bpp-phyl3 3.0.0
FromMixtureSubstitutionModel.cpp
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1// SPDX-FileCopyrightText: The Bio++ Development Group
2//
3// SPDX-License-Identifier: CECILL-2.1
4
5#include "FromMixtureSubstitutionModel.h"
6
7using namespace bpp;
8using namespace std;
9
10/******************************************************************************/
11
12FromMixtureSubstitutionModel::FromMixtureSubstitutionModel(
13 const MixedTransitionModelInterface& mixedModel,
14 const std::string& subModelName,
15 const std::string& mixtDesc) :
16 AbstractParameterAliasable(mixedModel.getName() + "_" + subModelName + "."),
17 AbstractWrappedModel(mixedModel.getName() + "_" + subModelName + "."),
18 AbstractWrappedTransitionModel(mixedModel.getName() + "_" + subModelName + "."),
19 AbstractTotallyWrappedTransitionModel(mixedModel.getName() + "_" + subModelName + "."),
20 AbstractWrappedSubstitutionModel(mixedModel.getName() + "_" + subModelName + "."),
21 AbstractTotallyWrappedSubstitutionModel(mixedModel.getName() + "_" + subModelName + "."),
22 subModel_(),
23 mixtName_(mixtDesc)
24{
25 try
26 {
27 auto& tm = mixedModel.model(subModelName);
28 try
29 {
30 auto& sm = dynamic_cast<const SubstitutionModelInterface&>(tm);
31 subModel_ = std::unique_ptr<SubstitutionModelInterface>(sm.clone());
32 subModel_->setNamespace(getNamespace());
33 subModel_->setRate(1);
34 addParameters_(subModel_->getParameters());
35 }
36 catch (bad_cast&)
37 {
38 throw Exception("FromMixtureSubstitutionModel::FromMixtureSubstitutionModel : model " + subModelName + " is not a substitution model.");
39 }
40 }
41 catch (NullPointerException&)
42 {
43 throw ParameterNotFoundException("FromMixtureSubstitutionModel::FromMixtureSubstitutionModel : unknown model name", subModelName);
44 }
45}
46
47FromMixtureSubstitutionModel::FromMixtureSubstitutionModel(
48 const MixedTransitionModelInterface& mixedModel,
49 size_t subModelNumber,
50 const std::string& mixtDesc) :
51 AbstractParameterAliasable(mixedModel.getName() + "_" + TextTools::toString(subModelNumber) + "."),
52 AbstractWrappedModel(mixedModel.getName() + "_" + TextTools::toString(subModelNumber) + "."),
53 AbstractWrappedTransitionModel(mixedModel.getName() + "_" + TextTools::toString(subModelNumber) + "."),
54 AbstractTotallyWrappedTransitionModel(mixedModel.getName() + "_" + TextTools::toString(subModelNumber) + "."),
55 AbstractWrappedSubstitutionModel(mixedModel.getName() + "_" + TextTools::toString(subModelNumber) + "."),
56 AbstractTotallyWrappedSubstitutionModel(mixedModel.getName() + "_" + TextTools::toString(subModelNumber) + "."),
57 subModel_(),
58 mixtName_(mixtDesc)
59{
60 if (subModelNumber >= mixedModel.getNumberOfModels())
61 throw ParameterNotFoundException("FromMixtureSubstitutionModel::FromMixtureSubstitutionModel : bad model number", TextTools::toString(subModelNumber));
62
63 auto& tm = mixedModel.nModel(subModelNumber);
64 try
65 {
66 auto& sm = dynamic_cast<const SubstitutionModelInterface&>(tm);
67 subModel_ = std::unique_ptr<SubstitutionModelInterface>(sm.clone());
68 subModel_->setNamespace(getNamespace());
69 subModel_->setRate(1);
70 addParameters_(subModel_->getParameters());
71 }
72 catch (bad_cast&)
73 {
74 throw Exception("FromMixtureSubstitutionModel::FromMixtureSubstitutionModel : model with number " + TextTools::toString(subModelNumber) + " is not a substitution model.");
75 }
76}
77
78
79/******************************************************************************/
80
81FromMixtureSubstitutionModel::FromMixtureSubstitutionModel(const FromMixtureSubstitutionModel& fmsm) :
82 AbstractParameterAliasable(fmsm),
83 AbstractWrappedModel(fmsm),
84 AbstractWrappedTransitionModel(fmsm),
85 AbstractTotallyWrappedTransitionModel(fmsm),
86 AbstractWrappedSubstitutionModel(fmsm),
87 AbstractTotallyWrappedSubstitutionModel(fmsm),
88 subModel_(fmsm.subModel_->clone()),
89 mixtName_(fmsm.mixtName_)
90{}
91
92
93/******************************************************************************/
94
95FromMixtureSubstitutionModel& FromMixtureSubstitutionModel::operator=(const FromMixtureSubstitutionModel& fmsm)
96{
97 AbstractTotallyWrappedSubstitutionModel::operator=(fmsm);
98
99 subModel_.reset(fmsm.subModel_->clone());
100 mixtName_ = fmsm.mixtName_;
101
102 return *this;
103}
bpp::AbstractParameterAliasable::addParameters_
void addParameters_(const ParameterList &parameters)
bpp::AbstractParameterAliasable::operator=
AbstractParameterAliasable & operator=(const AbstractParameterAliasable &ap)
bpp::AbstractParameterAliasable::getNamespace
std::string getNamespace() const override
bpp::AbstractWrappedModel
Abstract class of Wrapping model class, where all methods are redirected from model().
Definition: AbstractWrappedModel.h:24
bpp::FromMixtureSubstitutionModel
Model taken from a SubModel of a Mixture of SubstitutionModels.
Definition: FromMixtureSubstitutionModel.h:23
bpp::FromMixtureSubstitutionModel::operator=
FromMixtureSubstitutionModel & operator=(const FromMixtureSubstitutionModel &fmsm)
Definition: FromMixtureSubstitutionModel.cpp:95
bpp::FromMixtureSubstitutionModel::subModel_
std::unique_ptr< SubstitutionModelInterface > subModel_
The subModel taken from the AbstractTotallyWrappedSubstitutionModel.
Definition: FromMixtureSubstitutionModel.h:30
bpp::FromMixtureSubstitutionModel::mixtName_
std::string mixtName_
The name of the mixture model (for io purpose).
Definition: FromMixtureSubstitutionModel.h:35
bpp::FromMixtureSubstitutionModel::FromMixtureSubstitutionModel
FromMixtureSubstitutionModel(const MixedTransitionModelInterface &mixedModel, const std::string &subModelName, const std::string &mixtDesc)
Definition: FromMixtureSubstitutionModel.cpp:12
bpp::MixedTransitionModelInterface
Interface for Transition models, defined as a mixture of "simple" transition models.
Definition: MixedTransitionModel.h:24
bpp::MixedTransitionModelInterface::model
virtual const TransitionModelInterface & model(const std::string &name) const =0
Access the submodel with the given name.
bpp::MixedTransitionModelInterface::getNumberOfModels
virtual size_t getNumberOfModels() const =0
bpp::MixedTransitionModelInterface::nModel
virtual const TransitionModelInterface & nModel(size_t i) const =0
Returns a specific model from the mixture.
bpp::SubstitutionModelInterface
Interface for all substitution models.
Definition: SubstitutionModel.h:403
toString
std::string toString(T t)
bpp
Defines the basic types of data flow nodes.