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

Inheritance diagram for bpp::Phylip:

Collaboration diagram for bpp::Phylip:

Public Member Functions
	Phylip (bool extended=true, bool sequential=true, unsigned int charsByLine=100, bool checkSequenceNames=true, const std::string &split=" ")
	Build a new Phylip file reader. More...

virtual	~Phylip ()

unsigned int	getNumberOfSequences (const std::string &path) const throw (IOException)

bool	checkNames () const

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

const std::string &	getSplit () const

void	setSplit (const std::string &split)

const std::string	getDataType () const

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

The ISequence interface.
As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence interface by downcasting the interface.
virtual SequenceContainer *	readSequences (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Create a new container from a stream. More...

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

The OSequence interface.
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) const throw (Exception)
	Write a container to a file. More...

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

const std::string	getFormatDescription () const

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...

Protected Member Functions
const std::vector< std::string >	splitNameAndSequence (const std::string &s) const throw (Exception)

void	readSequential (std::istream &in, SiteContainer &asc) const throw (Exception)

void	readInterleaved (std::istream &in, SiteContainer &asc) const throw (Exception)

std::vector< std::string >	getSizedNames (const std::vector< std::string > &names) const

void	writeSequential (std::ostream &out, const SequenceContainer &sc) const

void	writeInterleaved (std::ostream &out, const SequenceContainer &sc) const

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 Attributes
bool	extended_

bool	sequential_

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

bool	checkNames_

std::string	namesSplit_

Detailed Description

The Phylip & co format.

An AlignedSequenceContainer is used instead of a VectorSequenceContainer.

This format is described on the Phylip package documentation website: http://evolution.genetics.washington.edu/phylip/doc/sequence.html

Definition at line 64 of file Phylip.h.

Constructor & Destructor Documentation

◆ Phylip()

bpp::Phylip::Phylip	(	bool	extended = `true`,
		bool	sequential = `true`,
		unsigned int	charsByLine = `100`,
		bool	checkSequenceNames = `true`,
		const std::string &	split = `" "`
	)

inline

Build a new Phylip file reader.

Parameters

extended	If true, sequences with names longer than 10 characters are allowed.
sequential	If false, sequences are supposed to be interlaved.
charsByLine	The number of base to display in a row.
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).
split	The string to use to split sequence name from content (only for 'extended' format). This will typically be " " (two spaces) or "\t" (a tabulation).

Definition at line 99 of file Phylip.h.

◆ ~Phylip()

virtual bpp::Phylip::~Phylip ( )

inlinevirtual

Definition at line 102 of file Phylip.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 Phylip::appendAlignmentFromStream	(	std::istream &	input,
		SiteContainer &	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::AbstractIAlignment.

Definition at line 174 of file Phylip.cpp.

◆ checkNames() [1/2]

bool bpp::Phylip::checkNames ( ) const

inline

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

Definition at line 163 of file Phylip.h.

References checkNames_.

◆ checkNames() [2/2]

void bpp::Phylip::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 170 of file Phylip.h.

References checkNames_.

◆ getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ getFormatDescription()

const std::string Phylip::getFormatDescription ( ) const

Definition at line 298 of file Phylip.cpp.

◆ getFormatName()

const std::string Phylip::getFormatName ( ) const

Definition at line 294 of file Phylip.cpp.

◆ getNumberOfSequences()

unsigned int Phylip::getNumberOfSequences	(	const std::string &	path	)	const
throw	(	IOException
	)

Returns: The number of sequences contained in the specified file.

This methods parses the firt line of the phylip file.

Parameters

path	The path of the file to parse.

Definition at line 185 of file Phylip.cpp.

◆ getSizedNames()

std::vector< std::string > Phylip::getSizedNames ( const std::vector< std::string > & names ) const

protected

Definition at line 201 of file Phylip.cpp.

◆ getSplit()

const std::string& bpp::Phylip::getSplit ( ) const

inline

Returns: The string used to split sequence name from content.

Definition at line 175 of file Phylip.h.

References namesSplit_.

◆ 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 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().

◆ readInterleaved()

void Phylip::readInterleaved	(	std::istream &	in,
		SiteContainer &	asc
	)		const
throw	(	Exception
	)

protected

Definition at line 132 of file Phylip.cpp.

◆ readSequences() [1/2]

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

inlinevirtual

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 122 of file Phylip.h.

References bpp::AbstractIAlignment::readAlignment().

◆ readSequences() [2/2]

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

inlinevirtual

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 125 of file Phylip.h.

References bpp::AbstractIAlignment::readAlignment().

◆ readSequential()

void Phylip::readSequential	(	std::istream &	in,
		SiteContainer &	asc
	)		const
throw	(	Exception
	)

protected

Definition at line 75 of file Phylip.cpp.

◆ setSplit()

void bpp::Phylip::setSplit ( const std::string & split )

inline

Parameters

split The string to be used to split sequence name from content.

Definition at line 180 of file Phylip.h.

References namesSplit_.

◆ splitNameAndSequence()

const std::vector< std::string > Phylip::splitNameAndSequence	(	const std::string &	s	)	const
throw	(	Exception
	)

protected

Definition at line 55 of file Phylip.cpp.

◆ writeAlignment() [1/2]

void Phylip::writeAlignment	(	std::ostream &	output,
		const SiteContainer &	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::AbstractOAlignment.

Definition at line 279 of file Phylip.cpp.

◆ writeAlignment() [2/2]

void bpp::Phylip::writeAlignment	(	const std::string &	path,
		const SiteContainer &	sc,
		bool	overwrite
	)		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::AbstractOAlignment.

Definition at line 144 of file Phylip.h.

References bpp::AbstractOAlignment::writeAlignment().

◆ writeInterleaved()

void Phylip::writeInterleaved	(	std::ostream &	out,
		const SequenceContainer &	sc
	)		const

protected

Definition at line 246 of file Phylip.cpp.

References bpp::SequenceContainer::getAlphabet(), bpp::SequenceContainer::getNumberOfSequences(), bpp::SequenceContainer::getSequence(), bpp::SequenceContainer::getSequencesNames(), bpp::Alphabet::getStateCodingSize(), and bpp::SequenceContainer::toString().

◆ writeSequential()

void Phylip::writeSequential	(	std::ostream &	out,
		const SequenceContainer &	sc
	)		const

protected

Definition at line 226 of file Phylip.cpp.

References bpp::SequenceContainer::getAlphabet(), bpp::SequenceContainer::getNumberOfSequences(), bpp::SequenceContainer::getSequence(), bpp::SequenceContainer::getSequencesNames(), bpp::Alphabet::getStateCodingSize(), and bpp::SequenceContainer::toString().

Member Data Documentation

◆ charsByLine_

unsigned int bpp::Phylip::charsByLine_

private

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

Definition at line 83 of file Phylip.h.

◆ checkNames_

bool bpp::Phylip::checkNames_

private

Definition at line 85 of file Phylip.h.

Referenced by checkNames().

◆ extended_

bool bpp::Phylip::extended_

private

Definition at line 75 of file Phylip.h.

◆ namesSplit_

std::string bpp::Phylip::namesSplit_

private

Definition at line 87 of file Phylip.h.

Referenced by getSplit(), and setSplit().

◆ sequential_

bool bpp::Phylip::sequential_

private

Definition at line 78 of file Phylip.h.

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

Bpp/Seq/Io/Phylip.h
Bpp/Seq/Io/Phylip.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Phylip()

◆ ~Phylip()

Member Function Documentation

◆ appendAlignmentFromFile()

◆ appendAlignmentFromStream()

◆ checkNames() [1/2]

◆ checkNames() [2/2]

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ getNumberOfSequences()

◆ getSizedNames()

◆ getSplit()

◆ readAlignment() [1/4]

◆ readAlignment() [2/4]

◆ readAlignment() [3/4]

◆ readAlignment() [4/4]

◆ readAlignmentFromFile()

◆ readAlignmentFromStream()

◆ readInterleaved()

◆ readSequences() [1/2]

◆ readSequences() [2/2]

◆ readSequential()

◆ setSplit()

◆ splitNameAndSequence()

◆ writeAlignment() [1/2]

◆ writeAlignment() [2/2]

◆ writeInterleaved()

◆ writeSequential()

Member Data Documentation

◆ charsByLine_

◆ checkNames_

◆ extended_

◆ namesSplit_

◆ sequential_