#include <Bpp/Seq/Io/ISequence.h>

Inheritance diagram for bpp::IAlignment:

Collaboration diagram for bpp::IAlignment:

Public Member Functions
	IAlignment ()

virtual	~IAlignment ()

virtual SiteContainer *	readAlignment (std::istream &input, const Alphabet *alpha) const =0 throw (Exception)
	Create a new container from a stream. More...

virtual SiteContainer *	readAlignment (const std::string &path, const Alphabet *alpha) const =0 throw (Exception)
	Create a new container from a file. More...

const std::string	getDataType () const

Detailed Description

The IAlignment interface.

This interface defines the basic methods for reading aligned sequences from a file.

Definition at line 99 of file ISequence.h.

Constructor & Destructor Documentation

◆ IAlignment()

bpp::IAlignment::IAlignment ( )

inline

Definition at line 103 of file ISequence.h.

◆ ~IAlignment()

virtual bpp::IAlignment::~IAlignment ( )

inlinevirtual

Definition at line 104 of file ISequence.h.

Member Function Documentation

◆ getDataType()

const std::string bpp::IOSequence::getDataType ( ) const

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ readAlignment() [1/2]

virtual SiteContainer* bpp::IAlignment::readAlignment	(	std::istream &	input,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

pure virtual

Create a new container from a stream.

Parameters

input	The input stream to read.
alpha	The alphabet to be associated to the container.

Returns: A new SiteContainer object.

Exceptions

Exception If the file is not in the specified format.

Implemented in bpp::AbstractIAlignment.

◆ readAlignment() [2/2]

virtual SiteContainer* bpp::IAlignment::readAlignment	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)