bpp::ISubstitutionModel Class Reference

General interface for distance matrix 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 SubstitutionModel *	read (const Alphabet *alphabet, const std::string &modelDescription, const SiteContainer *data=0, 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

Detailed Description

General interface for distance matrix readers.

Definition at line 75 of file IoSubstitutionModel.h.

Constructor & Destructor Documentation

ISubstitutionModel()

bpp::ISubstitutionModel::ISubstitutionModel ( )

inline

Definition at line 79 of file IoSubstitutionModel.h.

~ISubstitutionModel()

virtual bpp::ISubstitutionModel::~ISubstitutionModel ( )

inlinevirtual

Definition at line 80 of file IoSubstitutionModel.h.

Member Function Documentation

getDataType()

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

inlinevirtualinherited

Definition at line 69 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.

read()

virtual SubstitutionModel* bpp::ISubstitutionModel::read ( const Alphabet *  alphabet, const std::string &  modelDescription, const SiteContainer *  data = 0, bool  parseArguments = true  )

pure virtual

Read a substitution model from a string.

Parameters

alphabet	The alpabet to use in the model.
modelDescription	A string describing the model in the format.
data	A pointer toward a SiteContainer, which can be used to initial some parmaeters like frequencies.
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 occured.

Implemented in bpp::BppOSubstitutionModelFormat.

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

• Bpp/Phyl/Io/IoSubstitutionModel.h