TreeLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_TREELIKELIHOOD_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_TREELIKELIHOOD_H
 
#include <Bpp/Numeric/Function/Functions.h>
#include <Bpp/Numeric/ParameterList.h>
#include <Bpp/Numeric/Parametrizable.h>
#include <Bpp/Numeric/VectorTools.h>
 
#include "../../Model/SubstitutionModel.h"
#include "TreeLikelihoodData.h"
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Container/AlignmentData.h>
 
namespace bpp
{
class TreeLikelihoodInterface :
  public virtual SecondOrderDerivable
{
public:
  class BranchIterator
  {
public:
    virtual ~BranchIterator() {}
 
public:
    virtual int next() = 0;
    virtual bool hasNext() const = 0;
  };
 
  class SiteIterator
  {
public:
    virtual ~SiteIterator() {}
 
public:
    virtual size_t next() = 0;
    virtual bool hasNext() const = 0;
  };
 
  class ConstBranchModelDescription
  {
public:
    virtual ~ConstBranchModelDescription() {}
 
public:
    virtual const TransitionModelInterface& model() const = 0;
    virtual std::shared_ptr<const TransitionModelInterface> getModel() const = 0;
 
    virtual const SubstitutionModelInterface& substitutionModel() const = 0;
    virtual std::shared_ptr<const SubstitutionModelInterface> getSubstitutionModel() const = 0;
 
    virtual SiteIterator* getNewSiteIterator() const = 0;
  };
 
  class ConstBranchModelIterator
  {
public:
    virtual ~ConstBranchModelIterator() {}
 
public:
    virtual ConstBranchModelDescription* next() = 0;
    virtual bool hasNext() const = 0;
  };
 
  class ConstSiteModelDescription
  {
public:
    virtual ~ConstSiteModelDescription() {}
 
public:
    virtual const TransitionModelInterface& model() const = 0;
    virtual std::shared_ptr<const TransitionModelInterface> getModel() const = 0;
 
    virtual const SubstitutionModelInterface& substitutionModel() const = 0;
    virtual std::shared_ptr<const SubstitutionModelInterface> getSubstitutionModel() const = 0;
 
    virtual BranchIterator* getNewBranchIterator() const = 0;
  };
 
  class ConstSiteModelIterator
  {
public:
    virtual ~ConstSiteModelIterator() {}
 
public:
    virtual ConstSiteModelDescription* next() = 0;
    virtual bool hasNext() const = 0;
  };
 
public:
  TreeLikelihoodInterface() {}
  virtual ~TreeLikelihoodInterface() {}
 
  TreeLikelihoodInterface* clone() const override = 0;
 
public:
  virtual void setData(const AlignmentDataInterface& sites) = 0;
 
  virtual const AlignmentDataInterface& data() const = 0;
 
  virtual void initialize() = 0;
 
  virtual bool isInitialized() const = 0;
 
  virtual bool hasLikelihoodData() const = 0;
 
  virtual TreeLikelihoodData& likelihoodData() = 0;
 
  virtual const TreeLikelihoodData& likelihoodData() const = 0;
 
  virtual double getLikelihoodForASite(size_t site) const = 0;
 
  virtual double getLogLikelihoodForASite(size_t site) const = 0;
 
  virtual double getLikelihoodForASiteForAState(size_t site, int state) const = 0;
 
  virtual double getLogLikelihoodForASiteForAState(size_t site, int state) const = 0;
 
  virtual Vdouble getLikelihoodPerSite() const = 0;
 
  virtual Vdouble getLogLikelihoodPerSite() const = 0;
 
  virtual VVdouble getLikelihoodPerSitePerState() const = 0;
 
  virtual VVdouble getLogLikelihoodPerSitePerState() const = 0;
 
  virtual double getLikelihood() const = 0;
 
  virtual double getLogLikelihood() const = 0;
 
  virtual const Tree& tree() const = 0;
 
  virtual size_t getNumberOfSites() const = 0;
 
  virtual size_t getNumberOfStates() const = 0;
 
  virtual int getAlphabetStateAsInt(size_t i) const = 0;
 
  virtual std::string getAlphabetStateAsChar(size_t i) const = 0;
 
  virtual const std::vector<int>& getAlphabetStates() const = 0;
 
  virtual std::shared_ptr<const Alphabet> getAlphabet() const = 0;
 
  virtual ParameterList getBranchLengthsParameters() const = 0;
 
  virtual ParameterList getSubstitutionModelParameters() const = 0;
 
  virtual std::shared_ptr<const TransitionModelInterface> getModelForSite(int nodeId, size_t siteIndex) const = 0;
 
  virtual std::shared_ptr<TransitionModelInterface> getModelForSite(int nodeId, size_t siteIndex) = 0;
 
  virtual VVdouble getTransitionProbabilities(int nodeId, size_t siteIndex) const = 0;
 
  virtual ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const = 0;
 
  virtual ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const = 0;
 
  virtual size_t getSiteIndex(size_t site) const = 0;
 
  virtual const std::vector<double>& getRootFrequencies(size_t siteIndex) const = 0;
 
  virtual void enableDerivatives(bool yn) = 0;
 
  virtual ParameterList getDerivableParameters() const = 0;
 
  virtual ParameterList getNonDerivableParameters() const = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_TREELIKELIHOOD_H