The fasta sequence file format. More...

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

Inheritance diagram for bpp::Fasta:

Collaboration diagram for bpp::Fasta:

Classes
class	FileIndex
	The SequenceFileIndex class for Fasta format. More...

Public Member Functions
	Fasta (unsigned int charsByLine=100, bool checkSequenceNames=true, bool extended=false, bool strictSequenceNames=false)
	Build a new Fasta object. More...

virtual	~Fasta ()

bool	checkNames () const

void	checkNames (bool yn)
	Tell whether the sequence names should be checked when reading from files. More...

bool	strictNames () const

void	strictNames (bool yn)
	Tell wethed the sequence name should be restrected to the first non blank characters. More...

const std::string	getDataType () const

virtual bool	nextSequence (std::istream &input, SequenceType &seq) const =0
	Read sequence from stream. More...

virtual void	writeSequence (std::ostream &output, const SequenceType &seq) const =0
	Read sequence from stream. More...

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

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

The OSequence interface.
void	writeSequences (std::ostream &output, const SequenceContainerInterface &sc) const override
	Write a container to a stream. More...

void	writeSequences (const std::string &path, const SequenceContainerInterface &sc, bool overwrite=true) const override
	Write a container to a file. More...

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

const std::string	getFormatDescription () const override

The ISequenceStream interface.
bool	nextSequence (std::istream &input, Sequence &seq) const override

The OSequenceStream interface.
void	writeSequence (std::ostream &output, const Sequence &seq) const override

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...

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

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

std::unique_ptr< SiteContainerInterface >	readAlignment (const std::string &path, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a file. More...

std::unique_ptr< SiteContainerInterface >	readAlignment (std::istream &input, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a stream. More...

OAlignment methods:
As a SiteContainer is a specialization of SequenceContainer, it is assumed that a OSequence object can write aligned sequence just like a OAlignment object. Therefore it implements the OAlignment interface by down-casting the SiteContainer to a SequenceContainer.
void	writeAlignment (std::ostream &output, const SiteContainerInterface &sc) const override
	Write a container to a stream. More...

void	writeAlignment (const std::string &path, const SiteContainerInterface &sc, bool overwrite=true) const override
	Write a container to 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...

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

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

virtual std::unique_ptr< SiteContainerInterface >	readAlignmentFromFile (const std::string &path, std::shared_ptr< const Alphabet > alpha) const
	Read sequences from a file. More...

Protected Attributes
unsigned int	charsByLine_
	The maximum number of chars to be written on a line. More...

bool	checkNames_

bool	extended_

bool	strictNames_

Detailed Description

The fasta sequence file format.

Read and write from/to Fasta files.

Definition at line 26 of file Fasta.h.

Constructor & Destructor Documentation

◆ Fasta()

bpp::Fasta::Fasta	(	unsigned int	charsByLine = `100`,
		bool	checkSequenceNames = `true`,
		bool	extended = `false`,
		bool	strictSequenceNames = `false`
	)

inline

Build a new Fasta object.

Parameters

charsByLine	Number of character per line when writing files.
checkSequenceNames	Tells if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
extended	Tells if we should read general comments and sequence comments in HUPO-PSI format.
strictSequenceNames	Tells if the sequence names should be restricted to the characters between '>' and the first blank one.

Definition at line 51 of file Fasta.h.

◆ ~Fasta()

virtual bpp::Fasta::~Fasta ( )

inlinevirtual

Definition at line 54 of file Fasta.h.

Member Function Documentation

◆ appendAlignmentFromFile()

virtual void bpp::AbstractIAlignment::appendAlignmentFromFile	(	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 93 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIAlignment::readAlignment(), bpp::AbstractIAlignment::readAlignmentFromFile(), and bpp::AbstractIAlignment2::readSequences().

◆ appendAlignmentFromStream()

void bpp::Fasta::appendAlignmentFromStream	(	std::istream &	input,
		SequenceContainerInterface &	sc
	)		const

inlineoverridevirtual

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::AbstractIAlignment.

Definition at line 70 of file Fasta.h.

References appendSequencesFromStream().

◆ 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 Fasta::appendSequencesFromStream	(	std::istream &	input,
		SequenceContainerInterface &	sc
	)		const

overridevirtual

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 119 of file Fasta.cpp.

References bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::addSequence(), bpp::TemplateSequenceDataInterface< HashType >::getAlphabet(), and bpp::Commentable::setComments().

Referenced by appendAlignmentFromStream().

◆ checkNames() [1/2]

bool bpp::Fasta::checkNames ( ) const

inline

Returns: true if the names are to be checked when reading sequences from files.

Definition at line 121 of file Fasta.h.

References checkNames_.

◆ checkNames() [2/2]

void bpp::Fasta::checkNames ( bool yn )

inline

Tell whether the sequence names should be checked when reading from files.

Parameters

yn	whether the sequence names should be checked when reading from files.

Definition at line 128 of file Fasta.h.

References checkNames_.

◆ 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::Fasta::getFormatDescription ( ) const

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 96 of file Fasta.h.

◆ getFormatName()

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

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 94 of file Fasta.h.

◆ nextSequence() [1/2]

bool Fasta::nextSequence	(	std::istream &	input,
		Sequence &	seq
	)		const

override

Definition at line 18 of file Fasta.cpp.

References bpp::StringTokenizer::hasMoreToken(), bpp::TextTools::isWhiteSpaceCharacter(), bpp::StringTokenizer::nextToken(), bpp::TextTools::removeWhiteSpaces(), bpp::SimpleCommentable::setComments(), bpp::Sequence::setContent(), bpp::AbstractCoreSequence::setName(), and bpp::TextTools::toUpper().

Referenced by bpp::Fasta::FileIndex::getSequence().

◆ nextSequence() [2/2]

template<class SequenceType >

virtual bool bpp::TemplateISequenceStream< SequenceType >::nextSequence	(	std::istream &	input,
		SequenceType &	seq
	)		const

pure virtualinherited

Read sequence from stream.

Read one sequence from a stream.

Parameters

input	The stream to read.
seq	The sequence to fill.

Returns: true if a sequence was read or false if not.

Exceptions

Exception IOExecption and Sequence related Exceptions.

◆ readAlignment() [1/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	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::IAlignment.

Definition at line 57 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

◆ readAlignment() [2/4]

std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::readAlignment	(	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 SiteContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IAlignment.

Definition at line 62 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromFile().

◆ readAlignment() [3/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	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::IAlignment.

Definition at line 45 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIAlignment2::readSequences(), bpp::Clustal::readSequences(), bpp::DCSE::readSequences(), and bpp::Phylip::readSequences().

◆ readAlignment() [4/4]

std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::readAlignment	(	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 SiteContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IAlignment.

Definition at line 67 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromStream().

◆ readAlignmentFromFile()

virtual std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::readAlignmentFromFile	(	const std::string &	path,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineprotectedvirtualinherited

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 125 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

Referenced by bpp::AbstractIAlignment::readAlignment().

◆ readAlignmentFromStream()

virtual std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::readAlignmentFromStream	(	std::istream &	input,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineprotectedvirtualinherited

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 110 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIAlignment::readAlignment().

◆ 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().

◆ strictNames() [1/2]

bool bpp::Fasta::strictNames ( ) const

inline

Returns: true if the sequence name is restricted to be between '>' and the first space character.

Definition at line 133 of file Fasta.h.

References strictNames_.

Referenced by bpp::Fasta::FileIndex::getSequence().

◆ strictNames() [2/2]

void bpp::Fasta::strictNames ( bool yn )

inline

Tell wethed the sequence name should be restrected to the first non blank characters.

Parameters

yn	whether the sequence names should be restrected.

Definition at line 140 of file Fasta.h.

References strictNames_.

◆ writeAlignment() [1/2]

void bpp::AbstractOSequence2::writeAlignment	(	const std::string &	path,
		const SiteContainerInterface &	sc,
		bool	overwrite = `true`
	)		const

inlineoverridevirtualinherited

Write a container to a file.

Parameters

path	The path to the file to write.
sc	The container to write.
overwrite	If true the sequences are written at the beginning of the file instead of being appended. Any previous content will be lost.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::OAlignment.

Definition at line 78 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeAlignment() [2/2]

void bpp::AbstractOSequence2::writeAlignment	(	std::ostream &	output,
		const SiteContainerInterface &	sc
	)		const

inlineoverridevirtualinherited

Write a container to a stream.

Parameters

output	The output stream where to write.
sc	The container to write.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::OAlignment.

Definition at line 73 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeSequence() [1/2]

void Fasta::writeSequence	(	std::ostream &	output,
		const Sequence &	seq
	)		const

override

Definition at line 88 of file Fasta.cpp.

References bpp::Sequence::getChar(), bpp::SimpleCommentable::getComments(), bpp::AbstractCoreSequence::getName(), and bpp::AbstractTemplateSymbolList< T >::size().

◆ writeSequence() [2/2]

template<class SequenceType >

virtual void bpp::TemplateOSequenceStream< SequenceType >::writeSequence	(	std::ostream &	output,
		const SequenceType &	seq
	)		const

pure virtualinherited

Read sequence from stream.

Read one sequence from a stream.

Parameters

output	The stream where write.
seq	The sequence to write.

Exceptions

Exception IOExecption.

◆ writeSequences() [1/2]

void bpp::Fasta::writeSequences	(	const std::string &	path,
		const SequenceContainerInterface &	sc,
		bool	overwrite = `true`
	)		const

inlineoverridevirtual

Write a container to a file.

Parameters

path	The path to the file to write.
sc	The container to write.
overwrite	If true the sequences are written at the beginning of the file instead of being appended. Any previous content will be lost.

Exceptions

Exception If the file is not in the specified format.

Reimplemented from bpp::AbstractOSequence.

Definition at line 83 of file Fasta.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeSequences() [2/2]

void Fasta::writeSequences	(	std::ostream &	output,
		const SequenceContainerInterface &	sc
	)		const

overridevirtual

Write a container to a stream.

Parameters

output	The output stream where to write.
sc	The container to write.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::AbstractOSequence.

Definition at line 178 of file Fasta.cpp.

References bpp::Commentable::getComments(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceNames(), and bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence().

Member Data Documentation

◆ charsByLine_

unsigned int bpp::Fasta::charsByLine_

protected

The maximum number of chars to be written on a line.

Definition at line 37 of file Fasta.h.

◆ checkNames_

bool bpp::Fasta::checkNames_

protected

Definition at line 38 of file Fasta.h.

Referenced by checkNames().

◆ extended_

bool bpp::Fasta::extended_

protected

Definition at line 39 of file Fasta.h.

◆ strictNames_

bool bpp::Fasta::strictNames_

protected

Definition at line 40 of file Fasta.h.

Referenced by strictNames().

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

Bpp/Seq/Io/Fasta.h
Bpp/Seq/Io/Fasta.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Fasta()

◆ ~Fasta()

Member Function Documentation

◆ appendAlignmentFromFile()

◆ appendAlignmentFromStream()

◆ appendSequencesFromFile()

◆ appendSequencesFromStream()

◆ checkNames() [1/2]

◆ checkNames() [2/2]

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ nextSequence() [1/2]

◆ nextSequence() [2/2]

◆ readAlignment() [1/4]

◆ readAlignment() [2/4]

◆ readAlignment() [3/4]

◆ readAlignment() [4/4]

◆ readAlignmentFromFile()

◆ readAlignmentFromStream()

◆ readSequences() [1/4]

◆ readSequences() [2/4]

◆ readSequences() [3/4]

◆ readSequences() [4/4]

◆ readSequencesFromFile()

◆ readSequencesFromStream()

◆ strictNames() [1/2]

◆ strictNames() [2/2]

◆ writeAlignment() [1/2]

◆ writeAlignment() [2/2]

◆ writeSequence() [1/2]

◆ writeSequence() [2/2]

◆ writeSequences() [1/2]

◆ writeSequences() [2/2]

Member Data Documentation

◆ charsByLine_

◆ checkNames_

◆ extended_

◆ strictNames_