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

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

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

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

void	readSequences (const std::string &path, SequenceContainerInterface &sc) const override
	Add sequences to a 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...

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

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

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

std::unique_ptr< SequenceContainerInterface >	readSequencesFromFile (const std::string &path, std::shared_ptr< const Alphabet > &alpha) const
	Append sequences to a container from a file. More...

Detailed Description

Partial implementation of the ISequence interface.

Definition at line 23 of file AbstractISequence.h.

Constructor & Destructor Documentation

◆ AbstractISequence()

bpp::AbstractISequence::AbstractISequence ( )

inline

Definition at line 27 of file AbstractISequence.h.

◆ ~AbstractISequence()

virtual bpp::AbstractISequence::~AbstractISequence ( )

inlinevirtual

Definition at line 28 of file AbstractISequence.h.

Member Function Documentation

◆ appendSequencesFromFile()

virtual void bpp::AbstractISequence::appendSequencesFromFile	(	const std::string &	path,
		SequenceContainerInterface &	sc
	)		const

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 92 of file AbstractISequence.h.

References appendSequencesFromStream().

Referenced by readSequences(), and readSequencesFromFile().

◆ appendSequencesFromStream()

virtual void bpp::AbstractISequence::appendSequencesFromStream	(	std::istream &	input,
		SequenceContainerInterface &	sc
	)		const

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 29 of file IoSequence.h.

◆ readSequences() [1/4]

void bpp::AbstractISequence::readSequences	(	const std::string &	path,
		SequenceContainerInterface &	sc
	)		const

inlineoverridevirtual

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::ISequence.

Definition at line 57 of file AbstractISequence.h.

References appendSequencesFromFile().

◆ readSequences() [2/4]

std::unique_ptr<SequenceContainerInterface> bpp::AbstractISequence::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.

Definition at line 67 of file AbstractISequence.h.

References readSequencesFromFile().

◆ readSequences() [3/4]

void bpp::AbstractISequence::readSequences	(	std::istream &	input,
		SequenceContainerInterface &	sc
	)		const

inlineoverridevirtual

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::ISequence.

Definition at line 45 of file AbstractISequence.h.

References appendSequencesFromStream().

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

◆ readSequences() [4/4]

std::unique_ptr<SequenceContainerInterface> bpp::AbstractISequence::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.

Definition at line 62 of file AbstractISequence.h.

References readSequencesFromStream().

◆ readSequencesFromFile()

std::unique_ptr<SequenceContainerInterface> bpp::AbstractISequence::readSequencesFromFile	(	const std::string &	path,
		std::shared_ptr< const Alphabet > &	alpha
	)		const

inlineprotected

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 123 of file AbstractISequence.h.

References appendSequencesFromFile().

Referenced by readSequences().

◆ readSequencesFromStream()

std::unique_ptr<SequenceContainerInterface> bpp::AbstractISequence::readSequencesFromStream	(	std::istream &	input,
		std::shared_ptr< const Alphabet > &	alpha
	)		const

inlineprotected

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 109 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()