InvariantMixedDiscreteDistribution.cpp

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//
// File: InvariantMixedDiscreteDistribution.cpp
// Authors:
//   Julien Dutheil
// Created: 2007-12-24 12:02:00
//
 
/*
  Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
  
  This software is a computer program whose purpose is to provide classes
  for numerical calculus.
  
  This software is governed by the CeCILL license under French law and
  abiding by the rules of distribution of free software. You can use,
  modify and/ or redistribute the software under the terms of the CeCILL
  license as circulated by CEA, CNRS and INRIA at the following URL
  "http://www.cecill.info".
  
  As a counterpart to the access to the source code and rights to copy,
  modify and redistribute granted by the license, users are provided only
  with a limited warranty and the software's author, the holder of the
  economic rights, and the successive licensors have only limited
  liability.
  
  In this respect, the user's attention is drawn to the risks associated
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  software by the user in light of its specific status of free software,
  that may mean that it is complicated to manipulate, and that also
  therefore means that it is reserved for developers and experienced
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*/
 
 
#include "../../Utils/MapTools.h"
#include "InvariantMixedDiscreteDistribution.h"
 
using namespace bpp;
using namespace std;
 
/******************************************************************************/
 
InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(
  DiscreteDistribution* dist, double p, double invariant) :
  AbstractDiscreteDistribution(1, "Invariant."),
  dist_(dist),
  invariant_(invariant),
  p_(p),
  nestedPrefix_(dist->getNamespace())
{
  // We first change the namespace of the nested distribution:
  dist_->setNamespace("Invariant." + nestedPrefix_);
  addParameters_(dist_->getIndependentParameters());
  addParameter_(new Parameter("Invariant.p", p, Parameter::PROP_CONSTRAINT_IN));
 
  updateDistribution();
}
 
/******************************************************************************/
 
void InvariantMixedDiscreteDistribution::fireParameterChanged(const ParameterList& parameters)
{
  AbstractDiscreteDistribution::fireParameterChanged(parameters);
  p_ = getParameterValue("p");
  dist_->matchParametersValues(parameters);
 
  updateDistribution();
}
 
/******************************************************************************/
 
void InvariantMixedDiscreteDistribution::updateDistribution()
{
  distribution_.clear();
  bounds_.clear();
 
  size_t distNCat = dist_->getNumberOfCategories();
  vector<double> probs = dist_->getProbabilities();
  vector<double> cats  = dist_->getCategories();
 
  distribution_[invariant_] = p_;
  for (size_t i = 0; i < distNCat; i++)
  {
    if (cats[i] == invariant_)
      distribution_[invariant_] += (1. - p_) * probs[i];
    else
      distribution_[cats[i]] = (1. - p_) * probs[i];
  }
 
  intMinMax_->setLowerBound(dist_->getLowerBound(), !dist_->strictLowerBound());
  intMinMax_->setUpperBound(dist_->getUpperBound(), !dist_->strictUpperBound());
 
  if (invariant_ <= intMinMax_->getLowerBound())
    intMinMax_->setLowerBound(invariant_, true);
  if (invariant_ >= intMinMax_->getUpperBound())
    intMinMax_->setUpperBound(invariant_, true);
 
  numberOfCategories_ = distribution_.size();
 
  // bounds_
 
  // if invariant_ is between 2 values of dist_, bounds_ are set in the
  // middle of the 3 values
 
  bool nv = true;
 
  double a = dist_->getCategory(0), b;
  if (nv && (invariant_ < a))
  {
    bounds_.push_back((a + invariant_) / 2);
    nv = false;
  }
 
  for (size_t i = 1; i < distNCat; i++)
  {
    b = dist_->getCategory(i);
    if (nv && (invariant_ < b))
    {
      bounds_.push_back((a + invariant_) / 2);
      bounds_.push_back((invariant_ + b) / 2);
      nv = false;
    }
    else
      bounds_.push_back(dist_->getBound(i - 1));
    a = b;
  }
 
  if (nv)
    bounds_.push_back((a + invariant_) / 2);
}
 
/******************************************************************************/
 
void InvariantMixedDiscreteDistribution::setNamespace(const string& prefix)
{
  AbstractDiscreteDistribution::setNamespace(prefix);
  // We also need to update the namespace of the nested distribution:
  dist_->setNamespace(prefix + nestedPrefix_);
}
 
/******************************************************************************/
 
void InvariantMixedDiscreteDistribution::restrictToConstraint(const Constraint& c)
{
  if (!c.isCorrect(invariant_))
    throw ConstraintException("Impossible to restrict to Constraint", &getParameter_("p"), invariant_);
 
  dist_->restrictToConstraint(c);
  updateDistribution();
}