The GenBank sequence file format. More...

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

Inheritance diagram for bpp::GenBank:

Collaboration diagram for bpp::GenBank:

Public Member Functions
	GenBank ()
	Build a new GenBank object. More...

virtual	~GenBank ()

const std::string	getDataType () const

The AbstractISequence interface.
void	appendSequencesFromStream (std::istream &input, SequenceContainerInterface &sc) const
	Append sequences to a container from a stream. More...

The IOSequence interface.
const std::string	getFormatName () const

const std::string	getFormatDescription () const

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	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

The GenBank sequence file format.

For now, only read raw sequences. Features are not yet supported.

Definition at line 21 of file GenBank.h.

Constructor & Destructor Documentation

◆ GenBank()

bpp::GenBank::GenBank ( )

inline

Build a new GenBank object.

Definition at line 28 of file GenBank.h.

◆ ~GenBank()

virtual bpp::GenBank::~GenBank ( )

inlinevirtual

Definition at line 30 of file GenBank.h.

Member Function Documentation

◆ appendSequencesFromFile()

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

inlineprotectedvirtualinherited

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 bpp::AbstractISequence::appendSequencesFromStream().

Referenced by bpp::AbstractISequence::readSequences(), and bpp::AbstractISequence::readSequencesFromFile().

◆ appendSequencesFromStream()

void GenBank::appendSequencesFromStream	(	std::istream &	input,
		SequenceContainerInterface &	sc
	)		const

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.

Implements bpp::AbstractISequence.

Definition at line 15 of file GenBank.cpp.

References bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::addSequence(), bpp::TemplateSequenceDataInterface< HashType >::getAlphabet(), bpp::StringTokenizer::nextToken(), bpp::TextTools::removeSurroundingWhiteSpaces(), and bpp::TextTools::removeWhiteSpaces().

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 29 of file IoSequence.h.

◆ getFormatDescription()

const std::string bpp::GenBank::getFormatDescription ( ) const

inlinevirtual

Implements bpp::IOFormat.

Definition at line 47 of file GenBank.h.

◆ getFormatName()

const std::string bpp::GenBank::getFormatName ( ) const

inlinevirtual

Implements bpp::IOFormat.

Definition at line 46 of file GenBank.h.

◆ readSequences() [1/4]

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

inlineoverridevirtualinherited

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 bpp::AbstractISequence::appendSequencesFromFile().

◆ readSequences() [2/4]

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

inlineoverridevirtualinherited

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 bpp::AbstractISequence::readSequencesFromFile().

◆ readSequences() [3/4]

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

inlineoverridevirtualinherited

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 bpp::AbstractISequence::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

inlineoverridevirtualinherited

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 bpp::AbstractISequence::readSequencesFromStream().

◆ readSequencesFromFile()

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

inlineprotectedinherited

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 bpp::AbstractISequence::appendSequencesFromFile().

Referenced by bpp::AbstractISequence::readSequences().

◆ readSequencesFromStream()

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

inlineprotectedinherited

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 bpp::AbstractISequence::appendSequencesFromStream().

Referenced by bpp::AbstractISequence::readSequences().

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

Bpp/Seq/Io/GenBank.h
Bpp/Seq/Io/GenBank.cpp

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ GenBank()

◆ ~GenBank()

Member Function Documentation

◆ appendSequencesFromFile()

◆ appendSequencesFromStream()

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ readSequences() [1/4]

◆ readSequences() [2/4]

◆ readSequences() [3/4]

◆ readSequences() [4/4]

◆ readSequencesFromFile()

◆ readSequencesFromStream()