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

Inheritance diagram for bpp::AbstractIProbabilisticAlignment2:

Collaboration diagram for bpp::AbstractIProbabilisticAlignment2:

Public Member Functions
	AbstractIProbabilisticAlignment2 ()

virtual	~AbstractIProbabilisticAlignment2 ()

const std::string	getDataType () const

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

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

The IProbabilisticSequence interface.
As a ProbabilisticSiteContainer is a subclass of ProbabilisticSequenceContainer, we hereby implement the IProbabilisticSequence interface by downcasting the interface.
void	readSequences (std::istream &input, ProbabilisticSequenceContainerInterface &sc) const override
	Create a new container from a stream. More...

void	readSequences (const std::string &path, ProbabilisticSequenceContainerInterface &sc) const override
	Create a new container from a file. More...

std::unique_ptr< ProbabilisticSequenceContainerInterface >	readSequences (std::istream &input, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a stream. More...

std::unique_ptr< ProbabilisticSequenceContainerInterface >	readSequences (const std::string &path, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a file. More...

IProbabilisticAlignment methods:
void	readAlignment (std::istream &input, ProbabilisticSequenceContainerInterface &sc) const override
	Add sequences to a container from a stream. More...

void	readAlignment (const std::string &path, ProbabilisticSequenceContainerInterface &sc) const override
	Add sequences to a container from a file. More...

std::unique_ptr< ProbabilisticSiteContainerInterface >	readAlignment (const std::string &path, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a file. More...

std::unique_ptr< ProbabilisticSiteContainerInterface >	readAlignment (std::istream &input, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a stream. More...

Protected Member Functions
virtual void	appendAlignmentFromStream (std::istream &input, ProbabilisticSequenceContainerInterface &sc) const =0
	Append sequences to a container from a stream. More...

virtual void	appendAlignmentFromFile (const std::string &path, ProbabilisticSequenceContainerInterface &sc) const
	Append sequences to a container from a file. More...

virtual std::unique_ptr< ProbabilisticSiteContainerInterface >	readAlignmentFromStream (std::istream &input, std::shared_ptr< const Alphabet > &alpha) const
	Read sequences from a stream. More...

virtual std::unique_ptr< ProbabilisticSiteContainerInterface >	readAlignmentFromFile (const std::string &path, std::shared_ptr< const Alphabet > &alpha) const
	Read sequences from a file. More...

Detailed Description

Definition at line 289 of file AbstractIAlignment.h.

Constructor & Destructor Documentation

◆ AbstractIProbabilisticAlignment2()

bpp::AbstractIProbabilisticAlignment2::AbstractIProbabilisticAlignment2 ( )

inline

Definition at line 295 of file AbstractIAlignment.h.

◆ ~AbstractIProbabilisticAlignment2()

virtual bpp::AbstractIProbabilisticAlignment2::~AbstractIProbabilisticAlignment2 ( )

inlinevirtual

Definition at line 296 of file AbstractIAlignment.h.

Member Function Documentation

◆ appendAlignmentFromFile()

virtual void bpp::AbstractIProbabilisticAlignment::appendAlignmentFromFile	(	const std::string &	path,
		ProbabilisticSequenceContainerInterface &	sc
	)		const

inlineprotectedvirtualinherited

Append sequences to a container from a file.

Parameters

path	The path to the file to read.
sc	The sequence container to update.

Exceptions

Exception If the file is not in the specified format.

Definition at line 250 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIProbabilisticAlignment::readAlignment(), bpp::AbstractIProbabilisticAlignment::readAlignmentFromFile(), and readSequences().

◆ appendAlignmentFromStream()

virtual void bpp::AbstractIProbabilisticAlignment::appendAlignmentFromStream	(	std::istream &	input,
		ProbabilisticSequenceContainerInterface &	sc
	)		const

protectedpure virtualinherited

Append sequences to a container from a stream.

This is the unique method to implement!

Parameters

input	The input stream to read.
sc	The sequence container to update.

Implemented in bpp::Pasta.

Referenced by bpp::AbstractIProbabilisticAlignment::appendAlignmentFromFile(), bpp::AbstractIProbabilisticAlignment::readAlignment(), bpp::AbstractIProbabilisticAlignment::readAlignmentFromStream(), and readSequences().

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 44 of file IoSequence.h.

◆ readAlignment() [1/4]

void bpp::AbstractIProbabilisticAlignment::readAlignment	(	const std::string &	path,
		ProbabilisticSequenceContainerInterface &	sc
	)		const

inlineoverridevirtualinherited

Add sequences to a container from a file.

Parameters

path	The path to the file to read.
sc	The sequence container to update.

Implements bpp::IProbabilisticAlignment.

Definition at line 215 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromFile().

◆ readAlignment() [2/4]

std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::AbstractIProbabilisticAlignment::readAlignment	(	const std::string &	path,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtualinherited

Create a new container from a file.

Parameters

path	The path to the file to read.
alpha	The alphabet to be associated to the container.

Returns: A new ProbabilisticSiteContainer object.

Implements bpp::IProbabilisticAlignment.

Definition at line 220 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::readAlignmentFromFile().

◆ readAlignment() [3/4]

void bpp::AbstractIProbabilisticAlignment::readAlignment	(	std::istream &	input,
		ProbabilisticSequenceContainerInterface &	sc
	)		const

inlineoverridevirtualinherited

Add sequences to a container from a stream.

Parameters

input	The input stream to read.
sc	The sequence container to update.

Implements bpp::IProbabilisticAlignment.

Definition at line 204 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromStream().

Referenced by readSequences().

◆ readAlignment() [4/4]

std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::AbstractIProbabilisticAlignment::readAlignment	(	std::istream &	input,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtualinherited

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 ProbabilisticSiteContainer object.

Implements bpp::IProbabilisticAlignment.

Definition at line 225 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::readAlignmentFromStream().

◆ readAlignmentFromFile()

virtual std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::AbstractIProbabilisticAlignment::readAlignmentFromFile	(	const std::string &	path,
		std::shared_ptr< const Alphabet > &	alpha
	)		const

inlineprotectedvirtualinherited

Read sequences from a file.

Parameters

path	The path to the file to read.
alpha	The alphabet to use.

Returns: A sequence container.

Definition at line 280 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromFile().

Referenced by bpp::AbstractIProbabilisticAlignment::readAlignment().

◆ readAlignmentFromStream()

virtual std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::AbstractIProbabilisticAlignment::readAlignmentFromStream	(	std::istream &	input,
		std::shared_ptr< const Alphabet > &	alpha
	)		const

inlineprotectedvirtualinherited

Read sequences from a stream.

Parameters

input	The input stream to read.
alpha	The alphabet to use.

Returns: A sequence container.

Definition at line 266 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIProbabilisticAlignment::readAlignment().

◆ readSequences() [1/4]

void bpp::AbstractIProbabilisticAlignment2::readSequences	(	const std::string &	path,
		ProbabilisticSequenceContainerInterface &	container
	)		const

inlineoverridevirtual

Create a new container from a file.

Parameters

path	The path to the file to read.
container	The container where to add data.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IProbabilisticSequence.

Definition at line 312 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromFile().

◆ readSequences() [2/4]

std::unique_ptr<ProbabilisticSequenceContainerInterface> bpp::AbstractIProbabilisticAlignment2::readSequences	(	const std::string &	path,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtual

Create a new container from a file.

Parameters

path	The path to the file to read.
alpha	The alphabet to be associated to the container.

Returns: A new ProbabilisticSequenceContainer object.

Implements bpp::IProbabilisticSequence.

Definition at line 324 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::readAlignment().

◆ readSequences() [3/4]

void bpp::AbstractIProbabilisticAlignment2::readSequences	(	std::istream &	input,
		ProbabilisticSequenceContainerInterface &	container
	)		const

inlineoverridevirtual

Create a new container from a stream.

Parameters

input	The input stream to read.
container	The container where to add data.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IProbabilisticSequence.

Definition at line 307 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromStream().

◆ readSequences() [4/4]

std::unique_ptr<ProbabilisticSequenceContainerInterface> bpp::AbstractIProbabilisticAlignment2::readSequences	(	std::istream &	input,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtual

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 ProbabilisticSequenceContainer object.

Implements bpp::IProbabilisticSequence.

Definition at line 317 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::readAlignment().

The documentation for this class was generated from the following file:

Bpp/Seq/Io/AbstractIAlignment.h

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ AbstractIProbabilisticAlignment2()

◆ ~AbstractIProbabilisticAlignment2()

Member Function Documentation

◆ appendAlignmentFromFile()

◆ appendAlignmentFromStream()

◆ getDataType()

◆ readAlignment() [1/4]

◆ readAlignment() [2/4]

◆ readAlignment() [3/4]

◆ readAlignment() [4/4]

◆ readAlignmentFromFile()

◆ readAlignmentFromStream()

◆ readSequences() [1/4]

◆ readSequences() [2/4]

◆ readSequences() [3/4]

◆ readSequences() [4/4]