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

Inheritance diagram for bpp::ISequence:

Collaboration diagram for bpp::ISequence:

Public Member Functions
	ISequence ()

virtual	~ISequence ()

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

virtual SequenceContainer *	readSequences (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 ISequence interface.

This interface defines the basic methods for reading sequences from a file. NB: This interface is effective only if the VIRTUAL_COV option is enabled (default behavior).

Definition at line 64 of file ISequence.h.

Constructor & Destructor Documentation

◆ ISequence()

bpp::ISequence::ISequence ( )

inline

Definition at line 68 of file ISequence.h.

◆ ~ISequence()

virtual bpp::ISequence::~ISequence ( )

inlinevirtual

Definition at line 69 of file ISequence.h.

Member Function Documentation

◆ getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ readSequences() [1/2]

virtual SequenceContainer* bpp::ISequence::readSequences	(	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 SequenceContainer object.

Exceptions

Exception If the file is not in the specified format.

Implemented in bpp::Phylip, bpp::NexusIOSequence, bpp::AbstractISequence, bpp::Clustal, and bpp::DCSE.

◆ readSequences() [2/2]

virtual SequenceContainer* bpp::ISequence::readSequences	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)