bpp-phyl  2.4.0
AbstractTreeLikelihood.cpp
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1 //
2 // File: AbstractTreeLikelihood.cpp
3 // Created by: Julien Dutheil
4 // Created on: Fri Oct 17 17:57:21 2003
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
33 data to be ensured and, more generally, to use and operate it in the
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 "AbstractTreeLikelihood.h"
41 
42 using namespace bpp;
43 
44 /******************************************************************************/
45 
47 {
49  for (size_t i = 0; i < l.size(); i++) l[i] = getLikelihoodForASite(i);
50  return l;
51 }
52 
53 /******************************************************************************/
54 
56 {
58  for (size_t i = 0; i < l.size(); i++) l[i] = getLogLikelihoodForASite(i);
59  return l;
60 }
61 
62 /******************************************************************************/
63 
65 {
67  for (size_t i = 0; i < l.size(); i++)
68  {
69  Vdouble* l_i = & l[i];
70  l_i->resize(getNumberOfStates());
71  for (size_t x = 0; x < l_i->size(); x++)
72  {
73  (* l_i)[x] = getLikelihoodForASiteForAState(i, static_cast<int>(x));
74  }
75  }
76  return l;
77 }
78 
79 /******************************************************************************/
80 
82 {
84  for (size_t i = 0; i < l.size(); i++)
85  {
86  Vdouble* l_i = & l[i];
87  l_i->resize(getNumberOfStates());
88  for (size_t x = 0; x < l_i->size(); x++)
89  {
90  (* l_i)[x] = getLogLikelihoodForASiteForAState(i, static_cast<int>(x));
91  }
92  }
93  return l;
94 }
95 
96 /******************************************************************************/
97 
virtual size_t getNumberOfStates() const =0
virtual double getLikelihoodForASiteForAState(size_t site, int state) const =0
Get the likelihood for a site and for a state.
virtual double getLogLikelihoodForASite(size_t site) const =0
Get the logarithm of the likelihood for a site.
virtual double getLogLikelihoodForASiteForAState(size_t site, int state) const =0
Get the logarithm of the likelihood for a site and for a state.
virtual double getLikelihoodForASite(size_t site) const =0
Get the likelihood for a site.
std::vector< double > Vdouble
VVdouble getLikelihoodForEachSiteForEachState() const
Get the likelihood for each site and for each state.
VVdouble getLogLikelihoodForEachSiteForEachState() const
Get the logarithm of the likelihood for each site and for each state.
Vdouble getLikelihoodForEachSite() const
Get the likelihood for each site.
size_t getNumberOfSites() const
Get the number of sites in the dataset.
Vdouble getLogLikelihoodForEachSite() const
Get the logarithm of the likelihood for each site.
std::vector< Vdouble > VVdouble