The Pasta sequence file format. More...

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

Inheritance diagram for bpp::Pasta:

Collaboration diagram for bpp::Pasta:

Public Types
typedef Table< double >	DataTable

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

virtual	~Pasta ()

const std::string	getFormatName () const override
	Get the format name. More...

const std::string	getFormatDescription () const override

void	writeSequence (std::ostream &output, const ProbabilisticSequence &seq, bool header) const

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

const std::string	getDataType () const override

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

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

The "ISequenceStream interface"
bool	nextSequence (std::istream &input, ProbabilisticSequence &seq, bool hasLabels, const std::vector< size_t > &permutationMap) const

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

void	writeSequences (std::ostream &output, const SequenceContainerInterface &sc) const override=0

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

The "I/OProbabilisticSequence interface"
void	appendAlignmentFromStream (std::istream &input, ProbabilisticSequenceContainerInterface &psc) const override
	Append sequences to a container from a stream. More...

void	writeAlignment (std::ostream &output, const ProbabilisticSiteContainerInterface &psc) const override
	Write a container to a stream. More...

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

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

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

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

OProbabilisticAlignment methods:
void	writeAlignment (const std::string &path, const ProbabilisticSiteContainerInterface &psc, bool overwrite=true) const override
	Write a container to a file. 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...

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

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

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

virtual std::unique_ptr< ProbabilisticSiteContainerInterface >	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	extended_

bool	strictNames_

Detailed Description

The Pasta sequence file format.

Read and write from/to Pasta files – a format that is more general than the Fasta format : while the Fasta format contains sequence information in the form of character states at each site of the sequence, the Pasta format contains sequence information in the form of probability of presence of each character state at each site. See implementation of methods below for more details

Definition at line 30 of file Pasta.h.

Member Typedef Documentation

◆ DataTable

typedef Table<double> bpp::Pasta::DataTable

Definition at line 45 of file Pasta.h.

Constructor & Destructor Documentation

◆ Pasta()

bpp::Pasta::Pasta	(	unsigned int	charsByLine = `100`,
		bool	extended = `false`,
		bool	strictSequenceNames = `false`
	)

inline

Build a new Pasta object.

Parameters

charsByLine	Number of characters per line when writing files.
extended	Tell 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 54 of file Pasta.h.

◆ ~Pasta()

virtual bpp::Pasta::~Pasta ( )

inlinevirtual

Definition at line 57 of file Pasta.h.

Member Function Documentation

◆ appendAlignmentFromFile()

virtual void bpp::AbstractIProbabilisticAlignment::appendAlignmentFromFile	(	const std::string &	path,
		ProbabilisticSequenceContainerInterface &	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 250 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIProbabilisticAlignment::readAlignment(), bpp::AbstractIProbabilisticAlignment::readAlignmentFromFile(), and bpp::AbstractIProbabilisticAlignment2::readSequences().

◆ appendAlignmentFromStream()

void Pasta::appendAlignmentFromStream	(	std::istream &	input,
		ProbabilisticSequenceContainerInterface &	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.

Implements bpp::AbstractIProbabilisticAlignment.

Definition at line 156 of file Pasta.cpp.

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

◆ getDataType()

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

inlineoverridevirtual

Reimplemented from bpp::IOSequence.

Definition at line 131 of file Pasta.h.

◆ getFormatDescription()

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

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 66 of file Pasta.h.

◆ getFormatName()

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

inlineoverridevirtual

Get the format name.

Returns: format name

Implements bpp::IOFormat.

Definition at line 65 of file Pasta.h.

◆ nextSequence()

bool Pasta::nextSequence	(	std::istream &	input,
		ProbabilisticSequence &	seq,
		bool	hasLabels,
		const std::vector< size_t > &	permutationMap
	)		const

Definition at line 19 of file Pasta.cpp.

References bpp::Table< class >::addColumn(), bpp::ProbabilisticSymbolList::getAlphabet(), bpp::Table< class >::getData(), bpp::StringTokenizer::hasMoreToken(), bpp::TextTools::isWhiteSpaceCharacter(), bpp::StringTokenizer::nextToken(), bpp::SimpleCommentable::setComments(), bpp::ProbabilisticSymbolList::setContent(), and bpp::AbstractCoreSequence::setName().

◆ readAlignment() [1/4]

void bpp::AbstractIProbabilisticAlignment::readAlignment	(	const std::string &	path,
		ProbabilisticSequenceContainerInterface &	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.

Implements bpp::IProbabilisticAlignment.

Definition at line 215 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromFile().

◆ readAlignment() [2/4]

std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::AbstractIProbabilisticAlignment::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 ProbabilisticSiteContainer object.

Implements bpp::IProbabilisticAlignment.

Definition at line 220 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::readAlignmentFromFile().

◆ readAlignment() [3/4]

void bpp::AbstractIProbabilisticAlignment::readAlignment	(	std::istream &	input,
		ProbabilisticSequenceContainerInterface &	sc
	)		const

inlineoverridevirtualinherited

Add sequences to a container from a stream.

Parameters

input	The input stream to read.
sc	The sequence container to update.

Implements bpp::IProbabilisticAlignment.

Definition at line 204 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIProbabilisticAlignment2::readSequences().

◆ readAlignment() [4/4]

std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::AbstractIProbabilisticAlignment::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 ProbabilisticSiteContainer object.

Implements bpp::IProbabilisticAlignment.

Definition at line 225 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::readAlignmentFromStream().

◆ readAlignmentFromFile()

virtual std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::AbstractIProbabilisticAlignment::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.

Definition at line 280 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromFile().

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

◆ readAlignmentFromStream()

virtual std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::AbstractIProbabilisticAlignment::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.

Definition at line 266 of file AbstractIAlignment.h.

References bpp::AbstractIProbabilisticAlignment::appendAlignmentFromStream().

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

◆ writeAlignment() [1/6]

void bpp::AbstractOProbabilisticAlignment::writeAlignment	(	const std::string &	path,
		const ProbabilisticSiteContainerInterface &	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.

Implements bpp::OProbabilisticAlignment.

Definition at line 65 of file AbstractOAlignment.h.

References bpp::AbstractOProbabilisticAlignment::writeAlignment().

◆ writeAlignment() [2/6]

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() [3/6]

void bpp::AbstractOSequence2::writeAlignment

inlineoverride

Definition at line 78 of file AbstractOSequence.h.

◆ writeAlignment() [4/6]

void bpp::Pasta::writeAlignment	(	std::ostream &	output,
		const ProbabilisticSiteContainerInterface &	sc
	)		const

inlineoverridevirtual

Write a container to a stream.

Parameters

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

Implements bpp::AbstractOProbabilisticAlignment.

Definition at line 112 of file Pasta.h.

References bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(), and writeSequence().

◆ writeAlignment() [5/6]

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().

◆ writeAlignment() [6/6]

void bpp::AbstractOSequence2::writeAlignment

inlineoverride

Definition at line 73 of file AbstractOSequence.h.

◆ writeSequence() [1/2]

void Pasta::writeSequence	(	std::ostream &	output,
		const ProbabilisticSequence &	seq,
		bool	header
	)		const

Definition at line 276 of file Pasta.cpp.

References bpp::ProbabilisticSymbolList::getAlphabet(), bpp::SimpleCommentable::getComments(), bpp::ProbabilisticSymbolList::getContent(), bpp::AbstractCoreSequence::getName(), and bpp::VectorTools::print().

Referenced by writeAlignment(), and writeSequences().

◆ writeSequence() [2/2]

void Pasta::writeSequence	(	std::ostream &	output,
		const Sequence &	seq,
		bool	header
	)		const

Definition at line 318 of file Pasta.cpp.

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

◆ writeSequences() [1/4]

void bpp::AbstractOSequence::writeSequences	(	const std::string &	path,
		const SequenceContainerInterface &	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::OSequence.

Reimplemented in bpp::Mase, and bpp::Fasta.

Definition at line 38 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeSequences() [2/4]

void bpp::AbstractOSequence::writeSequences

inlineoverride

Definition at line 38 of file AbstractOSequence.h.

◆ writeSequences() [3/4]

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

inlineoverridevirtual

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 91 of file Pasta.h.

References bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(), and writeSequence().

◆ writeSequences() [4/4]

void bpp::AbstractOSequence::writeSequences

override

Member Data Documentation

◆ charsByLine_

unsigned int bpp::Pasta::charsByLine_

protected

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

Definition at line 39 of file Pasta.h.

◆ extended_

bool bpp::Pasta::extended_

protected

Definition at line 41 of file Pasta.h.

◆ strictNames_

bool bpp::Pasta::strictNames_

protected

Definition at line 42 of file Pasta.h.

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

Bpp/Seq/Io/Pasta.h
Bpp/Seq/Io/Pasta.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ DataTable

Constructor & Destructor Documentation

◆ Pasta()

◆ ~Pasta()

Member Function Documentation

◆ appendAlignmentFromFile()

◆ appendAlignmentFromStream()

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ nextSequence()

◆ readAlignment() [1/4]

◆ readAlignment() [2/4]

◆ readAlignment() [3/4]

◆ readAlignment() [4/4]

◆ readAlignmentFromFile()

◆ readAlignmentFromStream()

◆ writeAlignment() [1/6]

◆ writeAlignment() [2/6]

◆ writeAlignment() [3/6]

◆ writeAlignment() [4/6]

◆ writeAlignment() [5/6]

◆ writeAlignment() [6/6]

◆ writeSequence() [1/2]

◆ writeSequence() [2/2]

◆ writeSequences() [1/4]

◆ writeSequences() [2/4]

◆ writeSequences() [3/4]

◆ writeSequences() [4/4]

Member Data Documentation

◆ charsByLine_

◆ extended_

◆ strictNames_