bpp-phyl3 3.0.0
AbstractKroneckerCodonSubstitutionModel.cpp
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1// SPDX-FileCopyrightText: The Bio++ Development Group
2//
3// SPDX-License-Identifier: CECILL-2.1
4
5#include "AbstractKroneckerCodonSubstitutionModel.h"
6
7using namespace bpp;
8using namespace std;
9
10/******************************************************************************/
11
12AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(
13 std::shared_ptr<const GeneticCode> gCode,
14 std::unique_ptr<NucleotideSubstitutionModelInterface> pmod,
15 const string& prefix) :
16 AbstractParameterAliasable(prefix),
17 AbstractKroneckerWordSubstitutionModel(
18 gCode->getSourceAlphabet(),
19 std::shared_ptr<const StateMapInterface>(new CanonicalStateMap(gCode->getSourceAlphabet(), false)),
20 prefix),
21 gCode_(gCode)
22{
23 enableEigenDecomposition(true);
24
25 size_t i;
26 for (i = 0; i < 3; i++)
27 {
28 VSubMod_.push_back(std::move(pmod));
29 VnestedPrefix_.push_back(VSubMod_[i]->getNamespace());
30 }
31
32 VSubMod_[0]->setNamespace(prefix + "123_" + VnestedPrefix_[0]);
33 VSubMod_[0]->enableEigenDecomposition(0);
34 addParameters_(VSubMod_[0]->getParameters());
35
36 initGenerators_();
37}
38
39AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(
40 std::shared_ptr<const GeneticCode> gCode,
41 std::unique_ptr<NucleotideSubstitutionModelInterface> pmod,
42 const std::vector<std::set< size_t>>& vPos,
43 const std::string& prefix) :
44 AbstractParameterAliasable(prefix),
45 AbstractKroneckerWordSubstitutionModel(
46 gCode->getSourceAlphabet(),
47 std::shared_ptr<const StateMapInterface>(new CanonicalStateMap(gCode->getSourceAlphabet(), false)),
48 prefix),
49 gCode_(gCode)
50{
51 enableEigenDecomposition(true);
52
53 shared_ptr<NucleotideSubstitutionModelInterface> pmod2 = std::move(pmod);
54 size_t i;
55 for (i = 0; i < 3; i++)
56 {
57 VSubMod_.push_back(pmod2);
58 VnestedPrefix_.push_back(pmod2->getNamespace());
59 }
60 pmod2->setNamespace(prefix + "123_" + VnestedPrefix_[0]);
61 pmod2->enableEigenDecomposition(0);
62 addParameters_(pmod2->getParameters());
63
64 initGenerators_();
65 setChangingPositions(vPos);
66}
67
68AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(
69 std::shared_ptr<const GeneticCode> gCode,
70 std::unique_ptr<NucleotideSubstitutionModelInterface> pmod1,
71 std::unique_ptr<NucleotideSubstitutionModelInterface> pmod2,
72 std::unique_ptr<NucleotideSubstitutionModelInterface> pmod3,
73 const string& prefix) :
74 AbstractParameterAliasable(prefix),
75 AbstractKroneckerWordSubstitutionModel(
76 gCode->getSourceAlphabet(),
77 shared_ptr<const StateMapInterface>(new CanonicalStateMap(gCode->getSourceAlphabet(), false)),
78 prefix),
79 gCode_(gCode)
80{
81 enableEigenDecomposition(true);
82
83 VSubMod_.push_back(std::move(pmod1));
84 VnestedPrefix_.push_back(VSubMod_[0]->getNamespace());
85 VSubMod_[0]->setNamespace(prefix + "1_" + VnestedPrefix_[0]);
86 VSubMod_[0]->enableEigenDecomposition(0);
87 addParameters_(VSubMod_[0]->getParameters());
88
89 VSubMod_.push_back(std::move(pmod2));
90 VnestedPrefix_.push_back(VSubMod_[1]->getNamespace());
91 VSubMod_[1]->setNamespace(prefix + "2_" + VnestedPrefix_[1]);
92 VSubMod_[1]->enableEigenDecomposition(0);
93 addParameters_(VSubMod_[1]->getParameters());
94
95 VSubMod_.push_back(std::move(pmod3));
96 VnestedPrefix_.push_back(VSubMod_[2]->getNamespace());
97 VSubMod_[2]->setNamespace(prefix + "3_" + VnestedPrefix_[2]);
98 VSubMod_[2]->enableEigenDecomposition(0);
99 addParameters_(VSubMod_[2]->getParameters());
100
101 initGenerators_();
102}
103
104AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(
105 std::shared_ptr<const GeneticCode> gCode,
106 std::unique_ptr<NucleotideSubstitutionModelInterface> pmod1,
107 std::unique_ptr<NucleotideSubstitutionModelInterface> pmod2,
108 std::unique_ptr<NucleotideSubstitutionModelInterface> pmod3,
109 const std::vector<std::set< size_t>>& vPos,
110 const std::string& prefix) :
111 AbstractParameterAliasable(prefix),
112 AbstractKroneckerWordSubstitutionModel(
113 gCode->getSourceAlphabet(),
114 shared_ptr<const StateMapInterface>(new CanonicalStateMap(gCode->getSourceAlphabet(), false)),
115 prefix),
116 gCode_(gCode)
117{
118 enableEigenDecomposition(true);
119
120 VSubMod_.push_back(std::move(pmod1));
121 VnestedPrefix_.push_back(VSubMod_[0]->getNamespace());
122 VSubMod_[0]->setNamespace(prefix + "1_" + VnestedPrefix_[0]);
123 VSubMod_[0]->enableEigenDecomposition(0);
124 addParameters_(VSubMod_[0]->getParameters());
125
126 VSubMod_.push_back(std::move(pmod2));
127 VnestedPrefix_.push_back(VSubMod_[1]->getNamespace());
128 VSubMod_[1]->setNamespace(prefix + "2_" + VnestedPrefix_[1]);
129 VSubMod_[1]->enableEigenDecomposition(0);
130 addParameters_(VSubMod_[1]->getParameters());
131
132 VSubMod_.push_back(std::move(pmod3));
133 VnestedPrefix_.push_back(VSubMod_[2]->getNamespace());
134 VSubMod_[2]->setNamespace(prefix + "3_" + VnestedPrefix_[2]);
135 VSubMod_[2]->enableEigenDecomposition(0);
136 addParameters_(VSubMod_[2]->getParameters());
137
138 initGenerators_();
139 setChangingPositions(vPos);
140}
141
142
143void AbstractKroneckerCodonSubstitutionModel::completeMatrices_()
144{
145 size_t i, j;
146 size_t salph = getNumberOfStates();
147
148 for (i = 0; i < salph; i++)
149 {
150 for (j = 0; j < salph; j++)
151 {
152 if (gCode_->isStop(static_cast<int>(i)) || gCode_->isStop(static_cast<int>(j)))
153 {
154 generator_(i, j) = 0;
155 }
156 else
157 generator_(i, j) *= getCodonsMulRate(i, j);
158 }
159 }
160}
bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel
AbstractKroneckerCodonSubstitutionModel(std::shared_ptr< const GeneticCode > gCode, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod, const std::string &st)
Build a new AbstractKroneckerCodonSubstitutionModel object from a pointer to a NucleotideSubstitution...
Definition: AbstractKroneckerCodonSubstitutionModel.cpp:12
bpp::AbstractKroneckerCodonSubstitutionModel::completeMatrices_
void completeMatrices_() override
Method inherited from AbstractWordSubstitutionModel.
Definition: AbstractKroneckerCodonSubstitutionModel.cpp:143
bpp::AbstractKroneckerCodonSubstitutionModel::getCodonsMulRate
virtual double getCodonsMulRate(size_t i, size_t j) const override
Method inherited from CodonSubstitutionModel.
Definition: AbstractKroneckerCodonSubstitutionModel.h:155
bpp::AbstractKroneckerWordSubstitutionModel::setChangingPositions
void setChangingPositions(const std::vector< std::set< size_t > > &vPos)
Definition: AbstractKroneckerWordSubstitutionModel.cpp:133
bpp::AbstractParameterAliasable::addParameters_
void addParameters_(const ParameterList &parameters)
bpp::AbstractSubstitutionModel::generator_
RowMatrix< double > generator_
The generator matrix of the model.
Definition: AbstractSubstitutionModel.h:298
bpp::AbstractTransitionModel::getNumberOfStates
size_t getNumberOfStates() const override
Get the number of states.
Definition: AbstractSubstitutionModel.h:175
bpp::AbstractWordSubstitutionModel::VSubMod_
std::vector< std::shared_ptr< SubstitutionModelInterface > > VSubMod_
Definition: AbstractWordSubstitutionModel.h:115
bpp::CanonicalStateMap
This class implements a state map where all resolved states are modeled.
Definition: StateMap.h:168
bpp::ParameterAliasable::getNamespace
virtual std::string getNamespace() const=0
bpp::ParameterAliasable::getParameters
virtual const ParameterList & getParameters() const=0
bpp::StateMapInterface
Map the states of a given alphabet which have a model state.
Definition: StateMap.h:25
bpp::SubstitutionModelInterface::enableEigenDecomposition
virtual bool enableEigenDecomposition()=0
Tell if eigenValues and Vectors must be computed.
bpp
Defines the basic types of data flow nodes.