The so-called 'ExtendedNewick' parenthetic format for phylogenetic networks, where hybridization nodes are mandatory tagged and appear several times. More...

#include <Bpp/Phyl/Io/ExtendedNewick.h>

Inheritance diagram for bpp::ExtendedNewick:

Collaboration diagram for bpp::ExtendedNewick:

Public Member Functions
	ExtendedNewick (bool allowComments=false, bool writeId=false, bool verbose=false)
	Build a new ExtendedNewick reader/writer. More...

virtual	~ExtendedNewick ()

void	writePhyloDAGs (const std::vector< const PhyloDAG * > &dags, std::ostream &out) const override
	Write dags to a stream. More...

virtual void	writePhyloDAGs (const std::vector< const PhyloDAG * > &dags, std::ostream &out) const=0
	Write dags to a stream. More...

virtual void	writePhyloDAGs (const std::vector< const PhyloDAG * > &dags, const std::string &path, bool overwrite) const
	Write dags to a file. More...

virtual const std::string	getDataType () const

The IODAGraph interface
const std::string	getFormatName () const override

const std::string	getFormatDescription () const override

The ODAGraph interface
void	writePhyloDAG (const PhyloDAG &dag, std::ostream &out) const override
	Write a PhyloDAG to a stream. More...

virtual void	writePhyloDAG (const PhyloDAG &dag, std::ostream &out) const=0
	Write a PhyloDAG to a stream. More...

virtual void	writePhyloDAG (const PhyloDAG &dag, const std::string &path, bool overwrite) const
	Write a DAG to a file. More...

The IMultiDAGraph interface
void	readPhyloDAGs (std::istream &in, std::vector< std::unique_ptr< PhyloDAG > > &dags) const override
	Read dags from a stream. More...

virtual void	readPhyloDAGs (std::istream &in, std::vector< std::unique_ptr< PhyloDAG > > &dags) const override=0
	Read dags from a stream. More...

virtual void	readPhyloDAGs (const std::string &path, std::vector< std::unique_ptr< PhyloDAG > > &dags) const override
	Read dags from a file. More...

Protected Member Functions
void	write_ (const PhyloDAG &tree, std::ostream &out) const

void	write_ (const std::vector< const PhyloDAG * > &dags, std::ostream &out) const

Element	getElement (const std::string &elt) const override

std::string	edgeToParenthesis (const PhyloDAG &dag, std::shared_ptr< PhyloBranch > edge, std::vector< std::shared_ptr< PhyloNode > > &writtenNodes, bool writeId=false) const
	Get the ExtendedNewick description of a subdag. More...

std::string	dagToParenthesis (const PhyloDAG &dag, bool writeId=false) const
	Get the parenthesis description of a tree. More...

Protected Attributes
bool	allowComments_

bool	writeId_

bool	verbose_

The IDAGraph interface
std::unique_ptr< PhyloDAG >	readPhyloDAG (std::istream &in) const override
	Read a DAG from a stream. More...

std::unique_ptr< PhyloDAG >	parenthesisToPhyloDAG (const std::string &description, bool withId, bool verbose=false) const

std::unique_ptr< PhyloDAG >	readPhyloDAG (std::istream &in) const override=0
	Read a DAG from a stream. More...

std::unique_ptr< PhyloDAG >	readPhyloDAG (const std::string &path) const override
	Read a DAG from a file. More...

std::shared_ptr< PhyloNode >	parenthesisToNode (PhyloDAG &dag, std::shared_ptr< PhyloNode > father, const std::string &description, unsigned int &nodeCounter, unsigned int &branchCounter, std::map< std::string, std::shared_ptr< PhyloNode > > &mapEvent, bool withId, bool verbose) const

Detailed Description

The so-called 'ExtendedNewick' parenthetic format for phylogenetic networks, where hybridization nodes are mandatory tagged and appear several times.

Branch values are supported:

ex: ((A:0.1, ((B:0.2, (C:0.3, (D:0.2)Y::H1:0.2):0.1):0.2, (((Y::H1:0.1, E:0.4)h, 6)f)X::H2)c)a, ((X::H2, 7)d, 8)b)r;

Those values can be lengths, or probabilities for hybridization branches, depending on the biological meaning of the network.

Reference : Cardona, G, ó, F, Valiente, G (2008). Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinformatics, 9:532.

Definition at line 36 of file ExtendedNewick.h.

Constructor & Destructor Documentation

◆ ExtendedNewick()

bpp::ExtendedNewick::ExtendedNewick	(	bool	allowComments = `false`,
		bool	writeId = `false`,
		bool	verbose = `false`
	)

inline

Build a new ExtendedNewick reader/writer.

Some extendednewick format allow comments between hooks ('[' ']').

Parameters

allowComments	Tell if comments between [] are allowed in file.
writeId	If true, nodes ids will be written in place of bootstrap values.
verbose	If some info should be displayed, such as progress bar etc.

Definition at line 57 of file ExtendedNewick.h.

◆ ~ExtendedNewick()

virtual bpp::ExtendedNewick::~ExtendedNewick ( )

inlinevirtual

Definition at line 63 of file ExtendedNewick.h.

Member Function Documentation

◆ dagToParenthesis()

string ExtendedNewick::dagToParenthesis	(	const PhyloDAG &	dag,
		bool	writeId = `false`
	)		const

protected

Get the parenthesis description of a tree.

Parameters

dag	The dag to convert.
writeId	Tells if node ids must be printed. Leaves id will be added to the leave names, separated by a '_' character.

Returns: A string in the parenthesis format.

Definition at line 387 of file ExtendedNewick.cpp.

References edgeToParenthesis(), bpp::AssociationDAGraphImplObserver< class, class, class >::getOutgoingEdges(), bpp::AssociationDAGraphImplObserver< class, class, class >::getRoot(), and bpp::AssociationDAGraphImplObserver< class, class, class >::isRooted().

Referenced by write_().

◆ edgeToParenthesis()

string ExtendedNewick::edgeToParenthesis	(	const PhyloDAG &	dag,
		std::shared_ptr< PhyloBranch >	edge,
		std::vector< std::shared_ptr< PhyloNode > > &	writtenNodes,
		bool	writeId = `false`
	)		const

protected

Get the ExtendedNewick description of a subdag.

Parameters

dag	The dag to convert.
edge	The top of the subdag to convert.
writtenNodes	lists nodes already written.
writeId	Tells if node ids must be printed. Leaves id will be added to the leave names, separated by a '_' character.

Returns: A string in the parenthesis format.

Definition at line 340 of file ExtendedNewick.cpp.

References edgeToParenthesis(), bpp::AssociationDAGraphImplObserver< class, class, class >::getNodeIndex(), bpp::AssociationDAGraphImplObserver< class, class, class >::getNumberOfSons(), bpp::AssociationDAGraphImplObserver< class, class, class >::getOutgoingEdges(), bpp::AssociationDAGraphImplObserver< class, class, class >::getSon(), and bpp::AssociationDAGraphImplObserver< class, class, class >::isLeaf().

Referenced by dagToParenthesis(), and edgeToParenthesis().

◆ getDataType()

virtual const std::string bpp::IODAG::getDataType ( ) const

inlinevirtualinherited

Implements bpp::IOFormat.

Definition at line 48 of file IoDAG.h.

◆ getElement()

IODAG::Element ExtendedNewick::getElement ( const std::string & elt ) const

overrideprotectedvirtual

Reimplemented from bpp::AbstractIPhyloDAG.

Definition at line 104 of file ExtendedNewick.cpp.

References bpp::IODAG::Element::annotation, bpp::IODAG::Element::content, bpp::TextTools::isEmpty(), bpp::IODAG::Element::isLeaf, bpp::IODAG::Element::length, and bpp::TextTools::removeSurroundingWhiteSpaces().

Referenced by parenthesisToNode().

◆ getFormatDescription()

const string ExtendedNewick::getFormatDescription ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 30 of file ExtendedNewick.cpp.

◆ getFormatName()

const string ExtendedNewick::getFormatName ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 26 of file ExtendedNewick.cpp.

◆ parenthesisToNode()

shared_ptr< PhyloNode > ExtendedNewick::parenthesisToNode	(	PhyloDAG &	dag,
		std::shared_ptr< PhyloNode >	father,
		const std::string &	description,
		unsigned int &	nodeCounter,
		unsigned int &	branchCounter,
		std::map< std::string, std::shared_ptr< PhyloNode > > &	mapEvent,
		bool	withId,
		bool	verbose
	)		const

private

Definition at line 167 of file ExtendedNewick.cpp.

References bpp::IODAG::Element::annotation, bpp::IODAG::Element::content, bpp::AssociationDAGraphImplObserver< class, class, class >::createNode(), bpp::ApplicationTools::displayUnlimitedGauge(), getElement(), bpp::StringTokenizer::getToken(), bpp::NestedStringTokenizer::hasMoreToken(), bpp::AssociationDAGraphImplObserver< class, class, class >::hasNodeIndex(), bpp::NodeEvent::hybridizationEvent, bpp::TextTools::isEmpty(), bpp::IODAG::Element::isLeaf, bpp::IODAG::Element::length, bpp::AssociationDAGraphImplObserver< class, class, class >::link(), bpp::NestedStringTokenizer::nextToken(), bpp::StringTokenizer::numberOfRemainingTokens(), parenthesisToNode(), bpp::TextTools::removeSurroundingWhiteSpaces(), bpp::AssociationDAGraphImplObserver< class, class, class >::setEdgeIndex(), bpp::AssociationDAGraphImplObserver< class, class, class >::setNodeIndex(), bpp::TextTools::toDouble(), and bpp::TextTools::toInt().

Referenced by parenthesisToNode(), and parenthesisToPhyloDAG().

◆ parenthesisToPhyloDAG()

unique_ptr< PhyloDAG > ExtendedNewick::parenthesisToPhyloDAG	(	const std::string &	description,
		bool	withId,
		bool	verbose = `false`
	)		const

Definition at line 286 of file ExtendedNewick.cpp.

References bpp::ApplicationTools::message, and parenthesisToNode().

Referenced by readPhyloDAG(), and readPhyloDAGs().

◆ readPhyloDAG() [1/3]

std::unique_ptr< PhyloDAG > bpp::AbstractIPhyloDAG::readPhyloDAG ( const std::string & path ) const

inlineoverridevirtual

Read a DAG from a file.

Parameters

path	The file path.

Returns: a new PhyloDAG object.

Reimplemented from bpp::AbstractIPhyloDAG.

Definition at line 129 of file IoDAG.h.

◆ readPhyloDAG() [2/3]

unique_ptr< PhyloDAG > ExtendedNewick::readPhyloDAG ( std::istream & in ) const

overridevirtual

Read a DAG from a stream.

Parameters

in	The input stream.

Returns: A new PhyloDAG object.

Implements bpp::AbstractIPhyloDAG.

Definition at line 40 of file ExtendedNewick.cpp.

References allowComments_, bpp::TextTools::isEmpty(), parenthesisToPhyloDAG(), bpp::TextTools::removeSubstrings(), and verbose_.

◆ readPhyloDAG() [3/3]

std::unique_ptr< PhyloDAG > bpp::AbstractIPhyloDAG::readPhyloDAG ( std::istream & in ) const

overridevirtual

Read a DAG from a stream.

Parameters

in	The input stream.

Returns: A new PhyloDAG object.

Implements bpp::AbstractIPhyloDAG.

◆ readPhyloDAGs() [1/3]

virtual void bpp::AbstractIMultiPhyloDAG::readPhyloDAGs	(	const std::string &	path,
		std::vector< std::unique_ptr< PhyloDAG > > &	dags
	)		const

inlineoverridevirtual

Read dags from a file.

Parameters

path	The file path.
dags	The output dags vector.

Exceptions

Exception If an error occurred.

Reimplemented from bpp::AbstractIMultiPhyloDAG.

Definition at line 259 of file IoDAG.h.

◆ readPhyloDAGs() [2/3]

void ExtendedNewick::readPhyloDAGs	(	std::istream &	in,
		std::vector< std::unique_ptr< PhyloDAG > > &	dags
	)		const

overridevirtual

Read dags from a stream.

Parameters

in	The input stream.
dags	The output dags container.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractIMultiPhyloDAG.

Definition at line 73 of file ExtendedNewick.cpp.

References allowComments_, parenthesisToPhyloDAG(), bpp::TextTools::removeSubstrings(), and verbose_.

◆ readPhyloDAGs() [3/3]

virtual void bpp::AbstractIMultiPhyloDAG::readPhyloDAGs	(	std::istream &	in,
		std::vector< std::unique_ptr< PhyloDAG > > &	dags
	)		const

overridevirtual

Read dags from a stream.

Parameters

in	The input stream.
dags	The output dags container.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractIMultiPhyloDAG.

◆ write_() [1/2]

void ExtendedNewick::write_	(	const PhyloDAG &	tree,
		std::ostream &	out
	)		const

protected

Definition at line 312 of file ExtendedNewick.cpp.

References dagToParenthesis(), and writeId_.

Referenced by writePhyloDAG(), and writePhyloDAGs().

◆ write_() [2/2]

void ExtendedNewick::write_	(	const std::vector< const PhyloDAG * > &	dags,
		std::ostream &	out
	)		const

protected

Definition at line 325 of file ExtendedNewick.cpp.

References dagToParenthesis(), and writeId_.

◆ writePhyloDAG() [1/3]

virtual void bpp::AbstractOPhyloDAG::writePhyloDAG	(	const PhyloDAG &	dag,
		const std::string &	path,
		bool	overwrite
	)		const

inlinevirtual

Write a DAG to a file.

Parameters

dag	a PhyloDAG object.
path	The file path.
overwrite	Tell if existing file must be overwritten. Otherwise append to the file.

Exceptions

Exception If an error occurred.

Reimplemented from bpp::AbstractOPhyloDAG.

Definition at line 157 of file IoDAG.h.

◆ writePhyloDAG() [2/3]

void bpp::ExtendedNewick::writePhyloDAG	(	const PhyloDAG &	dag,
		std::ostream &	out
	)		const

inlineoverridevirtual

Write a PhyloDAG to a stream.

Parameters

dag	A PhyloDAG object.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOPhyloDAG.

Definition at line 113 of file ExtendedNewick.h.

References write_().

◆ writePhyloDAG() [3/3]

virtual void bpp::AbstractOPhyloDAG::writePhyloDAG	(	const PhyloDAG &	dag,
		std::ostream &	out
	)		const

virtual

Write a PhyloDAG to a stream.

Parameters

dag	A PhyloDAG object.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOPhyloDAG.

◆ writePhyloDAGs() [1/3]

virtual void bpp::AbstractOMultiPhyloDAG::writePhyloDAGs	(	const std::vector< const PhyloDAG * > &	dags,
		const std::string &	path,
		bool	overwrite
	)		const

inlinevirtual

Write dags to a file.

Parameters

dags	A vector of dag objects.
path	The file path.
overwrite	Tell if existing file must be overwritten. Otherwise append to the file.

Reimplemented from bpp::AbstractOMultiPhyloDAG.

Definition at line 280 of file IoDAG.h.

◆ writePhyloDAGs() [2/3]

void bpp::ExtendedNewick::writePhyloDAGs	(	const std::vector< const PhyloDAG * > &	dags,
		std::ostream &	out
	)		const

inlineoverridevirtual

Write dags to a stream.

Parameters

dags	A vector of dag objects.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOMultiPhyloDAG.

Definition at line 135 of file ExtendedNewick.h.

References write_().

◆ writePhyloDAGs() [3/3]

virtual void bpp::AbstractOMultiPhyloDAG::writePhyloDAGs	(	const std::vector< const PhyloDAG * > &	dags,
		std::ostream &	out
	)		const

virtual

Write dags to a stream.

Parameters

dags	A vector of dag objects.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOMultiPhyloDAG.

Member Data Documentation

◆ allowComments_

bool bpp::ExtendedNewick::allowComments_

protected

Definition at line 43 of file ExtendedNewick.h.

Referenced by readPhyloDAG(), and readPhyloDAGs().

◆ verbose_

bool bpp::ExtendedNewick::verbose_

protected

Definition at line 45 of file ExtendedNewick.h.

Referenced by readPhyloDAG(), and readPhyloDAGs().

◆ writeId_

bool bpp::ExtendedNewick::writeId_

protected

Definition at line 44 of file ExtendedNewick.h.

Referenced by write_().

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

Bpp/Phyl/Io/ExtendedNewick.h
Bpp/Phyl/Io/ExtendedNewick.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

The IDAGraph interface

Detailed Description

Constructor & Destructor Documentation

◆ ExtendedNewick()

◆ ~ExtendedNewick()

Member Function Documentation

◆ dagToParenthesis()

◆ edgeToParenthesis()

◆ getDataType()

◆ getElement()

◆ getFormatDescription()

◆ getFormatName()

◆ parenthesisToNode()

◆ parenthesisToPhyloDAG()

◆ readPhyloDAG() [1/3]

◆ readPhyloDAG() [2/3]

◆ readPhyloDAG() [3/3]

◆ readPhyloDAGs() [1/3]

◆ readPhyloDAGs() [2/3]

◆ readPhyloDAGs() [3/3]

◆ write_() [1/2]

◆ write_() [2/2]

◆ writePhyloDAG() [1/3]

◆ writePhyloDAG() [2/3]

◆ writePhyloDAG() [3/3]

◆ writePhyloDAGs() [1/3]

◆ writePhyloDAGs() [2/3]

◆ writePhyloDAGs() [3/3]

Member Data Documentation

◆ allowComments_

◆ verbose_

◆ writeId_