Partial implementation of the IAlignment and ISequence interface, dedicated to alignment readers. More...

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

Inheritance diagram for bpp::AbstractIAlignment2:

Collaboration diagram for bpp::AbstractIAlignment2:

Public Member Functions
	AbstractIAlignment2 ()

virtual	~AbstractIAlignment2 ()

const std::string	getDataType () const

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

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

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

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

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

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

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

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

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

std::unique_ptr< SiteContainerInterface >	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, SequenceContainerInterface &sc) const =0
	Append sequences to a container from a stream. More...

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

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

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

Detailed Description

Partial implementation of the IAlignment and ISequence interface, dedicated to alignment readers.

This implementation adds the ISequence interface, assuming that aligned sequences are no less than sequence themselves and can be read as such;

Definition at line 139 of file AbstractIAlignment.h.

Constructor & Destructor Documentation

◆ AbstractIAlignment2()

bpp::AbstractIAlignment2::AbstractIAlignment2 ( )

inline

Definition at line 145 of file AbstractIAlignment.h.

◆ ~AbstractIAlignment2()

virtual bpp::AbstractIAlignment2::~AbstractIAlignment2 ( )

inlinevirtual

Definition at line 146 of file AbstractIAlignment.h.

Member Function Documentation

◆ appendAlignmentFromFile()

virtual void bpp::AbstractIAlignment::appendAlignmentFromFile	(	const std::string &	path,
		SequenceContainerInterface &	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 93 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

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

◆ appendAlignmentFromStream()

virtual void bpp::AbstractIAlignment::appendAlignmentFromStream	(	std::istream &	input,
		SequenceContainerInterface &	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.

Exceptions

Exception If the file is not in the specified format.

Implemented in bpp::Phylip, bpp::NexusIOSequence, bpp::Mase, bpp::Fasta, bpp::DCSE, and bpp::Clustal.

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

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 29 of file IoSequence.h.

◆ readAlignment() [1/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		SequenceContainerInterface &	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.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IAlignment.

Definition at line 57 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

◆ readAlignment() [2/4]

std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::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 SiteContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IAlignment.

Definition at line 62 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromFile().

◆ readAlignment() [3/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		SequenceContainerInterface &	sc
	)		const

inlineoverridevirtualinherited

Add sequences to a container from a stream.

Parameters

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

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IAlignment.

Definition at line 45 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

Referenced by readSequences(), bpp::Clustal::readSequences(), bpp::DCSE::readSequences(), and bpp::Phylip::readSequences().

◆ readAlignment() [4/4]

std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::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 SiteContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IAlignment.

Definition at line 67 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromStream().

◆ readAlignmentFromFile()

virtual std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::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.

Exceptions

Exception If the file is not in the specified format.

Definition at line 125 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

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

◆ readAlignmentFromStream()

virtual std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::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.

Exceptions

Exception If the file is not in the specified format.

Definition at line 110 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

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

◆ readSequences() [1/4]

void bpp::AbstractIAlignment2::readSequences	(	const std::string &	path,
		SequenceContainerInterface &	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::ISequence.

Definition at line 162 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

◆ readSequences() [2/4]

std::unique_ptr<SequenceContainerInterface> bpp::AbstractIAlignment2::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 SequenceContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Reimplemented in bpp::Phylip, bpp::DCSE, and bpp::Clustal.

Definition at line 174 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignment().

◆ readSequences() [3/4]

void bpp::AbstractIAlignment2::readSequences	(	std::istream &	input,
		SequenceContainerInterface &	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::ISequence.

Definition at line 157 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

◆ readSequences() [4/4]

std::unique_ptr<SequenceContainerInterface> bpp::AbstractIAlignment2::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 SequenceContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Reimplemented in bpp::Phylip, bpp::DCSE, and bpp::Clustal.

Definition at line 167 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::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

◆ AbstractIAlignment2()

◆ ~AbstractIAlignment2()

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]