 
203  virtual VVVdouble getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const = 0;
204 
205  };
206 
207 } //end of namespace bpp.
208 
209 #endif //_DISCRETERATESACROSSSITESTREELIKELIHOOD_H_
210 
virtual VVdouble getLikelihoodForEachSiteForEachRateClass() const =0
Get the likelihood for each site and each rate class.
The TreeLikelihood interface.
virtual size_t getNumberOfClasses() const =0
Get the number of classes.
virtual double getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0
Get the likelihood for a site knowing its rate class and its ancestral state.
virtual double getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0
Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state...
virtual VVdouble getPosteriorProbabilitiesOfEachRate() const =0
Get the posterior probability for each site of belonging to a particular rate class.
virtual double getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0
Get the likelihood for a site knowing its rate class.
virtual VVVdouble getLogLikelihoodForEachSiteForEachRateClassForEachState() const =0
Get the logarithm of the likelihood for each site and each rate class and each state.
virtual std::vector< size_t > getRateClassWithMaxPostProbOfEachSite() const =0
Get the posterior rate class (the one with maximum posterior probability) for each site...
virtual ParameterList getRateDistributionParameters() const =0
Get the parameters associated to the rate distirbution.
virtual Vdouble getRateWithMaxPostProbOfEachSite() const =0
Get the posterior rate (the one with maximum posterior probability) for each site.
Interface for rate across sites (RAS) implementation.
std::vector< double > Vdouble
virtual VVdouble getLogLikelihoodForEachSiteForEachRateClass() const =0
Get the logarithm of the likelihood for each site and each rate class.
virtual double getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0
Get the logarithm of the likelihood for a site knowing its rate class.
virtual VVVdouble getLikelihoodForEachSiteForEachRateClassForEachState() const =0
Get the likelihood for each site and each rate class and each state.
virtual const DiscreteDistribution * getRateDistribution() const =0
Get the rate distribution used for the computation.
virtual Vdouble getPosteriorRateOfEachSite() const =0
Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities...
virtual VVVdouble getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const =0
Retrieves all Pij(t) for a particular branch, defined by the upper node.
std::vector< VVdouble > VVVdouble
std::vector< Vdouble > VVdouble