bpp::ISubstitutionModel Class Reference

General interface for model readers. More...

#include <Bpp/Phyl/Io/IoSubstitutionModel.h>

Inheritance diagram for bpp::ISubstitutionModel:

Collaboration diagram for bpp::ISubstitutionModel:

Public Member Functions
	ISubstitutionModel ()
virtual	~ISubstitutionModel ()
virtual std::unique_ptr< SubstitutionModelInterface >	readSubstitutionModel (std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, bool parseArguments=true)=0
	Read a substitution model from a string. More...
virtual const std::map< std::string, std::string > &	getUnparsedArguments () const =0
virtual const std::string	getDataType () const
virtual const std::string	getFormatName () const=0
virtual const std::string	getFormatDescription () const=0

Detailed Description

General interface for model readers.

Definition at line 42 of file IoSubstitutionModel.h.

Constructor & Destructor Documentation

ISubstitutionModel()

bpp::ISubstitutionModel::ISubstitutionModel ( )

inline

Definition at line 46 of file IoSubstitutionModel.h.

~ISubstitutionModel()

virtual bpp::ISubstitutionModel::~ISubstitutionModel ( )

inlinevirtual

Definition at line 47 of file IoSubstitutionModel.h.

Member Function Documentation

getDataType()

virtual const std::string bpp::IoSubstitutionModel::getDataType ( ) const

inlinevirtualinherited

Implements bpp::IOFormat.

Definition at line 35 of file IoSubstitutionModel.h.

getUnparsedArguments()

virtual const std::map<std::string, std::string>& bpp::ISubstitutionModel::getUnparsedArguments ( ) const

pure virtual

Returns

The arguments and their unparsed values from the last call of the read function, if there are any.

Implemented in bpp::BppOSubstitutionModelFormat.

readSubstitutionModel()

virtual std::unique_ptr<SubstitutionModelInterface> bpp::ISubstitutionModel::readSubstitutionModel ( std::shared_ptr< const Alphabet >  alphabet, const std::string &  modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &  mData, size_t  nData, bool  parseArguments = true  )

pure virtual

Read a substitution model from a string.

Parameters

alphabet	The alphabet to use in the model.
modelDescription	A string describing the model in the format.
mData	A map towards pointers of SiteContainer with the data to use to initialize frequency parameters
nData	Number of the SiteContainer in the mData. Can be set to 0, if none assigned.
parseArguments	Attempt to parse function arguments. If not, only store them and use default values instead.

Returns

A new SubstitutionModel object according to options specified.

Exceptions

Exception

if an error occurred.

Implemented in bpp::BppOSubstitutionModelFormat.

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

• Bpp/Phyl/Io/IoSubstitutionModel.h