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

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

Inheritance diagram for bpp::AbstractIAlignment:

Collaboration diagram for bpp::AbstractIAlignment:

Public Member Functions
	AbstractIAlignment ()

virtual	~AbstractIAlignment ()

const std::string	getDataType () const

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

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

virtual AlignedSequenceContainer *	readAlignment (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Create a new container from a file. More...

virtual AlignedSequenceContainer *	readAlignment (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Create a new container from a stream. More...

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

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

virtual AlignedSequenceContainer *	readAlignmentFromStream (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Read sequences from a stream. More...

virtual AlignedSequenceContainer *	readAlignmentFromFile (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Read sequences from a file. More...

Detailed Description

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

Definition at line 58 of file AbstractIAlignment.h.

Constructor & Destructor Documentation

◆ AbstractIAlignment()

bpp::AbstractIAlignment::AbstractIAlignment ( )

inline

Definition at line 63 of file AbstractIAlignment.h.

◆ ~AbstractIAlignment()

virtual bpp::AbstractIAlignment::~AbstractIAlignment ( )

inlinevirtual

Definition at line 64 of file AbstractIAlignment.h.

Member Function Documentation

◆ appendAlignmentFromFile()

virtual void bpp::AbstractIAlignment::appendAlignmentFromFile	(	const std::string &	path,
		SiteContainer &	sc
	)		const
throw	(	Exception
	)

inlineprotectedvirtual

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 143 of file AbstractIAlignment.h.

References appendAlignmentFromStream().

Referenced by readAlignment(), and readAlignmentFromFile().

◆ appendAlignmentFromStream()

virtual void bpp::AbstractIAlignment::appendAlignmentFromStream	(	std::istream &	input,
		SiteContainer &	sc
	)		const
throw	(	Exception
	)

protectedpure virtual

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

Referenced by appendAlignmentFromFile(), readAlignment(), and readAlignmentFromStream().

◆ getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ readAlignment() [1/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		SiteContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtual

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.

Definition at line 81 of file AbstractIAlignment.h.

References appendAlignmentFromStream().

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

◆ readAlignment() [2/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		SiteContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtual

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.

Definition at line 93 of file AbstractIAlignment.h.

References appendAlignmentFromFile().

◆ readAlignment() [3/4]

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlinevirtual

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 104 of file AbstractIAlignment.h.

References readAlignmentFromFile().

◆ readAlignment() [4/4]

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlinevirtual

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 115 of file AbstractIAlignment.h.

References readAlignmentFromStream().

◆ readAlignmentFromFile()

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignmentFromFile	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlineprotectedvirtual

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 173 of file AbstractIAlignment.h.

References appendAlignmentFromFile().

Referenced by readAlignment().

◆ readAlignmentFromStream()

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignmentFromStream	(	std::istream &	input,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlineprotectedvirtual

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 158 of file AbstractIAlignment.h.

References appendAlignmentFromStream().

Referenced by 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

◆ AbstractIAlignment()

◆ ~AbstractIAlignment()

Member Function Documentation

◆ appendAlignmentFromFile()

◆ appendAlignmentFromStream()

◆ getDataType()

◆ readAlignment() [1/4]

◆ readAlignment() [2/4]

◆ readAlignment() [3/4]

◆ readAlignment() [4/4]

◆ readAlignmentFromFile()

◆ readAlignmentFromStream()