Partial implementation of the OAlignment interface. More...

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

Inheritance diagram for bpp::AbstractOSequence2:

Collaboration diagram for bpp::AbstractOSequence2:

Public Member Functions
	AbstractOSequence2 ()

virtual	~AbstractOSequence2 ()

const std::string	getDataType () const

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

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

OAlignment methods:
As a SiteContainer is a specialization of SequenceContainer, it is assumed that a OSequence object can write aligned sequence just like a OAlignment object. Therefore it implements the OAlignment interface by down-casting the SiteContainer to a SequenceContainer.
void	writeAlignment (std::ostream &output, const SiteContainerInterface &sc) const override
	Write a container to a stream. More...

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

OSequence methods:
void	writeSequences (std::ostream &output, const SequenceContainerInterface &sc) const override=0
	Write a container to a stream. More...

void	writeSequences (const std::string &path, const SequenceContainerInterface &sc, bool overwrite=true) const override
	Write a container to a file. More...

Detailed Description

Partial implementation of the OAlignment interface.

This implementation is for sequence formats that can store both aligned and non-aligned sequences. Alignment sequences are written as simple sequences with gaps.

Definition at line 54 of file AbstractOSequence.h.

Constructor & Destructor Documentation

◆ AbstractOSequence2()

bpp::AbstractOSequence2::AbstractOSequence2 ( )

inline

Definition at line 60 of file AbstractOSequence.h.

◆ ~AbstractOSequence2()

virtual bpp::AbstractOSequence2::~AbstractOSequence2 ( )

inlinevirtual

Definition at line 61 of file AbstractOSequence.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]

void bpp::AbstractOSequence2::writeAlignment	(	const std::string &	path,
		const SiteContainerInterface &	sc,
		bool	overwrite = `true`
	)		const

inlineoverridevirtual

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.

Implements bpp::OAlignment.

Definition at line 78 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeAlignment() [2/2]

void bpp::AbstractOSequence2::writeAlignment	(	std::ostream &	output,
		const SiteContainerInterface &	sc
	)		const

inlineoverridevirtual

Write a container to a stream.

Parameters

output	The output stream where to write.
sc	The container to write.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::OAlignment.

Definition at line 73 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeSequences() [1/2]

void bpp::AbstractOSequence::writeSequences	(	const std::string &	path,
		const SequenceContainerInterface &	sc,
		bool	overwrite = `true`
	)		const

inlineoverridevirtualinherited

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.

Implements bpp::OSequence.

Reimplemented in bpp::Mase, and bpp::Fasta.

Definition at line 38 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().