The mase sequence file format. More...

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

Inheritance diagram for bpp::Mase:

Collaboration diagram for bpp::Mase:

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

virtual	~Mase ()

bool	checkNames () const

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

const std::string	getDataType () const

Reading method including header:
std::unique_ptr< SequenceContainerInterface >	readMeta (std::istream &input, std::shared_ptr< const Alphabet > &alpha, MaseHeader &header) const

std::unique_ptr< SequenceContainerInterface >	readMeta (std::string &path, std::shared_ptr< const Alphabet > &alpha, MaseHeader &header) const

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...

Writing methods including header:
void	writeMeta (std::ostream &output, const SequenceContainerInterface &sc, const MaseHeader &header) const

void	writeMeta (const std::string &path, const SequenceContainerInterface &sc, const MaseHeader &header, bool overwrite=true) const

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

const std::string	getFormatDescription () 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...

Private Member Functions
void	readHeader_ (std::istream &input, MaseHeader &header) const

void	writeHeader_ (std::ostream &output, const MaseHeader &header) const

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

bool	checkNames_

Detailed Description

The mase sequence file format.

In addition to traditional read and write method, this class offers overloaded method with MaseHeader objects, dedicated to header information storage. If used, then the header of the mase file will be parsed accordingly. Otherwise, the header lines will be stored as general comments.

See also: MaseTools for alternative way of parsing headers.

Definition at line 103 of file Mase.h.

Constructor & Destructor Documentation

◆ Mase()

bpp::Mase::Mase	(	unsigned int	charsByLine = `100`,
		bool	checkSequenceNames = `true`
	)

inline

Build a new Mase object.

Parameters

charsByLine	Number of character per line when writing files.
checkSequenceNames	Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).

Definition at line 122 of file Mase.h.

◆ ~Mase()

virtual bpp::Mase::~Mase ( )

inlinevirtual

Definition at line 125 of file Mase.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::Mase::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 161 of file Mase.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 Mase::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 13 of file Mase.cpp.

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

Referenced by appendAlignmentFromStream().

◆ checkNames() [1/2]

bool bpp::Mase::checkNames ( ) const

inline

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

Definition at line 217 of file Mase.h.

References checkNames_.

◆ checkNames() [2/2]

void bpp::Mase::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 224 of file Mase.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::Mase::getFormatDescription ( ) const

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 208 of file Mase.h.

◆ getFormatName()

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

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 206 of file Mase.h.

◆ 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().

◆ readHeader_()

void Mase::readHeader_	(	std::istream &	input,
		MaseHeader &	header
	)		const

private

Definition at line 159 of file Mase.cpp.

References bpp::MultiRange< class >::addRange(), bpp::TextTools::endsWith(), bpp::FileTools::getNextLine(), bpp::StringTokenizer::hasMoreToken(), bpp::StringTokenizer::nextToken(), bpp::TextTools::removeSurroundingWhiteSpaces(), bpp::MaseHeader::setSequenceSelection(), bpp::MaseHeader::setSiteSelection(), bpp::MaseHeader::setTree(), bpp::MultiRange< class >::size(), bpp::TextTools::toString(), and bpp::StringTokenizer::unparseRemainingTokens().

Referenced by readMeta().

◆ readMeta() [1/2]

std::unique_ptr<SequenceContainerInterface> bpp::Mase::readMeta	(	std::istream &	input,
		std::shared_ptr< const Alphabet > &	alpha,
		MaseHeader &	header
	)		const

inline

Definition at line 133 of file Mase.h.

References readHeader_(), and bpp::AbstractISequence::readSequences().

Referenced by readMeta().

◆ readMeta() [2/2]

std::unique_ptr<SequenceContainerInterface> bpp::Mase::readMeta	(	std::string &	path,
		std::shared_ptr< const Alphabet > &	alpha,
		MaseHeader &	header
	)		const

inline

Definition at line 139 of file Mase.h.

References readMeta().

◆ 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 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().

◆ 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().

◆ writeHeader_()

void Mase::writeHeader_	(	std::ostream &	output,
		const MaseHeader &	header
	)		const

private

Definition at line 270 of file Mase.cpp.

References bpp::Range< class >::begin(), bpp::Range< class >::end(), bpp::MultiRange< class >::getRange(), bpp::MaseHeader::getSequenceSelection(), bpp::MaseHeader::getSequenceSelectionNames(), bpp::MaseHeader::getSiteSelection(), bpp::MaseHeader::getSiteSelectionNames(), bpp::MaseHeader::getTree(), bpp::MaseHeader::getTreeNames(), bpp::MultiRange< class >::size(), and bpp::MultiRange< class >::totalLength().

Referenced by writeMeta().

◆ writeMeta() [1/2]

void bpp::Mase::writeMeta	(	const std::string &	path,
		const SequenceContainerInterface &	sc,
		const MaseHeader &	header,
		bool	overwrite = `true`
	)		const

inline

Definition at line 191 of file Mase.h.

References writeHeader_(), and writeSequences().

◆ writeMeta() [2/2]

void bpp::Mase::writeMeta	(	std::ostream &	output,
		const SequenceContainerInterface &	sc,
		const MaseHeader &	header
	)		const

inline

Definition at line 186 of file Mase.h.

References writeHeader_(), and writeSequences().

◆ writeSequences() [1/2]

void bpp::Mase::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 175 of file Mase.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeSequences() [2/2]

void Mase::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 93 of file Mase.cpp.

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

Referenced by writeMeta().

Member Data Documentation

◆ charsByLine_

unsigned int bpp::Mase::charsByLine_

private

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

Definition at line 112 of file Mase.h.

◆ checkNames_

bool bpp::Mase::checkNames_

private

Definition at line 113 of file Mase.h.

Referenced by checkNames().

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

Bpp/Seq/Io/Mase.h
Bpp/Seq/Io/Mase.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Mase()

◆ ~Mase()

Member Function Documentation

◆ appendAlignmentFromFile()

◆ appendAlignmentFromStream()

◆ appendSequencesFromFile()

◆ appendSequencesFromStream()

◆ checkNames() [1/2]

◆ checkNames() [2/2]

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ readAlignment() [1/4]

◆ readAlignment() [2/4]

◆ readAlignment() [3/4]

◆ readAlignment() [4/4]

◆ readAlignmentFromFile()

◆ readAlignmentFromStream()

◆ readHeader_()

◆ readMeta() [1/2]

◆ readMeta() [2/2]

◆ readSequences() [1/4]

◆ readSequences() [2/4]

◆ readSequences() [3/4]

◆ readSequences() [4/4]

◆ readSequencesFromFile()

◆ readSequencesFromStream()

◆ writeAlignment() [1/2]

◆ writeAlignment() [2/2]

◆ writeHeader_()

◆ writeMeta() [1/2]

◆ writeMeta() [2/2]

◆ writeSequences() [1/2]

◆ writeSequences() [2/2]

Member Data Documentation

◆ charsByLine_

◆ checkNames_