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)
	Build a new Newick reader/writer. More...

virtual	~Newick ()

void	enableExtendedBootstrapProperty (const std::string &propertyName)

void	disableExtendedBootstrapProperty ()

virtual const std::string	getDataType () const

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

const std::string	getFormatDescription () const

The ITree interface
TreeTemplate< Node > *	read (const std::string &path) const throw (Exception)
	Read a tree from a file. More...

TreeTemplate< Node > *	read (std::istream &in) const throw (Exception)
	Read a tree from a stream. More...

The OTree interface
void	write (const Tree &tree, const std::string &path, bool overwrite=true) const throw (Exception)
	Write a tree to a file. More...

void	write (const Tree &tree, std::ostream &out) const throw (Exception)
	Write a tree to a stream. More...

The IMultiTree interface
void	read (const std::string &path, std::vector< Tree *> &trees) const throw (Exception)
	Read trees from a file. More...

void	read (std::istream &in, std::vector< Tree *> &trees) const throw (Exception)
	Read trees from a stream. More...

The OMultiTree interface
void	write (const std::vector< Tree *> &trees, const std::string &path, bool overwrite=true) const throw (Exception)
	Write trees to a file. More...

void	write (const std::vector< Tree *> &trees, std::ostream &out) const throw (Exception)
	Write trees to a stream. More...

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

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

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

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

Protected Attributes
bool	allowComments_

bool	writeId_

bool	useBootstrap_

std::string	bootstrapPropertyName_

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.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 83 of file Newick.h.

Constructor & Destructor Documentation

◆ Newick()

bpp::Newick::Newick	(	bool	allowComments = `false`,
		bool	writeId = `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.

Definition at line 105 of file Newick.h.

◆ ~Newick()

virtual bpp::Newick::~Newick ( )

inlinevirtual

Definition at line 111 of file Newick.h.

Member Function Documentation

◆ disableExtendedBootstrapProperty()

void bpp::Newick::disableExtendedBootstrapProperty ( )

inline

Definition at line 120 of file Newick.h.

References bpp::TreeTools::BOOTSTRAP, bootstrapPropertyName_, and useBootstrap_.

◆ enableExtendedBootstrapProperty()

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

inline

Definition at line 115 of file Newick.h.

References bootstrapPropertyName_, and useBootstrap_.

◆ getDataType()

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

inlinevirtualinherited

Definition at line 68 of file IoTree.h.

◆ getFormatDescription()

const string Newick::getFormatDescription ( ) const

Definition at line 61 of file Newick.cpp.

◆ getFormatName()

const string Newick::getFormatName ( ) const

Definition at line 57 of file Newick.cpp.

◆ read() [1/4]

TreeTemplate<Node>* bpp::Newick::read	(	const std::string &	path	)	const
throw	(	Exception
	)

inlinevirtual

Read a tree from a file.

Parameters

path	The file path.

Returns: A new tree object.

Exceptions

Exception If an error occured.

Reimplemented from bpp::AbstractITree.

Definition at line 140 of file Newick.h.

References bpp::AbstractITree::read().

◆ read() [2/4]

TreeTemplate< Node > * Newick::read	(	std::istream &	in	)	const
throw	(	Exception
	)

virtual

Read a tree from a stream.

Parameters

in	The input stream.

Returns: A new tree object.

Exceptions

Exception If an error occured.

Implements bpp::AbstractITree.

Definition at line 74 of file Newick.cpp.

References bpp::TreeTemplateTools::parenthesisToTree().

◆ read() [3/4]

void bpp::Newick::read	(	const std::string &	path,
		std::vector< Tree *> &	trees
	)		const
throw	(	Exception
	)

inlinevirtual

Read trees from a file.

Parameters

path	The file path.
trees	The output trees container.

Exceptions

Exception If an error occured.

Reimplemented from bpp::AbstractIMultiTree.

Definition at line 169 of file Newick.h.

References bpp::AbstractIMultiTree::read().

◆ read() [4/4]

void Newick::read	(	std::istream &	in,
		std::vector< Tree *> &	trees
	)		const
throw	(	Exception
	)

virtual

Read trees from a stream.

Parameters

in	The input stream.
trees	The output trees container.

Exceptions

Exception If an error occured.

Implements bpp::AbstractIMultiTree.

Definition at line 134 of file Newick.cpp.

References bpp::TreeTemplateTools::parenthesisToTree().

◆ write() [1/4]

void bpp::Newick::write	(	const Tree &	tree,
		const std::string &	path,
		bool	overwrite = `true`
	)		const
throw	(	Exception
	)

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 occured.

Reimplemented from bpp::AbstractOTree.

Definition at line 153 of file Newick.h.

References bpp::AbstractOTree::write().

◆ write() [2/4]

void bpp::Newick::write	(	const Tree &	tree,
		std::ostream &	out
	)		const
throw	(	Exception
	)

inlinevirtual

Write a tree to a stream.

Parameters

tree	A tree object.
out	The output stream.

Exceptions

Exception If an error occured.

Implements bpp::AbstractOTree.

Definition at line 158 of file Newick.h.

References write_().

◆ write() [3/4]

void bpp::Newick::write	(	const std::vector< Tree *> &	trees,
		const std::string &	path,
		bool	overwrite = `true`
	)		const
throw	(	Exception
	)

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 occured.

Reimplemented from bpp::AbstractOMultiTree.

Definition at line 181 of file Newick.h.

References bpp::AbstractOMultiTree::write().

◆ write() [4/4]

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

inlinevirtual

Write trees to a stream.

Parameters

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

Exceptions

Exception If an error occured.

Implements bpp::AbstractOMultiTree.

Definition at line 185 of file Newick.h.

References write_().

◆ write_() [1/4]

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

protected

Definition at line 101 of file Newick.cpp.

References bpp::TreeTools::treeToParenthesis().

Referenced by write().

◆ write_() [2/4]

template<class N >

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

protected

Definition at line 118 of file Newick.cpp.

References bpp::TreeTemplateTools::treeToParenthesis().

◆ write_() [3/4]

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

protected

Definition at line 160 of file Newick.cpp.

References bpp::TreeTools::treeToParenthesis().

◆ write_() [4/4]

template<class N >

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

protected

Definition at line 180 of file Newick.cpp.

References bpp::TreeTemplateTools::treeToParenthesis().

Member Data Documentation

◆ allowComments_

bool bpp::Newick::allowComments_

protected

Definition at line 90 of file Newick.h.

◆ bootstrapPropertyName_

std::string bpp::Newick::bootstrapPropertyName_

protected

Definition at line 93 of file Newick.h.

Referenced by disableExtendedBootstrapProperty(), and enableExtendedBootstrapProperty().

◆ useBootstrap_

bool bpp::Newick::useBootstrap_

protected

Definition at line 92 of file Newick.h.

Referenced by disableExtendedBootstrapProperty(), and enableExtendedBootstrapProperty().

◆ writeId_

bool bpp::Newick::writeId_

protected

Definition at line 91 of file Newick.h.

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

Detailed Description

Constructor & Destructor Documentation

◆ Newick()

◆ ~Newick()

Member Function Documentation

◆ disableExtendedBootstrapProperty()

◆ enableExtendedBootstrapProperty()

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ read() [1/4]

◆ read() [2/4]

◆ read() [3/4]

◆ read() [4/4]

◆ write() [1/4]

◆ write() [2/4]

◆ write() [3/4]

◆ write() [4/4]

◆ write_() [1/4]

◆ write_() [2/4]

◆ write_() [3/4]

◆ write_() [4/4]

Member Data Documentation

◆ allowComments_

◆ bootstrapPropertyName_

◆ useBootstrap_

◆ writeId_