InvariantMixedDiscreteDistribution.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#ifndef BPP_NUMERIC_PROB_INVARIANTMIXEDDISCRETEDISTRIBUTION_H
#define BPP_NUMERIC_PROB_INVARIANTMIXEDDISCRETEDISTRIBUTION_H


#include "AbstractDiscreteDistribution.h"

namespace bpp
{
class InvariantMixedDiscreteDistribution :
  public AbstractDiscreteDistribution
{
private:
  std::unique_ptr<DiscreteDistributionInterface> dist_;
  double invariant_, p_;
  std::string nestedPrefix_;

public:
  InvariantMixedDiscreteDistribution(std::unique_ptr<DiscreteDistributionInterface> dist, double p, double invariant = 0.);

  virtual ~InvariantMixedDiscreteDistribution() {}

  InvariantMixedDiscreteDistribution(const InvariantMixedDiscreteDistribution& imdd) :
    AbstractDiscreteDistribution(imdd),
    dist_(imdd.dist_->clone()),
    invariant_(imdd.invariant_),
    p_(imdd.p_),
    nestedPrefix_(imdd.nestedPrefix_)
  {}

  InvariantMixedDiscreteDistribution& operator=(const InvariantMixedDiscreteDistribution& imdd)
  {
    AbstractDiscreteDistribution::operator=(imdd);
    dist_.reset(imdd.dist_->clone());
    invariant_    = imdd.invariant_;
    p_            = imdd.p_;
    nestedPrefix_ = imdd.nestedPrefix_;
    return *this;
  }

  InvariantMixedDiscreteDistribution* clone() const { return new InvariantMixedDiscreteDistribution(*this); }

public:
  std::string getName() const { return "Invariant"; }

  void fireParameterChanged(const ParameterList& parameters);

  void setNamespace(const std::string& prefix);

  void setNumberOfCategories(size_t nbClasses)
  {
    dist_->setNumberOfCategories(nbClasses);
    updateDistribution();
  }

  const DiscreteDistributionInterface& variableSubDistribution() const { return *dist_; }

  double qProb(double x) const
  {
    return (x >= p_ + (1 - p_) * dist_->pProb(invariant_)) ? dist_->qProb((x - p_) / (1 - p_)) : dist_->qProb(x / (1 - p_));
  }

  double pProb(double x) const
  {
    return (1 - p_) * dist_->pProb(x) + (x < invariant_ ? 0 : p_);
  }

  double Expectation(double a) const
  {
    return (1 - p_) * dist_->Expectation(a) + (a < invariant_ ? 0 : p_);
  }

  void setMedian(bool median)
  {
    if (median_ != median)
    {
      median_ = median;
      dist_->setMedian(median);
      updateDistribution();
    }
  }

  void discretize()
  {
    dist_->discretize();
    updateDistribution();
  }

  void restrictToConstraint(const ConstraintInterface& c);

protected:
  void updateDistribution();
};
} // end of namespace bpp.
#endif // BPP_NUMERIC_PROB_INVARIANTMIXEDDISCRETEDISTRIBUTION_H