#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, const std::string &split=" ")
	Build a new Phylip file reader. More...

virtual	~Phylip ()

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

const std::string &	getSplit () const

void	setSplit (const std::string &split)

const std::string	getDataType () const

The AbstractIAlignment2 interface.
void	appendAlignmentFromStream (std::istream &input, SequenceContainerInterface &sc) const override
	Append sequences to a container from a stream. More...

The AbstractISequence interface.
As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence interface by downcasting the interface.
virtual std::unique_ptr< SequenceContainerInterface >	readSequences (std::istream &input, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a stream. More...

virtual 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...

The AbstractOSequence interface.
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) 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 ISequence interface.
As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence interface by downcasting the interface.
void	readSequences (std::istream &input, SequenceContainerInterface &sc) const override
	Create a new container from a stream. More...

void	readSequences (const std::string &path, SequenceContainerInterface &sc) 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...

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

void	readSequential (std::istream &in, SequenceContainerInterface &asc) const

void	readInterleaved (std::istream &in, SequenceContainerInterface &asc) const

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

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

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

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 Attributes
bool	extended_

bool	sequential_

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

std::string	namesSplit_

Detailed Description

The Phylip & co format.

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

Definition at line 28 of file Phylip.h.

Constructor & Destructor Documentation

◆ Phylip()

bpp::Phylip::Phylip	(	bool	extended = `true`,
		bool	sequential = `true`,
		unsigned int	charsByLine = `100`,
		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.
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 58 of file Phylip.h.

References split().

◆ ~Phylip()

virtual bpp::Phylip::~Phylip ( )

inlinevirtual

Definition at line 61 of file Phylip.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 Phylip::appendAlignmentFromStream	(	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::AbstractIAlignment.

Definition at line 145 of file Phylip.cpp.

◆ 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 Phylip::getFormatDescription ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 290 of file Phylip.cpp.

◆ getFormatName()

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

overridevirtual

Implements bpp::IOFormat.

Definition at line 286 of file Phylip.cpp.

◆ getNumberOfSequences()

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

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

This methods parses the first line of the phylip file.

Parameters

path	The path of the file to parse.

Definition at line 161 of file Phylip.cpp.

References bpp::FileTools::getNextLine(), and bpp::StringTokenizer::nextToken().

◆ getSizedNames()

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

protected

Definition at line 180 of file Phylip.cpp.

References bpp::TextTools::resizeRight().

◆ getSplit()

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

inline

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

Definition at line 123 of file Phylip.h.

References namesSplit_.

◆ 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 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().

◆ readInterleaved()

void Phylip::readInterleaved	(	std::istream &	in,
		SequenceContainerInterface &	asc
	)		const

protected

Definition at line 101 of file Phylip.cpp.

References bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::addSequence(), bpp::TemplateSequenceDataInterface< HashType >::getAlphabet(), bpp::FileTools::getNextLine(), bpp::TextTools::isEmpty(), bpp::StringTokenizer::nextToken(), and bpp::TextTools::removeWhiteSpaces().

◆ readSequences() [1/4]

void bpp::AbstractIAlignment2::readSequences	(	const std::string &	path,
		SequenceContainerInterface &	container
	)		const

inlineoverridevirtualinherited

Create a new container from a file.

Parameters

path	The path to the file to read.
container	The container where to add data.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Definition at line 162 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

◆ readSequences() [2/4]

virtual std::unique_ptr<SequenceContainerInterface> bpp::Phylip::readSequences	(	const std::string &	path,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtual

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.

Reimplemented from bpp::AbstractIAlignment2.

Definition at line 84 of file Phylip.h.

References bpp::AbstractIAlignment::readAlignment().

◆ readSequences() [3/4]

void bpp::AbstractIAlignment2::readSequences	(	std::istream &	input,
		SequenceContainerInterface &	container
	)		const

inlineoverridevirtualinherited

Create a new container from a stream.

Parameters

input	The input stream to read.
container	The container where to add data.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Definition at line 157 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

◆ readSequences() [4/4]

virtual std::unique_ptr<SequenceContainerInterface> bpp::Phylip::readSequences	(	std::istream &	input,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtual

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.

Reimplemented from bpp::AbstractIAlignment2.

Definition at line 80 of file Phylip.h.

References bpp::AbstractIAlignment::readAlignment().

◆ readSequential()

void Phylip::readSequential	(	std::istream &	in,
		SequenceContainerInterface &	asc
	)		const

protected

Definition at line 42 of file Phylip.cpp.

References bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::addSequence(), bpp::TemplateSequenceDataInterface< HashType >::getAlphabet(), bpp::FileTools::getNextLine(), bpp::TextTools::isEmpty(), bpp::TextTools::removeSurroundingWhiteSpaces(), and bpp::TextTools::removeWhiteSpaces().

◆ 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 128 of file Phylip.h.

References namesSplit_, and split().

◆ splitNameAndSequence()

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

protected

Definition at line 21 of file Phylip.cpp.

References bpp::TextTools::removeFirstWhiteSpaces(), and bpp::TextTools::removeSurroundingWhiteSpaces().

◆ writeAlignment() [1/2]

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

Definition at line 104 of file Phylip.h.

References bpp::AbstractOAlignment::writeAlignment().

◆ writeAlignment() [2/2]

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

Definition at line 266 of file Phylip.cpp.

References bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences().

◆ writeInterleaved()

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

protected

Definition at line 233 of file Phylip.cpp.

References bpp::TemplateSequenceDataInterface< HashType >::getAlphabet(), bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceNames(), bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(), and bpp::TextTools::split().

◆ writeSequential()

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

protected

Definition at line 213 of file Phylip.cpp.

References bpp::TemplateSequenceDataInterface< HashType >::getAlphabet(), bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceNames(), bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence(), and bpp::TextTools::split().

Member Data Documentation

◆ charsByLine_

unsigned int bpp::Phylip::charsByLine_

private

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

Definition at line 45 of file Phylip.h.

◆ extended_

bool bpp::Phylip::extended_

private

Definition at line 37 of file Phylip.h.

◆ namesSplit_

std::string bpp::Phylip::namesSplit_

private

Definition at line 47 of file Phylip.h.

Referenced by getSplit(), and setSplit().

◆ sequential_

bool bpp::Phylip::sequential_

private

Definition at line 40 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()

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ getNumberOfSequences()

◆ getSizedNames()

◆ getSplit()

◆ readAlignment() [1/4]

◆ readAlignment() [2/4]

◆ readAlignment() [3/4]

◆ readAlignment() [4/4]

◆ readAlignmentFromFile()

◆ readAlignmentFromStream()

◆ readInterleaved()

◆ readSequences() [1/4]

◆ readSequences() [2/4]

◆ readSequences() [3/4]

◆ readSequences() [4/4]

◆ readSequential()

◆ setSplit()

◆ splitNameAndSequence()

◆ writeAlignment() [1/2]

◆ writeAlignment() [2/2]

◆ writeInterleaved()

◆ writeSequential()

Member Data Documentation

◆ charsByLine_

◆ extended_

◆ namesSplit_

◆ sequential_