#include <model.h>

Classes
struct	ModelParams

Public Member Functions
	Model (const cmaple::ModelBase::SubModel sub_model=cmaple::ModelBase::DEFAULT, const cmaple::SeqRegion::SeqType seqtype=cmaple::SeqRegion::SEQ_AUTO)
	Constructor from a model name.

	~Model ()
	Destructor.

void	fixParameters (const bool &fixed_model_params)
	Keep the model parameters unchanged. This API is useful when using one model for multiple trees - after the model parameters are estimated according to a tree, users can keep them unchanged, then use the model for other trees.

ModelParams	getParams ()
	Export the substitution model and its parameters to a ModelParams structure.

Detailed Description

Class represents a substitution model

Constructor & Destructor Documentation

◆ Model()

cmaple::Model::Model	(	const cmaple::ModelBase::SubModel	sub_model = `cmaple::ModelBase::DEFAULT`,
		const cmaple::SeqRegion::SeqType	seqtype = `cmaple::SeqRegion::SEQ_AUTO`
	)

Constructor from a model name.

Parameters

[in]	sub_model	a substitution model. Default: DEFAULT - GTR for DNA, and LG for Protein data. List of supported models: DNA models: JC, GTR, UNREST; Protein models: GTR20, NONREV, LG, WAG, JTT, Q_PFAM, Q_BIRD, Q_MAMMAL, Q_INSECT, Q_PLANT, Q_YEAST, JTTDCMUT, DCMUT, VT, PMB, BLOSUM62, DAYHOFF, MTREV, MTART, MTZOA, MTMET, MTVER, MTINV, MTMAM, FLAVI, HIVB, HIVW, FLU, RTREV, CPREV, NQ_PFAM, NQ_BIRD, NQ_MAMMAL, NQ_INSECT, NQ_PLANT, NQ_YEAST; See Substitution models* for references of those models.*
[in]	seqtype	Data type of sequences (optional): SEQ_DNA (nucleotide data), SEQ_PROTEIN (amino acid data), or SEQ_AUTO (auto detection)

Exceptions

std::invalid_argument

if any of the following situations occur.

sub_model is unknown/unsupported
sub_model is DEFAULT and seqtype is SEQ_AUTO

Member Function Documentation

◆ fixParameters()

void cmaple::Model::fixParameters ( const bool & fixed_model_params )

Keep the model parameters unchanged. This API is useful when using one model for multiple trees - after the model parameters are estimated according to a tree, users can keep them unchanged, then use the model for other trees.

Parameters

[in] fixed_model_params TRUE to keep the model parameters unchanged

◆ getParams()

ModelParams cmaple::Model::getParams ( )

Export the substitution model and its parameters to a ModelParams structure.

Returns: A ModelParams structure.

The documentation for this class was generated from the following file:

model/model.h