bpp-phyl
2.2.0
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Tools for automatically creating SubstitutionModelSet objects. More...
#include <Bpp/Phyl/Model/SubstitutionModelSetTools.h>
Static Public Member Functions | |
static SubstitutionModelSet * | createHomogeneousModelSet (SubstitutionModel *model, FrequenciesSet *rootFreqs, const Tree *tree) throw (AlphabetException, Exception) |
Create a SubstitutionModelSet object, corresponding to the homogeneous case. More... | |
static SubstitutionModelSet * | createNonHomogeneousModelSet (SubstitutionModel *model, FrequenciesSet *rootFreqs, const Tree *tree, const std::vector< std::string > &globalParameterNames) throw (AlphabetException, Exception) |
Create a SubstitutionModelSet object, with one model per branch. More... | |
Tools for automatically creating SubstitutionModelSet objects.
Definition at line 56 of file SubstitutionModelSetTools.h.
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Create a SubstitutionModelSet object, corresponding to the homogeneous case.
This class is mainly for testing purpose.
model | The model to use. |
rootFreqs | A FrequenciesSet object to parametrize root frequencies. |
tree | The tree to use for the construction of the set. |
Definition at line 48 of file SubstitutionModelSetTools.cpp.
References bpp::SubstitutionModelSet::addModel(), and bpp::SubstitutionModelSet::setRootFrequencies().
Referenced by bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator().
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Create a SubstitutionModelSet object, with one model per branch.
All branches share the same type of model, but allow one set of parameters per branch. This is also possible to specify some parameters to be common to all branches.
model | The model to use. |
rootFreqs | A FrequenciesSet object to parametrize root frequencies. |
tree | The tree to use for the construction of the set. |
globalParameterNames | Common parameters for all branches. All other parameters will be considered distinct for all branches. |
Definition at line 81 of file SubstitutionModelSetTools.cpp.
References bpp::MixedSubstitutionModelSet::addEmptyHyperNode(), bpp::SubstitutionModelSet::addModel(), bpp::MixedSubstitutionModelSet::addToHyperNode(), bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), bpp::MixedSubstitutionModel::getNumberOfModels(), and bpp::SubstitutionModelSet::setRootFrequencies().