bpp-phyl3 3.0.0
InMixedSubstitutionModel.cpp
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1// SPDX-FileCopyrightText: The Bio++ Development Group
2//
3// SPDX-License-Identifier: CECILL-2.1
4
5#include "InMixedSubstitutionModel.h"
6
7using namespace bpp;
8using namespace std;
9
10/******************************************************************************/
11
12InMixedSubstitutionModel::InMixedSubstitutionModel(
13 unique_ptr<MixedTransitionModelInterface> mixedModel,
14 const std::string& subModelName,
15 const std::string& mixtDesc) :
16 AbstractParameterAliasable(mixedModel->getNamespace()),
17 AbstractWrappedModel(mixedModel->getNamespace()),
18 AbstractWrappedTransitionModel(mixedModel->getNamespace()),
19 AbstractWrappedSubstitutionModel(mixedModel->getNamespace()),
20 mixedModelPtr_(std::move(mixedModel)),
21 subModelNumber_(0),
22 mixtName_(mixtDesc)
23{
24 Vuint vn = mixedModelPtr_->getSubmodelNumbers(subModelName);
25 subModelNumber_ = (size_t)vn[0];
26 addParameters_(mixedModelPtr_->getParameters());
27}
28
29
30InMixedSubstitutionModel::InMixedSubstitutionModel(
31 unique_ptr<MixedTransitionModelInterface> mixedModel,
32 size_t subModelNumber,
33 const std::string& mixtDesc) :
34 AbstractParameterAliasable(mixedModel->getNamespace()),
35 AbstractWrappedModel(mixedModel->getNamespace()),
36 AbstractWrappedTransitionModel(mixedModel->getNamespace()),
37 AbstractWrappedSubstitutionModel(mixedModel->getNamespace()),
38 mixedModelPtr_(std::move(mixedModel)),
39 subModelNumber_(subModelNumber),
40 mixtName_(mixtDesc)
41{
42 if (subModelNumber >= mixedModelPtr_->getNumberOfModels())
43 throw ParameterNotFoundException("InMixedSubstitutionModel::InMixedSubstitutionModel : bad model number", TextTools::toString(subModelNumber));
44
45 addParameters_(mixedModelPtr_->getParameters());
46}
47
48
49/******************************************************************************/
50
51InMixedSubstitutionModel::InMixedSubstitutionModel(const InMixedSubstitutionModel& fmsm) :
52 AbstractParameterAliasable(fmsm),
53 AbstractWrappedModel(fmsm),
54 AbstractWrappedTransitionModel(fmsm),
55 AbstractWrappedSubstitutionModel(fmsm),
56 mixedModelPtr_(fmsm.mixedModelPtr_->clone()),
57 subModelNumber_(fmsm.subModelNumber_),
58 mixtName_(fmsm.mixtName_)
59{}
60
61
62/******************************************************************************/
63
64InMixedSubstitutionModel& InMixedSubstitutionModel::operator=(const InMixedSubstitutionModel& fmsm)
65{
66 AbstractWrappedSubstitutionModel::operator=(fmsm);
67
68 mixedModelPtr_.reset(fmsm.mixedModelPtr_->clone());
69 subModelNumber_ = fmsm.subModelNumber_;
70 mixtName_ = fmsm.mixtName_;
71
72 return *this;
73}
bpp::AbstractParameterAliasable::addParameters_
void addParameters_(const ParameterList &parameters)
bpp::AbstractParameterAliasable::operator=
AbstractParameterAliasable & operator=(const AbstractParameterAliasable &ap)
bpp::AbstractWrappedModel
Abstract class of Wrapping model class, where all methods are redirected from model().
Definition: AbstractWrappedModel.h:24
bpp::InMixedSubstitutionModel
SubModel taken from a MixedTransitionModel, kept in the context of the MixedTransitionModel (see From...
Definition: InMixedSubstitutionModel.h:30
bpp::InMixedSubstitutionModel::subModelNumber_
size_t subModelNumber_
the number of the submodel
Definition: InMixedSubstitutionModel.h:40
bpp::InMixedSubstitutionModel::mixtName_
std::string mixtName_
The name of the mixture model (for io purpose).
Definition: InMixedSubstitutionModel.h:45
bpp::InMixedSubstitutionModel::operator=
InMixedSubstitutionModel & operator=(const InMixedSubstitutionModel &fmsm)
Definition: InMixedSubstitutionModel.cpp:64
bpp::InMixedSubstitutionModel::mixedModelPtr_
std::unique_ptr< MixedTransitionModelInterface > mixedModelPtr_
The MixedOfTransitionModels.
Definition: InMixedSubstitutionModel.h:35
bpp::TextTools::toString
std::string toString(T t)
bpp
Defines the basic types of data flow nodes.
bpp::Vuint
std::vector< unsigned int > Vuint