bpp::AbstractISequence Class Reference

Partial implementation of the ISequence interface. More...

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

Inheritance diagram for bpp::AbstractISequence:

Collaboration diagram for bpp::AbstractISequence:

List of all members.

Public Member Functions
	AbstractISequence ()
virtual	~AbstractISequence ()
const std::string	getDataType () const
virtual const std::string	getFormatName () const =0
virtual const std::string	getFormatDescription () const =0
ISequence methods:
virtual void	readSequences (std::istream &input, SequenceContainer &sc) const throw (Exception)
	Add sequences to a container from a stream.
virtual void	readSequences (const std::string &path, SequenceContainer &sc) const throw (Exception)
	Add sequences to a container from a file.
virtual VectorSequenceContainer *	readSequences (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Create a new container from a stream.
virtual VectorSequenceContainer *	readSequences (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Create a new container from a file.
Protected Member Functions
virtual void	appendSequencesFromStream (std::istream &input, SequenceContainer &sc) const =0 throw (Exception)
	Append sequences to a container from a stream.
virtual void	appendSequencesFromFile (const std::string &path, SequenceContainer &sc) const throw (Exception)
	Append sequences to a container from a file.
virtual VectorSequenceContainer *	readSequencesFromStream (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Read sequences from a stream.
virtual VectorSequenceContainer *	readSequencesFromFile (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Append sequences to a container from a file.

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Detailed Description

Partial implementation of the ISequence interface.

Definition at line 58 of file AbstractISequence.h.

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Constructor & Destructor Documentation

bpp::AbstractISequence::AbstractISequence

(

)

[inline]

Definition at line 63 of file AbstractISequence.h.

virtual bpp::AbstractISequence::~AbstractISequence

(

)

[inline, virtual]

Definition at line 64 of file AbstractISequence.h.

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Member Function Documentation

virtual void bpp::AbstractISequence::appendSequencesFromFile	(	const std::string &	path,
		SequenceContainer &	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 142 of file AbstractISequence.h.

References appendSequencesFromStream().

Referenced by readSequences(), and readSequencesFromFile().

virtual void bpp::AbstractISequence::appendSequencesFromStream	(	std::istream &	input,
		SequenceContainer &	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::Fasta, and bpp::GenBank.

Referenced by appendSequencesFromFile(), readSequences(), and readSequencesFromStream().

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

(

)

const [inline, virtual, inherited]

Implements bpp::IOFormat.

Definition at line 65 of file IoSequence.h.

virtual void bpp::AbstractISequence::readSequences	(	std::istream &	input,
		SequenceContainer &	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 82 of file AbstractISequence.h.

References appendSequencesFromStream().

Referenced by bpp::Mase::readMeta().

virtual void bpp::AbstractISequence::readSequences	(	const std::string &	path,
		SequenceContainer &	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 94 of file AbstractISequence.h.

References appendSequencesFromFile().

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequences	(	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 SequenceContainer object.

Exceptions:

Exception

If the file is not in the specified format.

Implements bpp::ISequence.

Definition at line 105 of file AbstractISequence.h.

References readSequencesFromStream().

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequences	(	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 SequenceContainer object.

Exceptions:

Exception

If the file is not in the specified format.

Implements bpp::ISequence.

Definition at line 116 of file AbstractISequence.h.

References readSequencesFromFile().

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequencesFromFile	(	const std::string &	path,
		const Alphabet *	alpha
	)		const throw (Exception) [inline, protected, virtual]

Append sequences to a container from a file.

Parameters:

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

Exceptions:

Exception

If the file is not in the specified format.

Definition at line 171 of file AbstractISequence.h.

References appendSequencesFromFile().

Referenced by readSequences().

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequencesFromStream	(	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 157 of file AbstractISequence.h.

References appendSequencesFromStream().

Referenced by readSequences().

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

• Bpp/Seq/Io/AbstractISequence.h