The so-called 'newick' parenthetic format. More...

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

Inheritance diagram for bpp::Newick:

Collaboration diagram for bpp::Newick:

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

virtual	~Newick ()

void	enableExtendedBootstrapProperty (const std::string &propertyName)

void	disableExtendedBootstrapProperty ()

std::unique_ptr< Tree >	readTree (std::istream &in) const override
	Read a tree from a stream. More...

std::unique_ptr< Tree >	readTree (const std::string &path) const override
	Read a tree from a file. More...

virtual const std::string	getDataType () const

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

const std::string	getFormatDescription () const override

The OTree interface
void	writeTree (const Tree &tree, std::ostream &out) const override
	Write a tree to a stream. More...

void	writePhyloTree (const PhyloTree &tree, std::ostream &out) const override
	Write a tree to a stream. More...

virtual void	writeTree (const Tree &tree, std::ostream &out) const=0
	Write a tree to a stream. More...

virtual void	writeTree (const Tree &tree, const std::string &path, bool overwrite) const
	Write a tree to a file. More...

virtual void	writePhyloTree (const PhyloTree &tree, std::ostream &out) const=0
	Write a tree to a stream. More...

virtual void	writePhyloTree (const PhyloTree &tree, const std::string &path, bool overwrite) const
	Write a tree to a file. More...

The IMultiTree interface
void	readTrees (std::istream &in, std::vector< std::unique_ptr< Tree > > &trees) const override
	Read trees from a stream. More...

void	readPhyloTrees (std::istream &in, std::vector< std::unique_ptr< PhyloTree > > &trees) const override
	Read trees from a stream. More...

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

virtual void	readTrees (const std::string &path, std::vector< std::unique_ptr< Tree > > &trees) const override
	Read trees from a file. More...

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

virtual void	readPhyloTrees (const std::string &path, std::vector< std::unique_ptr< PhyloTree > > &trees) const override
	Read trees from a file. More...

The OMultiTree interface
void	writeTrees (const std::vector< const Tree * > &trees, std::ostream &out) const override
	Write trees to a stream. More...

void	writePhyloTrees (const std::vector< const PhyloTree * > &trees, std::ostream &out) const override
	Write trees to a stream. More...

virtual void	writeTrees (const std::vector< const Tree * > &trees, std::ostream &out) const=0
	Write trees to a stream. More...

virtual void	writeTrees (const std::vector< const Tree * > &trees, const std::string &path, bool overwrite) const
	Write trees to a file. More...

virtual void	writePhyloTrees (const std::vector< const PhyloTree * > &trees, std::ostream &out) const=0
	Write trees to a stream. More...

virtual void	writePhyloTrees (const std::vector< const PhyloTree * > &trees, const std::string &path, bool overwrite) const
	Write trees to a file. More...

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

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

template<class N >
void	write_ (const TreeTemplate< N > &tree, std::ostream &out) const

void	write_ (const std::vector< const Tree * > &trees, std::ostream &out) const

void	write_ (const std::vector< const PhyloTree * > &trees, std::ostream &out) const

template<class N >
void	write_ (const std::vector< TreeTemplate< N > * > &trees, std::ostream &out) const

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

std::string	nodeToParenthesis (const PhyloTree &tree, std::shared_ptr< PhyloNode > node, bool writeId=false) const
	Get the Newick description of a subtree. More...

std::string	nodeToParenthesis (const PhyloTree &tree, std::shared_ptr< PhyloNode > node, bool bootstrap, const std::string &propertyName) const

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

std::string	treeToParenthesis (const PhyloTree &tree, bool bootstrap, const std::string &propertyName) const
	Get the parenthesis description of a tree. More...

Protected Attributes
bool	allowComments_

bool	writeId_

bool	useBootstrap_

std::string	bootstrapPropertyName_

bool	verbose_

The ITree interface
std::unique_ptr< TreeTemplate< Node > >	readTreeTemplate (std::istream &in) const override

std::unique_ptr< PhyloTree >	readPhyloTree (std::istream &in) const override
	Read a tree from a stream. More...

std::unique_ptr< PhyloTree >	parenthesisToPhyloTree (const std::string &description, bool bootstrap=false, const std::string &propertyName="", bool withId=false, bool verbose=false) const

virtual std::unique_ptr< TreeTemplate< Node > >	readTreeTemplate (std::istream &in) const=0

virtual std::unique_ptr< TreeTemplate< Node > >	readTreeTemplate (const std::string &path) const

std::unique_ptr< PhyloTree >	readPhyloTree (std::istream &in) const override=0
	Read a tree from a stream. More...

std::unique_ptr< PhyloTree >	readPhyloTree (const std::string &path) const override
	Read a tree from a file. More...

std::shared_ptr< PhyloNode >	parenthesisToNode (PhyloTree &tree, std::shared_ptr< PhyloNode > father, const std::string &description, unsigned int &nodeCounter, bool bootstrap, const std::string &propertyName, bool withId, bool verbose) const

Detailed Description

The so-called 'newick' parenthetic format.

Branch lengths and bootstraps are supported:

ex: ((A:0.1, B:0.15)90:0.2, C:0.27);

Code example:

#include <Phyl/Newick.h>
#include <Phyl/Tree/Tree.h>
 
Newick * newickReader = new Newick(false); //No comment allowed!
try {
 Tree * tree = newickReader->read("MyTestTree.dnd"); // Tree in file MyTestTree.dnd
 cout << "Tree has " << tree->getNumberOfLeaves() << " leaves." << endl;
} catch (Exception e) {
 cout << "Error when reading tree." << endl;
}
delete tree;
delete newickReader;

Bootstrap values are stored as node properties, as Number<double> objects and with the tag TreeTools::BOOTSTRAP.

This is also possible to read a "tagged" tree, where additional info is provided in place of bootstrap values: ((A,B)N2,(C,D)N3)N1; This is achieved by calling the enableExtendedBootstrapProperty method, and providing a property name to use. The additional information will be stored at each node as a property, in a String object. The disableExtendedBootstrapProperty method restores the default behavior.

Definition at line 49 of file Newick.h.

Constructor & Destructor Documentation

◆ Newick()

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

inline

Build a new Newick reader/writer.

Some newick 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 76 of file Newick.h.

◆ ~Newick()

virtual bpp::Newick::~Newick ( )

inlinevirtual

Definition at line 83 of file Newick.h.

Member Function Documentation

◆ disableExtendedBootstrapProperty()

void bpp::Newick::disableExtendedBootstrapProperty ( )

inline

Definition at line 92 of file Newick.h.

References bootstrapPropertyName_, and useBootstrap_.

◆ enableExtendedBootstrapProperty()

void bpp::Newick::enableExtendedBootstrapProperty ( const std::string & propertyName )

inline

Definition at line 86 of file Newick.h.

References bootstrapPropertyName_, and useBootstrap_.

Referenced by bpp::PhylogeneticsApplicationTools::writePhyloTrees().

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Definition at line 51 of file IoTree.h.

◆ getElement()

IOTree::Element Newick::getElement ( const std::string & elt ) const

overrideprotectedvirtual

Reimplemented from bpp::AbstractITree.

Definition at line 170 of file Newick.cpp.

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

Referenced by parenthesisToNode().

◆ getFormatDescription()

const string Newick::getFormatDescription ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 34 of file Newick.cpp.

◆ getFormatName()

const string Newick::getFormatName ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 30 of file Newick.cpp.

◆ nodeToParenthesis() [1/2]

string Newick::nodeToParenthesis	(	const PhyloTree &	tree,
		std::shared_ptr< PhyloNode >	node,
		bool	bootstrap,
		const std::string &	propertyName
	)		const

protected

Definition at line 528 of file Newick.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeToFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNumberOfSons(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSons(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasFather(), and nodeToParenthesis().

◆ nodeToParenthesis() [2/2]

string Newick::nodeToParenthesis	(	const PhyloTree &	tree,
		std::shared_ptr< PhyloNode >	node,
		bool	writeId = `false`
	)		const

protected

Get the Newick description of a subtree.

Parameters

tree	The tree to convert.
node	The top of the subtree to convert.
writeId	Tells if node ids must be printed. This will overwrite bootstrap values if there are ones. Leaves id will be added to the leave names, separated by a '_' character.

Returns: A string in the parenthesis format.

Definition at line 483 of file Newick.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeToFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNodeIndex(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNumberOfSons(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSons(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::isLeaf(), and nodeToParenthesis().

Referenced by nodeToParenthesis(), and treeToParenthesis().

◆ parenthesisToNode()

shared_ptr< PhyloNode > Newick::parenthesisToNode	(	PhyloTree &	tree,
		std::shared_ptr< PhyloNode >	father,
		const std::string &	description,
		unsigned int &	nodeCounter,
		bool	bootstrap,
		const std::string &	propertyName,
		bool	withId,
		bool	verbose
	)		const

private

Definition at line 233 of file Newick.cpp.

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

Referenced by parenthesisToNode(), and parenthesisToPhyloTree().

◆ parenthesisToPhyloTree()

unique_ptr< PhyloTree > Newick::parenthesisToPhyloTree	(	const std::string &	description,
		bool	bootstrap = `false`,
		const std::string &	propertyName = `""`,
		bool	withId = `false`,
		bool	verbose = `false`
	)		const

Definition at line 336 of file Newick.cpp.

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

Referenced by bpp::DistanceEstimation::computeMatrix(), readPhyloTree(), and readPhyloTrees().

◆ readPhyloTree() [1/3]

std::unique_ptr< PhyloTree > bpp::AbstractIPhyloTree::readPhyloTree ( const std::string & path ) const

inlineoverridevirtual

Read a tree from a file.

Parameters

path	The file path.

Returns: A new tree object.

Exceptions

Exception If an error occurred.

Reimplemented from bpp::AbstractIPhyloTree.

Definition at line 235 of file IoTree.h.

◆ readPhyloTree() [2/3]

unique_ptr< PhyloTree > Newick::readPhyloTree ( std::istream & in ) const

overridevirtual

Read a tree from a stream.

Parameters

in	The input stream.

Returns: A new tree object.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractIPhyloTree.

Definition at line 76 of file Newick.cpp.

References allowComments_, bootstrapPropertyName_, bpp::TextTools::isEmpty(), parenthesisToPhyloTree(), bpp::TextTools::removeSubstrings(), useBootstrap_, and verbose_.

Referenced by bpp::NexusIOTree::readPhyloTrees().

◆ readPhyloTree() [3/3]

std::unique_ptr< PhyloTree > bpp::AbstractIPhyloTree::readPhyloTree ( std::istream & in ) const

overridevirtual

Read a tree from a stream.

Parameters

in	The input stream.

Returns: A new tree object.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractIPhyloTree.

◆ readPhyloTrees() [1/3]

virtual void bpp::AbstractIMultiPhyloTree::readPhyloTrees	(	const std::string &	path,
		std::vector< std::unique_ptr< PhyloTree > > &	trees
	)		const

inlineoverridevirtual

Read trees from a file.

Parameters

path	The file path.
trees	The output trees container.

Exceptions

Exception If an error occurred.

Reimplemented from bpp::AbstractIMultiPhyloTree.

Definition at line 485 of file IoTree.h.

◆ readPhyloTrees() [2/3]

void Newick::readPhyloTrees	(	std::istream &	in,
		std::vector< std::unique_ptr< PhyloTree > > &	trees
	)		const

overridevirtual

Read trees from a stream.

Parameters

in	The input stream.
trees	The output trees container.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractIMultiPhyloTree.

Definition at line 139 of file Newick.cpp.

References allowComments_, bootstrapPropertyName_, parenthesisToPhyloTree(), bpp::TextTools::removeSubstrings(), useBootstrap_, and verbose_.

◆ readPhyloTrees() [3/3]

virtual void bpp::AbstractIMultiPhyloTree::readPhyloTrees	(	std::istream &	in,
		std::vector< std::unique_ptr< PhyloTree > > &	trees
	)		const

overridevirtual

Read trees from a stream.

Parameters

in	The input stream.
trees	The output trees container.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractIMultiPhyloTree.

◆ readTree() [1/2]

std::unique_ptr< Tree > bpp::AbstractITree::readTree ( const std::string & path ) const

inlineoverridevirtualinherited

Read a tree from a file.

Parameters

path	The file path.

Returns: A new tree object.

Exceptions

Exception If an error occurred.

Implements bpp::ITree.

Definition at line 201 of file IoTree.h.

References bpp::AbstractITree::readTree().

◆ readTree() [2/2]

std::unique_ptr< Tree > bpp::AbstractITree::readTree ( std::istream & in ) const

inlineoverridevirtualinherited

Read a tree from a stream.

Parameters

in	The input stream.

Returns: A new tree object.

Exceptions

Exception If an error occurred.

Implements bpp::ITree.

Definition at line 195 of file IoTree.h.

References bpp::AbstractITree::readTreeTemplate().

Referenced by bpp::AbstractITree::readTree().

◆ readTrees() [1/3]

virtual void bpp::AbstractIMultiTree::readTrees	(	const std::string &	path,
		std::vector< std::unique_ptr< Tree > > &	trees
	)		const

inlineoverridevirtual

Read trees from a file.

Parameters

path	The file path.
trees	The output trees container.

Exceptions

Exception If an error occurred.

Reimplemented from bpp::AbstractIMultiTree.

Definition at line 464 of file IoTree.h.

◆ readTrees() [2/3]

void Newick::readTrees	(	std::istream &	in,
		std::vector< std::unique_ptr< Tree > > &	trees
	)		const

overridevirtual

Read trees from a stream.

Parameters

in	The input stream.
trees	The output trees container.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractIMultiTree.

Definition at line 108 of file Newick.cpp.

References allowComments_, bootstrapPropertyName_, bpp::TreeTemplateTools::parenthesisToTree(), bpp::TextTools::removeSubstrings(), useBootstrap_, and verbose_.

◆ readTrees() [3/3]

virtual void bpp::AbstractIMultiTree::readTrees	(	std::istream &	in,
		std::vector< std::unique_ptr< Tree > > &	trees
	)		const

overridevirtual

Read trees from a stream.

Parameters

in	The input stream.
trees	The output trees container.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractIMultiTree.

◆ readTreeTemplate() [1/3]

virtual std::unique_ptr< TreeTemplate< Node > > bpp::AbstractITree::readTreeTemplate ( const std::string & path ) const

inlinevirtual

Reimplemented from bpp::AbstractITree.

Definition at line 211 of file IoTree.h.

◆ readTreeTemplate() [2/3]

unique_ptr< TreeTemplate< Node > > Newick::readTreeTemplate ( std::istream & in ) const

overridevirtual

Implements bpp::AbstractITree.

Definition at line 44 of file Newick.cpp.

References allowComments_, bootstrapPropertyName_, bpp::TextTools::isEmpty(), bpp::TreeTemplateTools::parenthesisToTree(), bpp::TextTools::removeSubstrings(), useBootstrap_, and verbose_.

◆ readTreeTemplate() [3/3]

virtual std::unique_ptr< TreeTemplate< Node > > bpp::AbstractITree::readTreeTemplate ( std::istream & in ) const

virtual

Implements bpp::AbstractITree.

◆ treeToParenthesis() [1/2]

string Newick::treeToParenthesis	(	const PhyloTree &	tree,
		bool	bootstrap,
		const std::string &	propertyName
	)		const

protected

Get the parenthesis description of a tree.

Parameters

tree	The tree to convert.
bootstrap	Tell is bootstrap values must be written. If so, the content of the property with name "bootstrap" will be written as bootstrap value. The property should be a Number<double> object. Otherwise, the content of the property with name 'propertyName' will be written. In this later case, the property should be a String object.
propertyName	The name of the property to use. Only used if bootstrap = false.

Returns: A string in the parenthesis format.

Definition at line 619 of file Newick.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeToFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getRoot(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSons(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::isRooted(), and nodeToParenthesis().

◆ treeToParenthesis() [2/2]

string Newick::treeToParenthesis	(	const PhyloTree &	tree,
		bool	writeId = `false`
	)		const

protected

Get the parenthesis description of a tree.

Parameters

tree	The tree to convert.
writeId	Tells if node ids must be printed. This will overwrite bootstrap values if there are ones. Leaves id will be added to the leave names, separated by a '_' character.

Returns: A string in the parenthesis format.

Definition at line 576 of file Newick.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeToFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getRoot(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSons(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::isRooted(), and nodeToParenthesis().

Referenced by write_().

◆ write_() [1/6]

void Newick::write_	(	const PhyloTree &	tree,
		std::ostream &	out
	)		const

protected

Definition at line 376 of file Newick.cpp.

References bootstrapPropertyName_, treeToParenthesis(), useBootstrap_, and writeId_.

◆ write_() [2/6]

void Newick::write_	(	const std::vector< const PhyloTree * > &	trees,
		std::ostream &	out
	)		const

protected

Definition at line 461 of file Newick.cpp.

References bootstrapPropertyName_, treeToParenthesis(), useBootstrap_, and writeId_.

◆ write_() [3/6]

void Newick::write_	(	const std::vector< const Tree * > &	trees,
		std::ostream &	out
	)		const

protected

Definition at line 416 of file Newick.cpp.

References bootstrapPropertyName_, bpp::TreeTools::treeToParenthesis(), useBootstrap_, and writeId_.

◆ write_() [4/6]

template<class N >

void Newick::write_	(	const std::vector< TreeTemplate< N > * > &	trees,
		std::ostream &	out
	)		const

protected

Definition at line 439 of file Newick.cpp.

References bootstrapPropertyName_, bpp::TreeTemplateTools::treeToParenthesis(), useBootstrap_, and writeId_.

◆ write_() [5/6]

void Newick::write_	(	const Tree &	tree,
		std::ostream &	out
	)		const

protected

Definition at line 359 of file Newick.cpp.

References bootstrapPropertyName_, bpp::TreeTools::treeToParenthesis(), useBootstrap_, and writeId_.

Referenced by writePhyloTree(), writePhyloTrees(), writeTree(), and writeTrees().

◆ write_() [6/6]

template<class N >

void Newick::write_	(	const TreeTemplate< N > &	tree,
		std::ostream &	out
	)		const

protected

Definition at line 396 of file Newick.cpp.

References bootstrapPropertyName_, bpp::TreeTemplateTools::treeToParenthesis(), useBootstrap_, and writeId_.

◆ writePhyloTree() [1/3]

virtual void bpp::AbstractOPhyloTree::writePhyloTree	(	const PhyloTree &	tree,
		const std::string &	path,
		bool	overwrite
	)		const

inlinevirtual

Write a tree to a file.

Parameters

tree	A tree 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::AbstractOPhyloTree.

Definition at line 297 of file IoTree.h.

◆ writePhyloTree() [2/3]

void bpp::Newick::writePhyloTree	(	const PhyloTree &	tree,
		std::ostream &	out
	)		const

inlineoverridevirtual

Write a tree to a stream.

Parameters

tree	A tree object.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOPhyloTree.

Definition at line 157 of file Newick.h.

References write_().

Referenced by bpp::NexusIOTree::write_().

◆ writePhyloTree() [3/3]

virtual void bpp::AbstractOPhyloTree::writePhyloTree	(	const PhyloTree &	tree,
		std::ostream &	out
	)		const

virtual

Write a tree to a stream.

Parameters

tree	A tree object.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOPhyloTree.

◆ writePhyloTrees() [1/3]

virtual void bpp::AbstractOMultiPhyloTree::writePhyloTrees	(	const std::vector< const PhyloTree * > &	trees,
		const std::string &	path,
		bool	overwrite
	)		const

inlinevirtual

Write trees to a file.

Parameters

trees	A vector of tree objects.
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::AbstractOMultiPhyloTree.

Definition at line 528 of file IoTree.h.

◆ writePhyloTrees() [2/3]

void bpp::Newick::writePhyloTrees	(	const std::vector< const PhyloTree * > &	trees,
		std::ostream &	out
	)		const

inlineoverridevirtual

Write trees to a stream.

Parameters

trees	A vector of tree objects.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOMultiPhyloTree.

Definition at line 198 of file Newick.h.

References write_().

◆ writePhyloTrees() [3/3]

virtual void bpp::AbstractOMultiPhyloTree::writePhyloTrees	(	const std::vector< const PhyloTree * > &	trees,
		std::ostream &	out
	)		const

virtual

Write trees to a stream.

Parameters

trees	A vector of tree objects.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOMultiPhyloTree.

◆ writeTree() [1/3]

virtual void bpp::AbstractOTree::writeTree	(	const Tree &	tree,
		const std::string &	path,
		bool	overwrite
	)		const

inlinevirtual

Write a tree to a file.

Parameters

tree	A tree 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::AbstractOTree.

Definition at line 263 of file IoTree.h.

◆ writeTree() [2/3]

void bpp::Newick::writeTree	(	const Tree &	tree,
		std::ostream &	out
	)		const

inlineoverridevirtual

Write a tree to a stream.

Parameters

tree	A tree object.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOTree.

Definition at line 150 of file Newick.h.

References write_().

◆ writeTree() [3/3]

virtual void bpp::AbstractOTree::writeTree	(	const Tree &	tree,
		std::ostream &	out
	)		const

virtual

Write a tree to a stream.

Parameters

tree	A tree object.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOTree.

◆ writeTrees() [1/3]

virtual void bpp::AbstractOMultiTree::writeTrees	(	const std::vector< const Tree * > &	trees,
		const std::string &	path,
		bool	overwrite
	)		const

inlinevirtual

Write trees to a file.

Parameters

trees	A vector of tree objects.
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::AbstractOMultiTree.

Definition at line 505 of file IoTree.h.

◆ writeTrees() [2/3]

void bpp::Newick::writeTrees	(	const std::vector< const Tree * > &	trees,
		std::ostream &	out
	)		const

inlineoverridevirtual

Write trees to a stream.

Parameters

trees	A vector of tree objects.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOMultiTree.

Definition at line 191 of file Newick.h.

References write_().

◆ writeTrees() [3/3]

virtual void bpp::AbstractOMultiTree::writeTrees	(	const std::vector< const Tree * > &	trees,
		std::ostream &	out
	)		const

virtual

Write trees to a stream.

Parameters

trees	A vector of tree objects.
out	The output stream.

Exceptions

Exception If an error occurred.

Implements bpp::AbstractOMultiTree.

Member Data Documentation

◆ allowComments_

bool bpp::Newick::allowComments_

protected

Definition at line 60 of file Newick.h.

Referenced by readPhyloTree(), readPhyloTrees(), readTrees(), and readTreeTemplate().

◆ bootstrapPropertyName_

std::string bpp::Newick::bootstrapPropertyName_

protected

Definition at line 63 of file Newick.h.

Referenced by disableExtendedBootstrapProperty(), enableExtendedBootstrapProperty(), readPhyloTree(), readPhyloTrees(), readTrees(), readTreeTemplate(), and write_().

◆ useBootstrap_

bool bpp::Newick::useBootstrap_

protected

Definition at line 62 of file Newick.h.

Referenced by disableExtendedBootstrapProperty(), enableExtendedBootstrapProperty(), readPhyloTree(), readPhyloTrees(), readTrees(), readTreeTemplate(), and write_().

◆ verbose_

bool bpp::Newick::verbose_

protected

Definition at line 64 of file Newick.h.

Referenced by readPhyloTree(), readPhyloTrees(), readTrees(), and readTreeTemplate().

◆ writeId_

bool bpp::Newick::writeId_

protected

Definition at line 61 of file Newick.h.

Referenced by write_().

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

Bpp/Phyl/Io/Newick.h
Bpp/Phyl/Io/Newick.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

The ITree interface

Detailed Description

Constructor & Destructor Documentation

◆ Newick()

◆ ~Newick()

Member Function Documentation

◆ disableExtendedBootstrapProperty()

◆ enableExtendedBootstrapProperty()

◆ getDataType()

◆ getElement()

◆ getFormatDescription()

◆ getFormatName()

◆ nodeToParenthesis() [1/2]

◆ nodeToParenthesis() [2/2]

◆ parenthesisToNode()

◆ parenthesisToPhyloTree()

◆ readPhyloTree() [1/3]

◆ readPhyloTree() [2/3]

◆ readPhyloTree() [3/3]

◆ readPhyloTrees() [1/3]

◆ readPhyloTrees() [2/3]

◆ readPhyloTrees() [3/3]

◆ readTree() [1/2]

◆ readTree() [2/2]

◆ readTrees() [1/3]

◆ readTrees() [2/3]

◆ readTrees() [3/3]

◆ readTreeTemplate() [1/3]

◆ readTreeTemplate() [2/3]

◆ readTreeTemplate() [3/3]

◆ treeToParenthesis() [1/2]

◆ treeToParenthesis() [2/2]

◆ write_() [1/6]

◆ write_() [2/6]

◆ write_() [3/6]

◆ write_() [4/6]

◆ write_() [5/6]

◆ write_() [6/6]

◆ writePhyloTree() [1/3]

◆ writePhyloTree() [2/3]

◆ writePhyloTree() [3/3]

◆ writePhyloTrees() [1/3]

◆ writePhyloTrees() [2/3]

◆ writePhyloTrees() [3/3]

◆ writeTree() [1/3]

◆ writeTree() [2/3]

◆ writeTree() [3/3]

◆ writeTrees() [1/3]

◆ writeTrees() [2/3]

◆ writeTrees() [3/3]

Member Data Documentation

◆ allowComments_

◆ bootstrapPropertyName_

◆ useBootstrap_

◆ verbose_

◆ writeId_