Partial implementation of the OProbabilisticAlignment interface. More...

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

Inheritance diagram for bpp::AbstractOProbabilisticSequence2:

Collaboration diagram for bpp::AbstractOProbabilisticSequence2:

Public Member Functions
	AbstractOProbabilisticSequence2 ()

virtual	~AbstractOProbabilisticSequence2 ()

const std::string	getDataType () const

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

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

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

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

OProbabilisticSequence methods:
void	writeSequences (std::ostream &output, const ProbabilisticSequenceContainerInterface &psc) const override=0
	Write a container to a stream. More...

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

Detailed Description

Partial implementation of the OProbabilisticAlignment interface.

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

Definition at line 120 of file AbstractOSequence.h.

Constructor & Destructor Documentation

◆ AbstractOProbabilisticSequence2()

bpp::AbstractOProbabilisticSequence2::AbstractOProbabilisticSequence2 ( )

inline

Definition at line 125 of file AbstractOSequence.h.

◆ ~AbstractOProbabilisticSequence2()

virtual bpp::AbstractOProbabilisticSequence2::~AbstractOProbabilisticSequence2 ( )

inlinevirtual

Definition at line 126 of file AbstractOSequence.h.

Member Function Documentation

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 44 of file IoSequence.h.

◆ writeAlignment() [1/2]

void bpp::AbstractOProbabilisticSequence2::writeAlignment	(	const std::string &	path,
		const ProbabilisticSiteContainerInterface &	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.

Implements bpp::OProbabilisticAlignment.

Definition at line 147 of file AbstractOSequence.h.

References bpp::AbstractOProbabilisticSequence::writeSequences().

◆ writeAlignment() [2/2]

void bpp::AbstractOProbabilisticSequence2::writeAlignment	(	std::ostream &	output,
		const ProbabilisticSiteContainerInterface &	sc
	)		const

inlineoverridevirtual

Write a container to a stream.

Parameters

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

Implements bpp::OProbabilisticAlignment.

Definition at line 142 of file AbstractOSequence.h.

References bpp::AbstractOProbabilisticSequence::writeSequences().

◆ writeSequences() [1/2]

void bpp::AbstractOProbabilisticSequence::writeSequences	(	const std::string &	path,
		const ProbabilisticSequenceContainerInterface &	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.

Implements bpp::OProbabilisticSequence.

Definition at line 103 of file AbstractOSequence.h.

References bpp::AbstractOProbabilisticSequence::writeSequences().