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

Inheritance diagram for bpp::OAlignment:

Collaboration diagram for bpp::OAlignment:

Public Member Functions
	OAlignment ()

virtual	~OAlignment ()

virtual void	writeAlignment (std::ostream &output, const SiteContainerInterface &sc) const =0
	Write a container to a stream. More...

virtual void	writeAlignment (const std::string &path, const SiteContainerInterface &sc, bool overwrite) const =0
	Write a container to a file. More...

const std::string	getDataType () const

virtual const std::string	getFormatName () const=0

virtual const std::string	getFormatDescription () const=0

Detailed Description

The OAlignment interface.

This interface defines the basic methods for writing alignments to a file.

Definition at line 56 of file OSequence.h.

Constructor & Destructor Documentation

◆ OAlignment()

bpp::OAlignment::OAlignment ( )

inline

Definition at line 60 of file OSequence.h.

◆ ~OAlignment()

virtual bpp::OAlignment::~OAlignment ( )

inlinevirtual

Definition at line 61 of file OSequence.h.

Member Function Documentation

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 29 of file IoSequence.h.

◆ writeAlignment() [1/2]

virtual void bpp::OAlignment::writeAlignment	(	const std::string &	path,
		const SiteContainerInterface &	sc,
		bool	overwrite
	)		const

pure virtual

Write a container to a file.

Parameters

path	The path to the file to write.
sc	The container to write.
overwrite	If true the sequences are written at the beginning of the file instead of being appended. Any previous content will be lost.

Exceptions

Exception If the file is not in the specified format.

Implemented in bpp::Stockholm, bpp::Clustal, bpp::AbstractOSequence2, bpp::AbstractOAlignment, and bpp::Phylip.

◆ writeAlignment() [2/2]

virtual void bpp::OAlignment::writeAlignment	(	std::ostream &	output,
		const SiteContainerInterface &	sc
	)		const