bpp-phyl  2.4.0
RASTools.cpp
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1 //
2 // File: RASTools.cpp
3 // Created by: Julien Dutheil <Julien.Dutheil@univ-montp2.fr>
4 // Created on: May 24 2004
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,
15  modify and/ or redistribute the software under the terms of the CeCILL
16  license as circulated by CEA, CNRS and INRIA at the following URL
17  "http://www.cecill.info".
18 
19  As a counterpart to the access to the source code and rights to copy,
20  modify and redistribute granted by the license, users are provided only
21  with a limited warranty and the software's author, the holder of the
22  economic rights, and the successive licensors have only limited
23  liability.
24 
25  In this respect, the user's attention is drawn to the risks associated
26  with loading, using, modifying and/or developing or reproducing the
27  software by the user in light of its specific status of free software,
28  that may mean that it is complicated to manipulate, and that also
29  therefore means that it is reserved for developers and experienced
30  professionals having in-depth computer knowledge. Users are therefore
31  encouraged to load and test the software's suitability as regards their
32  requirements in conditions enabling the security of their systems and/or
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34  same conditions as regards security.
35 
36  The fact that you are presently reading this means that you have had
37  knowledge of the CeCILL license and that you accept its terms.
38  */
39 
40 #include "RASTools.h"
41 
43 
44 using namespace bpp;
45 
46 // From the STL
47 #include <map>
48 
49 using namespace std;
50 
52  const DiscreteRatesAcrossSitesTreeLikelihood& treeLikelihood)
53 {
54  // Get all posterior rate classes for each sites:
55  vector<size_t> classes = treeLikelihood.getRateClassWithMaxPostProbOfEachSite();
56  map<size_t, size_t> counts;
57  for (size_t i = 0; i < classes.size(); i++)
58  {
59  counts[classes[i]]++;
60  }
61 
62  // Now compute the distribution:
63  const DiscreteDistribution* rDist = treeLikelihood.getRateDistribution();
64  map<double, double> distribution;
65  for (map<size_t, size_t>::iterator i = counts.begin(); i != counts.end(); i++)
66  {
67  distribution[rDist->getCategory(i->first)] = (double)i->second / (double)classes.size();
68  }
69 
70  // Build a new distribution and return it:
71  return new SimpleDiscreteDistribution(distribution);
72 }
73 
STL namespace.
virtual std::vector< size_t > getRateClassWithMaxPostProbOfEachSite() const =0
Get the posterior rate class (the one with maximum posterior probability) for each site...
virtual double getCategory(size_t categoryIndex) const =0
Interface for rate across sites (RAS) implementation.
virtual const DiscreteDistribution * getRateDistribution() const =0
Get the rate distribution used for the computation.
static DiscreteDistribution * getPosteriorRateDistribution(const DiscreteRatesAcrossSitesTreeLikelihood &treeLikelihood)
Get the rate distribution estimated from a dataset.
Definition: RASTools.cpp:51