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:
VectorSequenceContainer *	readMeta (std::istream &input, const Alphabet *alpha, MaseHeader &header) const throw (Exception)

VectorSequenceContainer *	readMeta (std::string &path, const Alphabet *alpha, MaseHeader &header) const throw (Exception)

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

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

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

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

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

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

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

const std::string	getFormatDescription () const

ISequence methods:
virtual void	readSequences (std::istream &input, SequenceContainer &sc) const throw (Exception)
	Add sequences to a container from a stream. More...

virtual void	readSequences (const std::string &path, SequenceContainer &sc) const throw (Exception)
	Add sequences to a container from a file. More...

virtual VectorSequenceContainer *	readSequences (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Create a new container from a stream. More...

virtual VectorSequenceContainer *	readSequences (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Create a new container from a file. More...

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

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

virtual AlignedSequenceContainer *	readAlignment (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Create a new container from a file. More...

virtual AlignedSequenceContainer *	readAlignment (std::istream &input, const Alphabet *alpha) const throw (Exception)
	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 SiteContainer &sc) const throw (Exception)
	Write a container to a stream. More...

void	writeAlignment (const std::string &path, const SiteContainer &sc, bool overwrite=true) const throw (Exception)
	Write a container to a file. More...

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

virtual VectorSequenceContainer *	readSequencesFromStream (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Read sequences from a stream. More...

virtual VectorSequenceContainer *	readSequencesFromFile (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Append sequences to a container from a file. More...

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

virtual AlignedSequenceContainer *	readAlignmentFromStream (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Read sequences from a stream. More...

virtual AlignedSequenceContainer *	readAlignmentFromFile (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Read sequences from a file. More...

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

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 125 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 146 of file Mase.h.

◆ ~Mase()

virtual bpp::Mase::~Mase ( )

inlinevirtual

Definition at line 149 of file Mase.h.

Member Function Documentation

◆ appendAlignmentFromFile()

virtual void bpp::AbstractIAlignment::appendAlignmentFromFile	(	const std::string &	path,
		SiteContainer &	sc
	)		const
throw	(	Exception
	)

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 143 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

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

◆ appendAlignmentFromStream()

void bpp::Mase::appendAlignmentFromStream	(	std::istream &	input,
		SiteContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtual

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 185 of file Mase.h.

References appendSequencesFromStream().

◆ appendSequencesFromFile()

virtual void bpp::AbstractISequence::appendSequencesFromFile	(	const std::string &	path,
		SequenceContainer &	sc
	)		const
throw	(	Exception
	)

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 142 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromStream().

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

◆ appendSequencesFromStream()

void Mase::appendSequencesFromStream	(	std::istream &	input,
		SequenceContainer &	sc
	)		const
throw	(	Exception
	)

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 49 of file Mase.cpp.

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 239 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 246 of file Mase.h.

References checkNames_.

◆ getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ getFormatDescription()

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

inline

Definition at line 230 of file Mase.h.

◆ getFormatName()

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

inline

Definition at line 228 of file Mase.h.

◆ readAlignment() [1/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		SiteContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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.

Definition at line 81 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

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

◆ readAlignment() [2/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		SiteContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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.

Definition at line 93 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

◆ readAlignment() [3/4]

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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 104 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromFile().

◆ readAlignment() [4/4]

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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 115 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromStream().

◆ readAlignmentFromFile()

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignmentFromFile	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

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 173 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

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

◆ readAlignmentFromStream()

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignmentFromStream	(	std::istream &	input,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

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 158 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

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

◆ readHeader_()

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

private

Definition at line 181 of file Mase.cpp.

Referenced by readMeta().

◆ readMeta() [1/2]

VectorSequenceContainer* bpp::Mase::readMeta	(	std::istream &	input,
		const Alphabet *	alpha,
		MaseHeader &	header
	)		const
throw	(	Exception
	)

inline

Definition at line 158 of file Mase.h.

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

Referenced by readMeta().

◆ readMeta() [2/2]

VectorSequenceContainer* bpp::Mase::readMeta	(	std::string &	path,
		const Alphabet *	alpha,
		MaseHeader &	header
	)		const
throw	(	Exception
	)

inline

Definition at line 163 of file Mase.h.

References readMeta().

◆ readSequences() [1/4]

virtual void bpp::AbstractISequence::readSequences	(	std::istream &	input,
		SequenceContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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.

Definition at line 82 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromStream().

Referenced by readMeta().

◆ readSequences() [2/4]

virtual void bpp::AbstractISequence::readSequences	(	const std::string &	path,
		SequenceContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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.

Definition at line 94 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromFile().

◆ readSequences() [3/4]

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequences	(	std::istream &	input,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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 105 of file AbstractISequence.h.

References bpp::AbstractISequence::readSequencesFromStream().

◆ readSequences() [4/4]

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequences	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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 116 of file AbstractISequence.h.

References bpp::AbstractISequence::readSequencesFromFile().

◆ readSequencesFromFile()

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequencesFromFile	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlineprotectedvirtualinherited

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 171 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromFile().

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

◆ readSequencesFromStream()

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequencesFromStream	(	std::istream &	input,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

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 157 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromStream().

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

◆ writeAlignment() [1/2]

void bpp::AbstractOSequence::writeAlignment	(	std::ostream &	output,
		const SiteContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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 92 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeAlignment() [2/2]

void bpp::AbstractOSequence::writeAlignment	(	const std::string &	path,
		const SiteContainer &	sc,
		bool	overwrite = `true`
	)		const
throw	(	Exception
	)

inlinevirtualinherited

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 96 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeHeader_()

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

private

Definition at line 273 of file Mase.cpp.

References bpp::MaseHeader::getSequenceSelection(), bpp::MaseHeader::getSequenceSelectionNames(), bpp::MaseHeader::getSiteSelection(), bpp::MaseHeader::getSiteSelectionNames(), bpp::MaseHeader::getTree(), and bpp::MaseHeader::getTreeNames().

Referenced by writeMeta().

◆ writeMeta() [1/2]

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

inline

Definition at line 208 of file Mase.h.

References writeHeader_(), and writeSequences().

◆ writeMeta() [2/2]

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

inline

Definition at line 213 of file Mase.h.

References writeHeader_(), and writeSequences().

◆ writeSequences() [1/2]

void Mase::writeSequences	(	std::ostream &	output,
		const SequenceContainer &	sc
	)		const
throw	(	Exception
	)

virtual

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 119 of file Mase.cpp.

Referenced by writeMeta().

◆ writeSequences() [2/2]

void bpp::Mase::writeSequences	(	const std::string &	path,
		const SequenceContainer &	sc,
		bool	overwrite = `true`
	)		const
throw	(	Exception
	)

inlinevirtual

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 197 of file Mase.h.

References bpp::AbstractOSequence::writeSequences().

Member Data Documentation

◆ charsByLine_

unsigned int bpp::Mase::charsByLine_

private

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

Definition at line 136 of file Mase.h.

◆ checkNames_

bool bpp::Mase::checkNames_

private

Definition at line 137 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_