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	Property

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

virtual	~Nhx ()

std::unique_ptr< TreeTemplate< Node > >	parenthesisToTree (const std::string &description) const

std::unique_ptr< PhyloTree >	parenthesisToPhyloTree (const std::string &description) const

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

std::string	treeToParenthesis (const PhyloTree &tree) const

void	registerProperty (const Property &property)

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

void	changeTagsToNames (PhyloTree &tree, std::shared_ptr< PhyloNode > node) const

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

void	changeNamesToTags (PhyloTree &tree, std::shared_ptr< PhyloNode > node) const

void	useTagsAsPropertyNames (bool yn)

bool	useTagsAsPropertyNames () const

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

std::string	propertiesToParenthesis (const PhyloTree &tree, const std::shared_ptr< PhyloNode > node) const

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 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
	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...

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 Node &node) const

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

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

bool	setNodeProperties (PhyloTree &tree, std::shared_ptr< PhyloNode > node, const std::string properties) const

void	checkNodesId_ (PhyloTree &tree) const
	check and fill all nodes ids. More...

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

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

Private Member Functions
Node *	parenthesisToNode (const std::string &description) const

std::shared_ptr< PhyloNode >	parenthesisToNode (PhyloTree &tree, std::shared_ptr< PhyloNode > father, const std::string &description) const

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/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 53 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 29 of file Nhx.cpp.

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

◆ ~Nhx()

virtual bpp::Nhx::~Nhx ( )

inlinevirtual

Definition at line 111 of file Nhx.h.

Member Function Documentation

◆ changeNamesToTags() [1/2]

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 619 of file Nhx.cpp.

References changeNamesToTags(), 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_.

Referenced by changeNamesToTags().

◆ changeNamesToTags() [2/2]

void Nhx::changeNamesToTags	(	PhyloTree &	tree,
		std::shared_ptr< PhyloNode >	node
	)		const

Definition at line 685 of file Nhx.cpp.

References changeNamesToTags(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeToFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSons(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasFather(), and supportedProperties_.

◆ changeTagsToNames() [1/2]

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 590 of file Nhx.cpp.

References changeTagsToNames(), 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_.

Referenced by changeTagsToNames().

◆ changeTagsToNames() [2/2]

void Nhx::changeTagsToNames	(	PhyloTree &	tree,
		std::shared_ptr< PhyloNode >	node
	)		const

Definition at line 648 of file Nhx.cpp.

References changeTagsToNames(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeToFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSons(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasFather(), and supportedProperties_.

◆ checkNodesId_()

void Nhx::checkNodesId_ ( PhyloTree & tree ) const

protected

check and fill all nodes ids.

Definition at line 431 of file Nhx.cpp.

Referenced by parenthesisToPhyloTree().

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Definition at line 51 of file IoTree.h.

◆ getElement()

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

overrideprotectedvirtual

Reimplemented from bpp::AbstractITree.

Definition at line 203 of file Nhx.cpp.

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

Referenced by parenthesisToNode().

◆ getFormatDescription()

const string Nhx::getFormatDescription ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 60 of file Nhx.cpp.

◆ getFormatName()

const string Nhx::getFormatName ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 56 of file Nhx.cpp.

◆ nodeToParenthesis() [1/2]

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

protected

Definition at line 802 of file Nhx.cpp.

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

Referenced by nodeToParenthesis(), and treeToParenthesis().

◆ nodeToParenthesis() [2/2]

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

protected

Definition at line 861 of file Nhx.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(), nodeToParenthesis(), and propertiesToParenthesis().

◆ parenthesisToNode() [1/2]

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

private

◆ parenthesisToNode() [2/2]

std::shared_ptr< PhyloNode > Nhx::parenthesisToNode	(	PhyloTree &	tree,
		std::shared_ptr< PhyloNode >	father,
		const std::string &	description
	)		const

private

Definition at line 353 of file Nhx.cpp.

References bpp::IOTree::Element::annotation, bpp::IOTree::Element::content, bpp::AssociationTreeGraphImplObserver< class, class, class >::createNode(), getElement(), hasIds_, bpp::NestedStringTokenizer::hasMoreToken(), bpp::TextTools::isEmpty(), bpp::IOTree::Element::isLeaf, bpp::IOTree::Element::length, bpp::NestedStringTokenizer::nextToken(), parenthesisToNode(), bpp::TextTools::removeSurroundingWhiteSpaces(), setNodeProperties(), and bpp::TextTools::toDouble().

◆ parenthesisToPhyloTree()

unique_ptr< PhyloTree > Nhx::parenthesisToPhyloTree ( const std::string & description ) const

Definition at line 407 of file Nhx.cpp.

References checkNodesId_(), hasIds_, and parenthesisToNode().

Referenced by readPhyloTree(), and readPhyloTrees().

◆ parenthesisToTree()

unique_ptr< TreeTemplate< Node > > Nhx::parenthesisToTree ( const std::string & description ) const

Definition at line 334 of file Nhx.cpp.

References hasIds_, and parenthesisToNode().

Referenced by readTrees(), and readTreeTemplate().

◆ propertiesToParenthesis() [1/2]

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

Definition at line 725 of file Nhx.cpp.

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

Referenced by nodeToParenthesis(), and treeToParenthesis().

◆ propertiesToParenthesis() [2/2]

string Nhx::propertiesToParenthesis	(	const PhyloTree &	tree,
		const std::shared_ptr< PhyloNode >	node
	)		const

Definition at line 761 of file Nhx.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeToFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNodeIndex(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasFather(), propertyToString_(), supportedProperties_, bpp::TextTools::toString(), and useTagsAsPropertyNames_.

◆ propertyToString_()

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

staticprotected

Definition at line 1024 of file Nhx.cpp.

References bpp::BppBoolean::getValue(), Number< double >::getValue(), Number< int >::getValue(), bpp::BppString::toSTL(), and bpp::TextTools::toString().

Referenced by propertiesToParenthesis().

◆ 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 > Nhx::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 102 of file Nhx.cpp.

References parenthesisToPhyloTree(), and bpp::TextTools::removeSubstrings().

◆ 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 Nhx::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 168 of file Nhx.cpp.

References parenthesisToPhyloTree(), and bpp::TextTools::removeSubstrings().

◆ 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 Nhx::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 133 of file Nhx.cpp.

References parenthesisToTree(), and bpp::TextTools::removeSubstrings().

◆ 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 > > Nhx::readTreeTemplate ( std::istream & in ) const

overridevirtual

Implements bpp::AbstractITree.

Definition at line 71 of file Nhx.cpp.

References parenthesisToTree(), and bpp::TextTools::removeSubstrings().

◆ readTreeTemplate() [3/3]

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

virtual

Implements bpp::AbstractITree.

◆ registerProperty()

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

inline

Definition at line 201 of file Nhx.h.

References supportedProperties_.

Referenced by Nhx().

◆ setNodeProperties() [1/2]

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

protected

Definition at line 479 of file Nhx.cpp.

References bpp::StringTokenizer::hasMoreToken(), bpp::TextTools::hasSubstring(), bpp::TextTools::isDecimalNumber(), bpp::StringTokenizer::nextToken(), bpp::TextTools::removeChar(), bpp::Node::setBranchProperty(), bpp::Node::setId(), bpp::Node::setNodeProperty(), stringToProperty_(), supportedProperties_, bpp::TextTools::toInt(), and useTagsAsPropertyNames_.

Referenced by parenthesisToNode().

◆ setNodeProperties() [2/2]

bool Nhx::setNodeProperties	(	PhyloTree &	tree,
		std::shared_ptr< PhyloNode >	node,
		const std::string	properties
	)		const

protected

Definition at line 530 of file Nhx.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeToFather(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasFather(), bpp::StringTokenizer::hasMoreToken(), bpp::TextTools::hasSubstring(), bpp::TextTools::isDecimalNumber(), bpp::StringTokenizer::nextToken(), bpp::TextTools::removeChar(), bpp::AssociationTreeGraphImplObserver< class, class, class >::setEdgeIndex(), bpp::AssociationTreeGraphImplObserver< class, class, class >::setNodeIndex(), stringToProperty_(), supportedProperties_, bpp::TextTools::toInt(), and useTagsAsPropertyNames_.

◆ stringToProperty_()

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

staticprotected

Definition at line 1066 of file Nhx.cpp.

References bpp::TextTools::toDouble(), bpp::TextTools::toInt(), and bpp::TextTools::toString().

Referenced by setNodeProperties().

◆ treeToParenthesis() [1/2]

string Nhx::treeToParenthesis ( const PhyloTree & tree ) const

Definition at line 896 of file Nhx.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(), nodeToParenthesis(), and propertiesToParenthesis().

◆ treeToParenthesis() [2/2]

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

Definition at line 827 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::hasNoSon(), nodeToParenthesis(), and propertiesToParenthesis().

Referenced by write_().

◆ useTagsAsPropertyNames() [1/2]

bool bpp::Nhx::useTagsAsPropertyNames ( ) const

inline

Definition at line 231 of file Nhx.h.

References useTagsAsPropertyNames_.

◆ useTagsAsPropertyNames() [2/2]

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

inline

Definition at line 230 of file Nhx.h.

References useTagsAsPropertyNames_.

◆ write_() [1/6]

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

protected

Definition at line 951 of file Nhx.cpp.

References treeToParenthesis().

◆ write_() [2/6]

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

protected

Definition at line 990 of file Nhx.cpp.

References treeToParenthesis().

◆ write_() [3/6]

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

protected

Definition at line 976 of file Nhx.cpp.

References treeToParenthesis().

◆ write_() [4/6]

template<class N >

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

protected

Definition at line 1008 of file Nhx.cpp.

References treeToParenthesis().

◆ write_() [5/6]

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

protected

Definition at line 940 of file Nhx.cpp.

References treeToParenthesis().

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

◆ write_() [6/6]

template<class N >

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

protected

Definition at line 964 of file Nhx.cpp.

References treeToParenthesis().

◆ 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::Nhx::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 152 of file Nhx.h.

References 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::Nhx::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 187 of file Nhx.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::Nhx::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 145 of file Nhx.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::Nhx::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 180 of file Nhx.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

◆ hasIds_

bool bpp::Nhx::hasIds_

mutableprivate

Definition at line 100 of file Nhx.h.

Referenced by parenthesisToNode(), parenthesisToPhyloTree(), and parenthesisToTree().

◆ supportedProperties_

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

private

Definition at line 98 of file Nhx.h.

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

◆ useTagsAsPropertyNames_

bool bpp::Nhx::useTagsAsPropertyNames_

private

Definition at line 99 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 Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Nhx()

◆ ~Nhx()

Member Function Documentation

◆ changeNamesToTags() [1/2]

◆ changeNamesToTags() [2/2]

◆ changeTagsToNames() [1/2]

◆ changeTagsToNames() [2/2]

◆ checkNodesId_()

◆ getDataType()

◆ getElement()

◆ getFormatDescription()

◆ getFormatName()

◆ nodeToParenthesis() [1/2]

◆ nodeToParenthesis() [2/2]

◆ parenthesisToNode() [1/2]

◆ parenthesisToNode() [2/2]

◆ parenthesisToPhyloTree()

◆ parenthesisToTree()

◆ propertiesToParenthesis() [1/2]

◆ propertiesToParenthesis() [2/2]

◆ propertyToString_()

◆ 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]

◆ registerProperty()

◆ setNodeProperties() [1/2]

◆ setNodeProperties() [2/2]

◆ stringToProperty_()

◆ treeToParenthesis() [1/2]

◆ treeToParenthesis() [2/2]

◆ useTagsAsPropertyNames() [1/2]

◆ useTagsAsPropertyNames() [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

◆ hasIds_

◆ supportedProperties_

◆ useTagsAsPropertyNames_