bpp-phyl  2.4.0
ProbabilisticSubstitutionMapping.h
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1 //
2 // File: ProbabilisticSubstitutionMapping.h
3 // Created by: Julien Dutheil
4 // Created on: Wed Apr 5 10:47 2006
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (November 16, 2004, 2005, 2006)
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
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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
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38 */
39 
40 #ifndef _PROBABILISTICSUBSTITUTIONMAPPING_H_
41 #define _PROBABILISTICSUBSTITUTIONMAPPING_H_
42 
43 #include "SubstitutionMapping.h"
44 #include "SubstitutionCount.h"
45 #include "../TreeExceptions.h"
46 
47 #include <Bpp/Text/TextTools.h>
48 
49 // From the STL:
50 #include <vector>
51 
52 namespace bpp
53 {
54 
65 {
66  private:
73  std::vector< std::vector< std::vector<double> > > mapping_;
74 
75  public:
76 
86  ProbabilisticSubstitutionMapping(const Tree& tree, const SubstitutionCount* sc, size_t numberOfSites) :
87  AbstractMapping(tree), AbstractSubstitutionMapping(tree), substitutionCount_(sc), mapping_(0)
88  {
89  setNumberOfSites(numberOfSites);
90  }
91 
98  AbstractMapping(tree), AbstractSubstitutionMapping(tree), substitutionCount_(0), mapping_(0)
99  {}
100 
101 
103 
105  AbstractMapping(psm), AbstractSubstitutionMapping(psm), substitutionCount_(psm.substitutionCount_), mapping_(psm.mapping_)
106  {}
107 
109  {
111  substitutionCount_ = psm.substitutionCount_;
112  mapping_ = psm.mapping_;
113  return *this;
114  }
115 
117 
118  public:
119 
121  {
122  if (!substitutionCount_) return 1;
123  return substitutionCount_->getNumberOfSubstitutionTypes();
124  }
125 
126  virtual double getNumberOfSubstitutions(int nodeId, size_t siteIndex, size_t type) const
127  {
128  return mapping_[siteIndex][getNodeIndex(nodeId)][type];
129  }
130 
131  virtual std::vector<double> getNumberOfSubstitutions(int nodeId, size_t siteIndex) const
132  {
133  return mapping_[siteIndex][getNodeIndex(nodeId)];
134  }
135 
141  virtual void setTree(const Tree& tree);
142 
143  virtual void setNumberOfSites(size_t numberOfSites);
144 
150  virtual double& operator()(size_t nodeIndex, size_t siteIndex, size_t type)
151  {
152  return mapping_[siteIndex][nodeIndex][type];
153  }
154 
160  virtual const double& operator()(size_t nodeIndex, size_t siteIndex, size_t type) const
161  {
162  return mapping_[siteIndex][nodeIndex][type];
163  }
164 
170  std::vector< std::vector<double> >& operator[](size_t siteIndex)
171  {
172  return mapping_[siteIndex];
173  }
174 
180  const std::vector< std::vector<double> >& operator[](size_t siteIndex) const
181  {
182  return mapping_[siteIndex];
183  }
184 };
185 
186 } //end of namespace bpp.
187 
188 #endif //_PROBABILISTICSUBSTITUTIONMAPPING_H_
189 
Partial implementation of the substitution mapping interface.
virtual void setNumberOfSites(size_t numberOfSites)
virtual void setTree(const Tree &tree)
(Re)-set the phylogenetic tree associated to this mapping.
Data storage class for probabilistic substitution mappings.
ProbabilisticSubstitutionMapping(const Tree &tree)
Build a new ProbabilisticSubstitutionMapping object.
ProbabilisticSubstitutionMapping(const ProbabilisticSubstitutionMapping &psm)
Interface for phylogenetic tree objects.
Definition: Tree.h:148
virtual double & operator()(size_t nodeIndex, size_t siteIndex, size_t type)
Direct access to substitution numbers.
ProbabilisticSubstitutionMapping & operator=(const ProbabilisticSubstitutionMapping &psm)
std::vector< std::vector< std::vector< double > > > mapping_
Substitution numbers storage.
virtual std::vector< double > getNumberOfSubstitutions(int nodeId, size_t siteIndex) const
ProbabilisticSubstitutionMapping * clone() const
virtual size_t getNumberOfSubstitutionTypes() const
Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes().
The SubstitutionsCount interface.
ProbabilisticSubstitutionMapping(const Tree &tree, const SubstitutionCount *sc, size_t numberOfSites)
Build a new ProbabilisticSubstitutionMapping object.
const std::vector< std::vector< double > > & operator[](size_t siteIndex) const
Direct access to substitution numbers.
std::vector< std::vector< double > > & operator[](size_t siteIndex)
Direct access to substitution numbers.
virtual const double & operator()(size_t nodeIndex, size_t siteIndex, size_t type) const
Direct access to substitution numbers.
virtual double getNumberOfSubstitutions(int nodeId, size_t siteIndex, size_t type) const
Partial implementation of the mapping interface.
Definition: Mapping.h:128
virtual size_t getNodeIndex(int nodeId) const
Definition: Mapping.h:226
AbstractSubstitutionMapping & operator=(const AbstractSubstitutionMapping &absm)