Partial implementation of the ISequence interface. More...

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

Inheritance diagram for bpp::AbstractISequence:

Collaboration diagram for bpp::AbstractISequence:

Public Member Functions
	AbstractISequence ()

virtual	~AbstractISequence ()

const std::string	getDataType () const

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

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

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

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

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

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

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

virtual VectorSequenceContainer *	readSequencesFromFile (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Append sequences to a container from a file. More...

Detailed Description

Partial implementation of the ISequence interface.

Definition at line 58 of file AbstractISequence.h.

Constructor & Destructor Documentation

◆ AbstractISequence()

bpp::AbstractISequence::AbstractISequence ( )

inline

Definition at line 63 of file AbstractISequence.h.

◆ ~AbstractISequence()

virtual bpp::AbstractISequence::~AbstractISequence ( )

inlinevirtual

Definition at line 64 of file AbstractISequence.h.

Member Function Documentation

◆ appendSequencesFromFile()

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

References appendSequencesFromStream().

Referenced by readSequences(), and readSequencesFromFile().

◆ appendSequencesFromStream()

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

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

◆ getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ readSequences() [1/4]

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

References appendSequencesFromStream().

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

◆ readSequences() [2/4]

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

References appendSequencesFromFile().

◆ readSequences() [3/4]

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequences	(	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 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().

◆ readSequences() [4/4]

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequences	(	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 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().

◆ readSequencesFromFile()

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

inlineprotectedvirtual

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().

◆ readSequencesFromStream()

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

References appendSequencesFromStream().

Referenced by readSequences().

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

Bpp/Seq/Io/AbstractISequence.h

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ AbstractISequence()

◆ ~AbstractISequence()

Member Function Documentation

◆ appendSequencesFromFile()

◆ appendSequencesFromStream()

◆ getDataType()

◆ readSequences() [1/4]

◆ readSequences() [2/4]

◆ readSequences() [3/4]

◆ readSequences() [4/4]

◆ readSequencesFromFile()

◆ readSequencesFromStream()