a simple parser for reading trees from a Nexus file. More...

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

Inheritance diagram for bpp::NexusIOTree:

Collaboration diagram for bpp::NexusIOTree:

Public Member Functions
	NexusIOTree ()
	Build a new Nexus tree parser. More...

virtual	~NexusIOTree ()

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)

Detailed Description

a simple parser for reading trees from a Nexus file.

This reader is not supposed to be a full parser of the Nexus files, but only extract the tree data. Only a basic subset of the options are and will be supported.

This format is described in the following paper: Maddison D, Swofford D, and Maddison W (1997), Syst Biol 46(4):590-621

Author: Julien Dutheil

Definition at line 61 of file NexusIoTree.h.

Constructor & Destructor Documentation

◆ NexusIOTree()

bpp::NexusIOTree::NexusIOTree ( )

inline

Build a new Nexus tree parser.

Definition at line 72 of file NexusIoTree.h.

◆ ~NexusIOTree()

virtual bpp::NexusIOTree::~NexusIOTree ( )

inlinevirtual

Definition at line 74 of file NexusIoTree.h.

Member Function Documentation

◆ getDataType()

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

inlinevirtualinherited

Definition at line 68 of file IoTree.h.

◆ getFormatDescription()

const string NexusIOTree::getFormatDescription ( ) const

Definition at line 68 of file NexusIoTree.cpp.

◆ getFormatName()

const string NexusIOTree::getFormatName ( ) const

Definition at line 64 of file NexusIoTree.cpp.

◆ read() [1/4]

TreeTemplate<Node>* bpp::NexusIOTree::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 98 of file NexusIoTree.h.

References bpp::AbstractITree::read().

◆ read() [2/4]

TreeTemplate< Node > * NexusIOTree::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 80 of file NexusIoTree.cpp.

◆ read() [3/4]

void bpp::NexusIOTree::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 132 of file NexusIoTree.h.

References bpp::AbstractIMultiTree::read().

◆ read() [4/4]

void NexusIOTree::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 93 of file NexusIoTree.cpp.

References bpp::TreeTemplate< N >::getLeaves(), and bpp::TreeTemplateTools::parenthesisToTree().

◆ write() [1/4]

void bpp::NexusIOTree::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 117 of file NexusIoTree.h.

References bpp::AbstractOTree::write().

◆ write() [2/4]

void bpp::NexusIOTree::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 121 of file NexusIoTree.h.

References write_().

◆ write() [3/4]

void bpp::NexusIOTree::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 144 of file NexusIoTree.h.

References bpp::AbstractOMultiTree::write().

◆ write() [4/4]

void bpp::NexusIOTree::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 148 of file NexusIoTree.h.

References write_().

◆ write_() [1/4]

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

protected

Definition at line 172 of file NexusIoTree.cpp.

Referenced by write().

◆ write_() [2/4]

template<class N >

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

protected

Definition at line 182 of file NexusIoTree.cpp.

◆ write_() [3/4]

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

protected

Definition at line 191 of file NexusIoTree.cpp.

References bpp::Tree::getNodeName(), bpp::Tree::setNodeName(), and bpp::TreeTools::treeToParenthesis().

◆ write_() [4/4]

template<class N >

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

protected

Definition at line 256 of file NexusIoTree.cpp.

References bpp::Tree::getNodeName(), bpp::Tree::setNodeName(), and bpp::TreeTemplateTools::treeToParenthesis().

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

Bpp/Phyl/Io/NexusIoTree.h
Bpp/Phyl/Io/NexusIoTree.cpp

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ NexusIOTree()

◆ ~NexusIOTree()

Member Function Documentation

◆ 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]