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 ()

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

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

virtual const std::string	getDataType () const

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

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

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

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

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

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

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

const std::string	getFormatDescription () const override

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...

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

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

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

virtual void	writePhyloTree (const PhyloTree &tree, std::ostream &out) const=0

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

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

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

virtual void	readPhyloTrees (std::istream &in, std::vector< std::unique_ptr< PhyloTree >> &trees) const override=0

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

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

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

virtual void	writePhyloTrees (const std::vector< const PhyloTree * > &trees, std::ostream &out) const=0

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

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

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 27 of file NexusIoTree.h.

Constructor & Destructor Documentation

◆ NexusIOTree()

bpp::NexusIOTree::NexusIOTree ( )

inline

Build a new Nexus tree parser.

Definition at line 41 of file NexusIoTree.h.

◆ ~NexusIOTree()

virtual bpp::NexusIOTree::~NexusIOTree ( )

inlinevirtual

Definition at line 43 of file NexusIoTree.h.

Member Function Documentation

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Definition at line 51 of file IoTree.h.

◆ getElement() [1/2]

virtual Element bpp::AbstractITree::getElement ( const std::string & elt ) const

inlinevirtualinherited

Reimplemented in bpp::Nhx, and bpp::Newick.

Definition at line 219 of file IoTree.h.

◆ getElement() [2/2]

Element bpp::AbstractIPhyloTree::getElement ( const std::string & elt ) const

inlineinherited

Definition at line 245 of file IoTree.h.

◆ getFormatDescription()

const string NexusIOTree::getFormatDescription ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 36 of file NexusIoTree.cpp.

◆ getFormatName()

const string NexusIOTree::getFormatName ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 32 of file NexusIoTree.cpp.

◆ readPhyloTree() [1/4]

std::unique_ptr<PhyloTree> bpp::AbstractIPhyloTree::readPhyloTree ( 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::IPhyloTree.

Definition at line 235 of file IoTree.h.

References bpp::AbstractIPhyloTree::readPhyloTree().

◆ readPhyloTree() [2/4]

std::unique_ptr<PhyloTree> bpp::AbstractIPhyloTree::readPhyloTree

inlineoverride

Definition at line 235 of file IoTree.h.

◆ readPhyloTree() [3/4]

unique_ptr< PhyloTree > NexusIOTree::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 140 of file NexusIoTree.cpp.

◆ readPhyloTree() [4/4]

std::unique_ptr<PhyloTree> bpp::AbstractIPhyloTree::readPhyloTree

override

◆ readPhyloTrees() [1/4]

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

inlineoverridevirtualinherited

Read trees from a file.

Parameters

path	The file path.
trees	The output trees container.

Exceptions

Exception If an error occurred.

Implements bpp::IMultiPhyloTree.

Definition at line 485 of file IoTree.h.

References bpp::AbstractIMultiPhyloTree::readPhyloTrees().

◆ readPhyloTrees() [2/4]

virtual void bpp::AbstractIMultiPhyloTree::readPhyloTrees

inlineoverride

Definition at line 485 of file IoTree.h.

◆ readPhyloTrees() [3/4]

void NexusIOTree::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 151 of file NexusIoTree.cpp.

References bpp::NexusTools::getNextCommand(), bpp::FileTools::getNextLine(), bpp::StringTokenizer::hasMoreToken(), bpp::NestedStringTokenizer::nextToken(), bpp::StringTokenizer::nextToken(), bpp::NestedStringTokenizer::numberOfRemainingTokens(), bpp::Newick::readPhyloTree(), bpp::TextTools::removeSurroundingWhiteSpaces(), and bpp::TextTools::toUpper().

◆ readPhyloTrees() [4/4]

virtual void bpp::AbstractIMultiPhyloTree::readPhyloTrees

override

◆ 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() [1/4]

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

inlineoverridevirtualinherited

Read trees from a file.

Parameters

path	The file path.
trees	The output trees container.

Exceptions

Exception If an error occurred.

Implements bpp::IMultiTree.

Definition at line 464 of file IoTree.h.

References bpp::AbstractIMultiTree::readTrees().

◆ readTrees() [2/4]

virtual void bpp::AbstractIMultiTree::readTrees

inlineoverride

Definition at line 464 of file IoTree.h.

◆ readTrees() [3/4]

void NexusIOTree::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 57 of file NexusIoTree.cpp.

References bpp::NexusTools::getNextCommand(), bpp::FileTools::getNextLine(), bpp::StringTokenizer::hasMoreToken(), bpp::NestedStringTokenizer::nextToken(), bpp::StringTokenizer::nextToken(), bpp::NestedStringTokenizer::numberOfRemainingTokens(), bpp::TreeTemplateTools::parenthesisToTree(), bpp::TextTools::removeSurroundingWhiteSpaces(), and bpp::TextTools::toUpper().

◆ readTrees() [4/4]

virtual void bpp::AbstractIMultiTree::readTrees

override

◆ readTreeTemplate() [1/4]

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

inlinevirtualinherited

Definition at line 211 of file IoTree.h.

References bpp::AbstractITree::readTreeTemplate().

◆ readTreeTemplate() [2/4]

virtual std::unique_ptr<TreeTemplate<Node> > bpp::AbstractITree::readTreeTemplate

inline

Definition at line 211 of file IoTree.h.

◆ readTreeTemplate() [3/4]

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

overridevirtual

Implements bpp::AbstractITree.

Definition at line 45 of file NexusIoTree.cpp.

◆ readTreeTemplate() [4/4]

virtual std::unique_ptr<TreeTemplate<Node> > bpp::AbstractITree::readTreeTemplate

◆ write_() [1/6]

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

protected

Definition at line 249 of file NexusIoTree.cpp.

◆ write_() [2/6]

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

protected

Definition at line 335 of file NexusIoTree.cpp.

References bpp::PhyloTree::clone(), count(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNode(), bpp::TextTools::toString(), bpp::VectorTools::vectorUnion(), and bpp::Newick::writePhyloTree().

◆ write_() [3/6]

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

protected

Definition at line 268 of file NexusIoTree.cpp.

References count(), bpp::Tree::getNodeName(), bpp::Tree::setNodeName(), bpp::TextTools::toString(), bpp::TreeTools::treeToParenthesis(), and bpp::VectorTools::vectorUnion().

◆ write_() [4/6]

template<class N >

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

protected

Definition at line 409 of file NexusIoTree.cpp.

References count(), bpp::Tree::getNodeName(), bpp::Tree::setNodeName(), bpp::TextTools::toString(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::VectorTools::vectorUnion().

◆ write_() [5/6]

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

protected

Definition at line 240 of file NexusIoTree.cpp.

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

◆ write_() [6/6]

template<class N >

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

protected

Definition at line 259 of file NexusIoTree.cpp.

◆ writePhyloTree() [1/4]

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

inlinevirtualinherited

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.

Implements bpp::OPhyloTree.

Definition at line 297 of file IoTree.h.

References bpp::IOException::what(), and bpp::AbstractOPhyloTree::writePhyloTree().

◆ writePhyloTree() [2/4]

virtual void bpp::AbstractOPhyloTree::writePhyloTree

inline

Definition at line 297 of file IoTree.h.

◆ writePhyloTree() [3/4]

void bpp::NexusIOTree::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 84 of file NexusIoTree.h.

References write_().

◆ writePhyloTree() [4/4]

virtual void bpp::AbstractOPhyloTree::writePhyloTree

◆ writePhyloTrees() [1/4]

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

inlinevirtualinherited

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.

Implements bpp::OMultiPhyloTree.

Definition at line 528 of file IoTree.h.

References bpp::AbstractOMultiPhyloTree::writePhyloTrees().

◆ writePhyloTrees() [2/4]

virtual void bpp::AbstractOMultiPhyloTree::writePhyloTrees

inline

Definition at line 528 of file IoTree.h.

◆ writePhyloTrees() [3/4]

void bpp::NexusIOTree::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 118 of file NexusIoTree.h.

References write_().

◆ writePhyloTrees() [4/4]

virtual void bpp::AbstractOMultiPhyloTree::writePhyloTrees

◆ writeTree() [1/4]

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

inlinevirtualinherited

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.

Implements bpp::OTree.

Definition at line 263 of file IoTree.h.

References bpp::IOException::what(), and bpp::AbstractOTree::writeTree().

◆ writeTree() [2/4]

virtual void bpp::AbstractOTree::writeTree

inline

Definition at line 263 of file IoTree.h.

◆ writeTree() [3/4]

void bpp::NexusIOTree::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 77 of file NexusIoTree.h.

References write_().

◆ writeTree() [4/4]

virtual void bpp::AbstractOTree::writeTree

◆ writeTrees() [1/4]

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

inlinevirtualinherited

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.

Implements bpp::OMultiTree.

Definition at line 505 of file IoTree.h.

References bpp::AbstractOMultiTree::writeTrees().

◆ writeTrees() [2/4]

virtual void bpp::AbstractOMultiTree::writeTrees

inline

Definition at line 505 of file IoTree.h.

◆ writeTrees() [3/4]

void bpp::NexusIOTree::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 111 of file NexusIoTree.h.

References write_().

◆ writeTrees() [4/4]

virtual void bpp::AbstractOMultiTree::writeTrees

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()

◆ getElement() [1/2]

◆ getElement() [2/2]

◆ getFormatDescription()

◆ getFormatName()

◆ readPhyloTree() [1/4]

◆ readPhyloTree() [2/4]

◆ readPhyloTree() [3/4]

◆ readPhyloTree() [4/4]

◆ readPhyloTrees() [1/4]

◆ readPhyloTrees() [2/4]

◆ readPhyloTrees() [3/4]

◆ readPhyloTrees() [4/4]

◆ readTree() [1/2]

◆ readTree() [2/2]

◆ readTrees() [1/4]

◆ readTrees() [2/4]

◆ readTrees() [3/4]

◆ readTrees() [4/4]

◆ readTreeTemplate() [1/4]

◆ readTreeTemplate() [2/4]

◆ readTreeTemplate() [3/4]

◆ readTreeTemplate() [4/4]

◆ write_() [1/6]

◆ write_() [2/6]

◆ write_() [3/6]

◆ write_() [4/6]

◆ write_() [5/6]

◆ write_() [6/6]

◆ writePhyloTree() [1/4]

◆ writePhyloTree() [2/4]

◆ writePhyloTree() [3/4]

◆ writePhyloTree() [4/4]

◆ writePhyloTrees() [1/4]

◆ writePhyloTrees() [2/4]

◆ writePhyloTrees() [3/4]

◆ writePhyloTrees() [4/4]

◆ writeTree() [1/4]

◆ writeTree() [2/4]

◆ writeTree() [3/4]

◆ writeTree() [4/4]

◆ writeTrees() [1/4]

◆ writeTrees() [2/4]

◆ writeTrees() [3/4]

◆ writeTrees() [4/4]