bpp::AbstractIAlignment Class Reference

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:

List of all members.

Public Member Functions
	AbstractIAlignment ()
virtual	~AbstractIAlignment ()
const std::string	getDataType () const
virtual const std::string	getFormatName () const =0
virtual const std::string	getFormatDescription () const =0
IAlignment methods:
virtual void	readAlignment (std::istream &input, SiteContainer &sc) const throw (Exception)
	Add sequences to a container from a stream.
virtual void	readAlignment (const std::string &path, SiteContainer &sc) const throw (Exception)
	Add sequences to a container from a file.
virtual AlignedSequenceContainer *	readAlignment (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Create a new container from a file.
virtual AlignedSequenceContainer *	readAlignment (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Create a new container from a stream.
Protected Member Functions
virtual void	appendAlignmentFromStream (std::istream &input, SiteContainer &sc) const =0 throw (Exception)
	Append sequences to a container from a stream.
virtual void	appendAlignmentFromFile (const std::string &path, SiteContainer &sc) const throw (Exception)
	Append sequences to a container from a file.
virtual AlignedSequenceContainer *	readAlignmentFromStream (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Read sequences from a stream.
virtual AlignedSequenceContainer *	readAlignmentFromFile (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Read sequences from a file.

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Detailed Description

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

Definition at line 58 of file AbstractIAlignment.h.

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Constructor & Destructor Documentation

bpp::AbstractIAlignment::AbstractIAlignment

(

)

[inline]

Definition at line 63 of file AbstractIAlignment.h.

virtual bpp::AbstractIAlignment::~AbstractIAlignment

(

)

[inline, virtual]

Definition at line 64 of file AbstractIAlignment.h.

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Member Function Documentation

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

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().

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

const std::string bpp::IOSequence::getDataType

(

)

const [inline, virtual, inherited]

Implements bpp::IOFormat.

Definition at line 65 of file IoSequence.h.

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

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().

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

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().

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

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().

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

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().

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

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().

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

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().

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

• Bpp/Seq/Io/AbstractIAlignment.h