The so-called 'Nhx - New Hampshire eXtended' parenthetic format. More...

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

Inheritance diagram for bpp::Nhx:

Collaboration diagram for bpp::Nhx:

Classes
struct	Element

struct	Property

Public Member Functions
	Nhx (bool useTagsAsPptNames=true)
	Build a new Nhx reader/writer. More...

virtual	~Nhx ()

TreeTemplate< Node > *	parenthesisToTree (const std::string &description) const throw (Exception)

std::string	treeToParenthesis (const TreeTemplate< Node > &tree) const

void	registerProperty (const Property &property)

void	changeTagsToNames (Node &node) const
	Convert property names from tag to names. More...

void	changeNamesToTags (Node &node) const
	Convert property names from names to tags. More...

void	useTagsAsPropertyNames (bool yn)

bool	useTagsAsPropertyNames () const

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)

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

Node *	parenthesisToNode (const std::string &description) const

std::string	propertiesToParenthesis (const Node &node) const

std::string	nodeToParenthesis (const Node &node) const

bool	setNodeProperties (Node &node, const std::string properties) const

Static Protected Member Functions
static std::string	propertyToString_ (const Clonable *pptObject, short type) throw (Exception)

static Clonable *	stringToProperty_ (const std::string &pptDesc, short type) throw (Exception)

Private Attributes
std::set< Property >	supportedProperties_

bool	useTagsAsPropertyNames_

bool	hasIds_

Detailed Description

The so-called 'Nhx - New Hampshire eXtended' parenthetic format.

See http://www.phylosoft.org/Nhx/ for details.

Branch lengths and node annotations are supported:

ex: ((A:0.1[&&NHX:S=human], B:0.15[&&NHX:S=chimp]):0.2[&&NHX:B=90:D=N:S=primates], C:0.27[&&NHX:S=mouse]);

Where e.g. "S=human" means that the sequence A comes from species "human", "B=90" stands for a support value, and "D=N" means that there was no duplication at the node. Other tags are allowed, see http://www.phylosoft.org/NHX/. By default, comments between "[" and "]" are removed, unless the opening bracket is followed by "&&NHX".

Code example:

#include <Phyl/Nhx.h>
#include <Phyl/Tree.h>
Nhx * NhxReader = new Nhx();
try {
  Tree * tree = nhxReader->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 nhxReader;

All node annotations are stored as node properties, with type bppString for all properties except for support values, where a Number is used.

Definition at line 87 of file Nhx.h.

Constructor & Destructor Documentation

◆ Nhx()

Nhx::Nhx ( bool useTagsAsPptNames = true )

Build a new Nhx reader/writer.

Comments between hooks ('[' ']') are ignored.

Parameters

useTagsAsPptNames Tells if the NHX tag should be used as a property name in the parsed tree.

Definition at line 60 of file Nhx.cpp.

References bpp::TreeTools::BOOTSTRAP, and registerProperty().

◆ ~Nhx()

virtual bpp::Nhx::~Nhx ( )

inlinevirtual

Definition at line 152 of file Nhx.h.

Member Function Documentation

◆ changeNamesToTags()

void Nhx::changeNamesToTags ( Node & node ) const

Convert property names from names to tags.

If a tree has been parsed using useTagsAsPropertyNames=false, this method allows to convert the tree as is it was parsed using the option set to true.

Parameters

node	The root node of the subtree to convert.

Definition at line 553 of file Nhx.cpp.

References bpp::Node::deleteBranchProperty(), bpp::Node::deleteNodeProperty(), bpp::Node::getBranchProperty(), bpp::Node::getNodeProperty(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasBranchProperty(), bpp::Node::hasNodeProperty(), bpp::Node::setBranchProperty(), bpp::Node::setNodeProperty(), and supportedProperties_.

◆ changeTagsToNames()

void Nhx::changeTagsToNames ( Node & node ) const

Convert property names from tag to names.

If a tree has been parsed using useTagsAsPropertyNames=true, this method allows to convert the tree as is it was parsed using the option set to false.

Parameters

node	The root node of the subtree to convert.

Definition at line 533 of file Nhx.cpp.

References bpp::Node::deleteBranchProperty(), bpp::Node::deleteNodeProperty(), bpp::Node::getBranchProperty(), bpp::Node::getNodeProperty(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasBranchProperty(), bpp::Node::hasNodeProperty(), bpp::Node::setBranchProperty(), bpp::Node::setNodeProperty(), and supportedProperties_.

◆ getDataType()

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

inlinevirtualinherited

Definition at line 68 of file IoTree.h.

◆ getElement()

Nhx::Element Nhx::getElement	(	const std::string &	elt	)	const
throw	(	IOException
	)

protected

Definition at line 206 of file Nhx.cpp.

References bpp::Nhx::Element::annotation, bpp::Nhx::Element::content, bpp::Nhx::Element::isLeaf, and bpp::Nhx::Element::length.

Referenced by parenthesisToNode().

◆ getFormatDescription()

const string Nhx::getFormatDescription ( ) const

Definition at line 91 of file Nhx.cpp.

◆ getFormatName()

const string Nhx::getFormatName ( ) const

Definition at line 87 of file Nhx.cpp.

◆ nodeToParenthesis()

string Nhx::nodeToParenthesis ( const Node & node ) const

protected

Definition at line 433 of file Nhx.cpp.

References bpp::Node::getDistanceToFather(), bpp::Node::getName(), bpp::Node::getNumberOfSons(), bpp::Node::hasDistanceToFather(), bpp::Node::isLeaf(), and propertiesToParenthesis().

Referenced by treeToParenthesis().

◆ parenthesisToNode()

Node * Nhx::parenthesisToNode ( const std::string & description ) const

protected

Definition at line 287 of file Nhx.cpp.

References bpp::Node::addSon(), bpp::Nhx::Element::annotation, bpp::Nhx::Element::content, getElement(), hasIds_, bpp::Nhx::Element::isLeaf, bpp::Nhx::Element::length, bpp::Node::setDistanceToFather(), bpp::Node::setName(), and setNodeProperties().

◆ parenthesisToTree()

TreeTemplate< Node > * Nhx::parenthesisToTree	(	const std::string &	description	)	const
throw	(	Exception
	)

Definition at line 334 of file Nhx.cpp.

References bpp::TreeTemplate< N >::resetNodesId(), and bpp::TreeTemplate< N >::setRootNode().

◆ propertiesToParenthesis()

string Nhx::propertiesToParenthesis ( const Node & node ) const

protected

Definition at line 404 of file Nhx.cpp.

References bpp::Node::getBranchProperty(), bpp::Node::getId(), bpp::Node::getNodeProperty(), bpp::Node::hasBranchProperty(), bpp::Node::hasNodeProperty(), propertyToString_(), supportedProperties_, and useTagsAsPropertyNames_.

Referenced by nodeToParenthesis(), and treeToParenthesis().

◆ propertyToString_()

string Nhx::propertyToString_	(	const Clonable *	pptObject,
		short	type
	)
throw	(	Exception
	)

staticprotected

Definition at line 353 of file Nhx.cpp.

Referenced by propertiesToParenthesis().

◆ read() [1/4]

TreeTemplate<Node>* bpp::Nhx::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 170 of file Nhx.h.

References bpp::AbstractITree::read().

◆ read() [2/4]

TreeTemplate< Node > * Nhx::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 104 of file Nhx.cpp.

◆ read() [3/4]

void bpp::Nhx::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 199 of file Nhx.h.

References bpp::AbstractIMultiTree::read().

◆ read() [4/4]

void Nhx::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 150 of file Nhx.cpp.

◆ registerProperty()

void bpp::Nhx::registerProperty ( const Property & property )

inline

Definition at line 225 of file Nhx.h.

References supportedProperties_.

Referenced by Nhx().

◆ setNodeProperties()

bool Nhx::setNodeProperties	(	Node &	node,
		const std::string	properties
	)		const

protected

Definition at line 490 of file Nhx.cpp.

References bpp::Node::setBranchProperty(), bpp::Node::setId(), bpp::Node::setNodeProperty(), stringToProperty_(), supportedProperties_, and useTagsAsPropertyNames_.

Referenced by parenthesisToNode().

◆ stringToProperty_()

Clonable * Nhx::stringToProperty_	(	const std::string &	pptDesc,
		short	type
	)
throw	(	Exception
	)

staticprotected

Definition at line 386 of file Nhx.cpp.

Referenced by setNodeProperties().

◆ treeToParenthesis()

string Nhx::treeToParenthesis ( const TreeTemplate< Node > & tree ) const

Definition at line 457 of file Nhx.cpp.

References bpp::Node::getDistanceToFather(), bpp::Node::getName(), bpp::Node::getNumberOfSons(), bpp::TreeTemplate< N >::getRootNode(), bpp::Node::getSon(), bpp::Node::hasDistanceToFather(), bpp::Node::isLeaf(), nodeToParenthesis(), and propertiesToParenthesis().

◆ useTagsAsPropertyNames() [1/2]

void bpp::Nhx::useTagsAsPropertyNames ( bool yn )

inline

Definition at line 251 of file Nhx.h.

References useTagsAsPropertyNames_.

◆ useTagsAsPropertyNames() [2/2]

bool bpp::Nhx::useTagsAsPropertyNames ( ) const

inline

Definition at line 252 of file Nhx.h.

References useTagsAsPropertyNames_.

◆ write() [1/4]

void bpp::Nhx::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 183 of file Nhx.h.

References bpp::AbstractOTree::write().

◆ write() [2/4]

void bpp::Nhx::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 188 of file Nhx.h.

References write_().

◆ write() [3/4]

void bpp::Nhx::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 211 of file Nhx.h.

References bpp::AbstractOMultiTree::write().

◆ write() [4/4]

void bpp::Nhx::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 215 of file Nhx.h.

References write_().

◆ write_() [1/4]

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

protected

Definition at line 131 of file Nhx.cpp.

Referenced by write().

◆ write_() [2/4]

template<class N >

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

protected

Definition at line 141 of file Nhx.cpp.

◆ write_() [3/4]

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

protected

Definition at line 181 of file Nhx.cpp.

◆ write_() [4/4]

template<class N >

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

protected

Definition at line 194 of file Nhx.cpp.

Member Data Documentation

◆ hasIds_

bool bpp::Nhx::hasIds_

mutableprivate

Definition at line 140 of file Nhx.h.

Referenced by parenthesisToNode().

◆ supportedProperties_

std::set<Property> bpp::Nhx::supportedProperties_

private

Definition at line 138 of file Nhx.h.

Referenced by changeNamesToTags(), changeTagsToNames(), propertiesToParenthesis(), registerProperty(), and setNodeProperties().

◆ useTagsAsPropertyNames_

bool bpp::Nhx::useTagsAsPropertyNames_

private

Definition at line 139 of file Nhx.h.

Referenced by propertiesToParenthesis(), setNodeProperties(), and useTagsAsPropertyNames().

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

Bpp/Phyl/Io/Nhx.h
Bpp/Phyl/Io/Nhx.cpp

Classes

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Nhx()

◆ ~Nhx()

Member Function Documentation

◆ changeNamesToTags()

◆ changeTagsToNames()

◆ getDataType()

◆ getElement()

◆ getFormatDescription()

◆ getFormatName()

◆ nodeToParenthesis()

◆ parenthesisToNode()

◆ parenthesisToTree()

◆ propertiesToParenthesis()

◆ propertyToString_()

◆ read() [1/4]

◆ read() [2/4]

◆ read() [3/4]

◆ read() [4/4]

◆ registerProperty()

◆ setNodeProperties()

◆ stringToProperty_()

◆ treeToParenthesis()

◆ useTagsAsPropertyNames() [1/2]

◆ useTagsAsPropertyNames() [2/2]

◆ 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

◆ hasIds_

◆ supportedProperties_

◆ useTagsAsPropertyNames_