/usr/include/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h is in libbpp-core-dev 2.1.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 | //
// File: InvariantMixedDiscreteDistribution.h
// Created by: Julien Dutheil
// Created on: Mon Dec 24 12:02 2007
//
/*
Copyright or © or Copr. CNRS, (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
with loading, using, modifying and/or developing or reproducing the
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
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _INVARIANTMIXEDDISCRETEDISTRIBUTION_H_
#define _INVARIANTMIXEDDISCRETEDISTRIBUTION_H_
#include "AbstractDiscreteDistribution.h"
namespace bpp
{
/**
* @brief Discrete mixed distribution, with a one-category fixed value (called "invariant") and a user-specified multi-categories distribution.
*
* The term "invariant" comes from the use of such distributions in phylogenetics:
* the fixed category corresponds to a value of 0 and describes invariant positions in an alignment.
*/
class InvariantMixedDiscreteDistribution:
public AbstractDiscreteDistribution
{
private:
DiscreteDistribution* dist_;
double invariant_, p_;
std::string nestedPrefix_;
public:
/**
* @brief Build a new InvariantMixedDiscreteDistribution object.
*
* @param dist The distribution to use. The mixed distribution will "own" this distribution object.
* This means that the distribution will be cloned in case of copy of this instance, and will be
* deleted with this instance.
* @param p The probability of being in the invariant category.
* @param invariant The value of the invariant category (typically 0, but other values may be specified).
*/
InvariantMixedDiscreteDistribution(DiscreteDistribution* dist, double p, double invariant = 0.);
virtual ~InvariantMixedDiscreteDistribution()
{
delete dist_;
}
InvariantMixedDiscreteDistribution(const InvariantMixedDiscreteDistribution& imdd):
AbstractParameterAliasable(imdd),
AbstractDiscreteDistribution(imdd),
dist_(dynamic_cast<DiscreteDistribution *>(imdd.dist_->clone())),
invariant_(imdd.invariant_), p_(imdd.p_),
nestedPrefix_(imdd.nestedPrefix_)
{}
InvariantMixedDiscreteDistribution& operator=(const InvariantMixedDiscreteDistribution& imdd)
{
AbstractParameterAliasable::operator=(imdd);
AbstractDiscreteDistribution::operator=(imdd);
dist_ = dynamic_cast<DiscreteDistribution *>(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);
/*
*@ brief Sets the number of categories of the embedded
*distribution. The number of categories of this class equals this
*plus one if the invariant_ is not in the embedded distribution
*values.
*
*/
void setNumberOfCategories(unsigned int nbClasses) {
dist_->setNumberOfCategories(nbClasses);
updateDistribution();
}
/**
* @return The nested, conditional, sub-distribution.
*/
const DiscreteDistribution * getVariableSubDistribution() 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 Constraint& c);
protected:
void updateDistribution();
};
} //end of namespace bpp.
#endif //_INVARIANTMIXEDDISCRETEDISTRIBUTION_H_
|