#include <Bpp/Phyl/Mapping/PhyloBranchMapping.h>

Inheritance diagram for bpp::PhyloBranchMapping:

Collaboration diagram for bpp::PhyloBranchMapping:

Public Member Functions
	PhyloBranchMapping ()
	Constructors. More...

	PhyloBranchMapping (double length)

	PhyloBranchMapping (const PhyloBranch &branch)

	PhyloBranchMapping (const PhyloBranchMapping &branch)
	Copy constructor. More...

PhyloBranchMapping &	operator= (const PhyloBranchMapping &branch)
	Assignation operator. More...

PhyloBranchMapping *	clone () const

	~PhyloBranchMapping ()
	destructor. In Graph, nothing is changed. More...

void	setNumberOfSites (size_t nbSites)
	Sets a number of sites. If the number of types is already defined, it is kept. More...

void	setNumberOfTypes (size_t nbTypes)
	Define a number of types. More...

void	setNumberOfSitesAndTypes (size_t nbSites, size_t nbTypes)
	Define a number of types. More...

size_t	getNumberOfSites () const
	Gets the number of sites. More...

size_t	getNumberOfTypes () const
	Gets the number of types. More...

Vdouble &	getSiteCount (size_t site)
	Gets the counts at a given site. More...

const Vdouble &	getSiteCount (size_t site) const

double	getSiteTypeCount (size_t site, size_t type) const
	Gets the counts at a given site on a given type. More...

void	setSiteTypeCount (size_t site, size_t type, double value)
	Sets the counts at a given site on a given type. More...

double	operator() (size_t site, size_t type) const
	Without check. More...

double &	operator() (size_t site, size_t type)

const VVdouble &	getCounts () const
	return counts More...

VVdouble &	getCounts ()

bool	hasLength () const
	Has the length been set? More...

void	deleteLength ()
	Delete length. More...

double	getLength () const
	What is the branch length? More...

void	setLength (double newLength)

void	setProperty (const std::string &name, const Clonable &property)
	Set/add a branch property. More...

Clonable *	getProperty (const std::string &name)

const Clonable *	getProperty (const std::string &name) const

Clonable *	removeProperty (const std::string &name)

void	deleteProperty (const std::string &name)

void	removeProperties ()
	Remove all branch properties. More...

void	deleteProperties ()
	Delete all branch properties. More...

bool	hasProperty (const std::string &name) const

std::vector< std::string >	getPropertyNames () const

bool	hasBootstrapValue () const

double	getBootstrapValue () const

Protected Attributes
VVdouble	counts_

bool	isLengthDefined_

double	length_

std::map< std::string, Clonable * >	properties_

Detailed Description

Definition at line 25 of file PhyloBranchMapping.h.

Constructor & Destructor Documentation

◆ PhyloBranchMapping() [1/4]

bpp::PhyloBranchMapping::PhyloBranchMapping ( )

inline

Constructors.

Warning: phyloTree_ does not know the edge exists.

Definition at line 44 of file PhyloBranchMapping.h.

Referenced by clone().

◆ PhyloBranchMapping() [2/4]

bpp::PhyloBranchMapping::PhyloBranchMapping ( double length )

inline

Definition at line 49 of file PhyloBranchMapping.h.

◆ PhyloBranchMapping() [3/4]

bpp::PhyloBranchMapping::PhyloBranchMapping ( const PhyloBranch & branch )

inline

Definition at line 54 of file PhyloBranchMapping.h.

◆ PhyloBranchMapping() [4/4]

bpp::PhyloBranchMapping::PhyloBranchMapping ( const PhyloBranchMapping & branch )

inline

Copy constructor.

Parameters

branch The branch to copy.

Definition at line 65 of file PhyloBranchMapping.h.

◆ ~PhyloBranchMapping()

bpp::PhyloBranchMapping::~PhyloBranchMapping ( )

inline

destructor. In Graph, nothing is changed.

Definition at line 89 of file PhyloBranchMapping.h.

Member Function Documentation

◆ clone()

PhyloBranchMapping * bpp::PhyloBranchMapping::clone ( ) const

inline

Definition at line 83 of file PhyloBranchMapping.h.

References PhyloBranchMapping().

◆ deleteLength()

void bpp::PhyloBranch::deleteLength ( )

inlineinherited

Delete length.

Definition at line 88 of file PhyloBranch.h.

References bpp::PhyloBranch::isLengthDefined_.

◆ deleteProperties()

void bpp::PhyloBranch::deleteProperties ( )

inlineinherited

Delete all branch properties.

Definition at line 187 of file PhyloBranch.h.

References bpp::PhyloBranch::properties_.

Referenced by bpp::PhyloBranch::~PhyloBranch().

◆ deleteProperty()

void bpp::PhyloBranch::deleteProperty ( const std::string & name )

inlineinherited

Definition at line 163 of file PhyloBranch.h.

References bpp::PhyloBranch::hasProperty(), and bpp::PhyloBranch::properties_.

◆ getBootstrapValue()

double bpp::PhyloBranch::getBootstrapValue ( ) const

inlineinherited

Definition at line 205 of file PhyloBranch.h.

References bpp::PhyloBranch::hasBootstrapValue(), and bpp::PhyloBranch::properties_.

◆ getCounts() [1/2]

VVdouble & bpp::PhyloBranchMapping::getCounts ( )

inline

Definition at line 203 of file PhyloBranchMapping.h.

References counts_.

◆ getCounts() [2/2]

const VVdouble & bpp::PhyloBranchMapping::getCounts ( ) const

inline

return counts

Definition at line 198 of file PhyloBranchMapping.h.

References counts_.

◆ getLength()

double bpp::PhyloBranch::getLength ( ) const

inlineinherited

What is the branch length?

Returns: a double representing the branch length, 0 if length is not defined.

Definition at line 99 of file PhyloBranch.h.

References bpp::PhyloBranch::isLengthDefined_, and bpp::PhyloBranch::length_.

Referenced by bpp::PhyloBranchParam::PhyloBranchParam().

◆ getNumberOfSites()

size_t bpp::PhyloBranchMapping::getNumberOfSites ( ) const

inline

Gets the number of sites.

Definition at line 121 of file PhyloBranchMapping.h.

References counts_.

Referenced by getSiteTypeCount(), and setSiteTypeCount().

◆ getNumberOfTypes()

size_t bpp::PhyloBranchMapping::getNumberOfTypes ( ) const

inline

Gets the number of types.

Definition at line 129 of file PhyloBranchMapping.h.

References counts_.

Referenced by getSiteTypeCount(), and setSiteTypeCount().

◆ getProperty() [1/2]

Clonable * bpp::PhyloBranch::getProperty ( const std::string & name )

inlineinherited

Definition at line 135 of file PhyloBranch.h.

References bpp::PhyloBranch::hasProperty(), and bpp::PhyloBranch::properties_.

◆ getProperty() [2/2]

const Clonable * bpp::PhyloBranch::getProperty ( const std::string & name ) const

inlineinherited

Definition at line 143 of file PhyloBranch.h.

References bpp::PhyloBranch::hasProperty(), and bpp::PhyloBranch::properties_.

◆ getPropertyNames()

std::vector< std::string > bpp::PhyloBranch::getPropertyNames ( ) const

inlineinherited

Definition at line 198 of file PhyloBranch.h.

References bpp::MapTools::getKeys(), and bpp::PhyloBranch::properties_.

◆ getSiteCount() [1/2]

Vdouble & bpp::PhyloBranchMapping::getSiteCount ( size_t site )

inline

Gets the counts at a given site.

Definition at line 138 of file PhyloBranchMapping.h.

References counts_.

◆ getSiteCount() [2/2]

const Vdouble & bpp::PhyloBranchMapping::getSiteCount ( size_t site ) const

inline

Definition at line 143 of file PhyloBranchMapping.h.

References counts_.

◆ getSiteTypeCount()

double bpp::PhyloBranchMapping::getSiteTypeCount	(	size_t	site,
		size_t	type
	)		const

inline

Gets the counts at a given site on a given type.

With check

Definition at line 157 of file PhyloBranchMapping.h.

References counts_, getNumberOfSites(), and getNumberOfTypes().

◆ hasBootstrapValue()

bool bpp::PhyloBranch::hasBootstrapValue ( ) const

inlineinherited

Definition at line 200 of file PhyloBranch.h.

References bpp::PhyloBranch::properties_.

Referenced by bpp::PhyloBranch::getBootstrapValue().

◆ hasLength()

bool bpp::PhyloBranch::hasLength ( ) const

inlineinherited

Has the length been set?

Returns: true if a length has been defined

Definition at line 79 of file PhyloBranch.h.

References bpp::PhyloBranch::isLengthDefined_.

Referenced by bpp::PhyloBranchParam::PhyloBranchParam().

◆ hasProperty()

bool bpp::PhyloBranch::hasProperty ( const std::string & name ) const

inlineinherited

Definition at line 196 of file PhyloBranch.h.

References bpp::PhyloBranch::properties_.

Referenced by bpp::PhyloBranch::deleteProperty(), bpp::PhyloBranch::getProperty(), bpp::PhyloBranch::removeProperty(), and bpp::PhyloBranch::setProperty().

◆ operator()() [1/2]

double & bpp::PhyloBranchMapping::operator()	(	size_t	site,
		size_t	type
	)

inline

Definition at line 189 of file PhyloBranchMapping.h.

References counts_.

◆ operator()() [2/2]

double bpp::PhyloBranchMapping::operator()	(	size_t	site,
		size_t	type
	)		const

inline

Without check.

Definition at line 184 of file PhyloBranchMapping.h.

References counts_.

◆ operator=()

PhyloBranchMapping & bpp::PhyloBranchMapping::operator= ( const PhyloBranchMapping & branch )

inline

Assignation operator.

Parameters

branch the branch to copy.

Returns: A reference toward this branch.

Definition at line 76 of file PhyloBranchMapping.h.

References counts_, and bpp::PhyloBranch::operator=().

◆ removeProperties()

void bpp::PhyloBranch::removeProperties ( )

inlineinherited

Remove all branch properties.

Attached objects will not be deleted.

Definition at line 179 of file PhyloBranch.h.

References bpp::PhyloBranch::properties_.

◆ removeProperty()

Clonable * bpp::PhyloBranch::removeProperty ( const std::string & name )

inlineinherited

Definition at line 151 of file PhyloBranch.h.

References bpp::PhyloBranch::hasProperty(), and bpp::PhyloBranch::properties_.

◆ setLength()

void bpp::PhyloBranch::setLength ( double newLength )

inlineinherited

Define a new branch length

Parameters

newLength a double repserenting the new length of the branch

Definition at line 112 of file PhyloBranch.h.

References bpp::PhyloBranch::isLengthDefined_, and bpp::PhyloBranch::length_.

◆ setNumberOfSites()

void bpp::PhyloBranchMapping::setNumberOfSites ( size_t nbSites )

inline

Sets a number of sites. If the number of types is already defined, it is kept.

Definition at line 96 of file PhyloBranchMapping.h.

References counts_, and bpp::VectorTools::resize2().

◆ setNumberOfSitesAndTypes()

void bpp::PhyloBranchMapping::setNumberOfSitesAndTypes	(	size_t	nbSites,
		size_t	nbTypes
	)

inline

Define a number of types.

Definition at line 112 of file PhyloBranchMapping.h.

References counts_, and bpp::VectorTools::resize2().

◆ setNumberOfTypes()

void bpp::PhyloBranchMapping::setNumberOfTypes ( size_t nbTypes )

inline

Define a number of types.

Definition at line 104 of file PhyloBranchMapping.h.

References counts_, and bpp::VectorTools::resize2().

◆ setProperty()

void bpp::PhyloBranch::setProperty	(	const std::string &	name,
		const Clonable &	property
	)

inlineinherited

Set/add a branch property.

If no property with the same name is found, the new property will be added to the list. Conversely, the property will be deleted and replaced by the new one. If you want to keep a copy of the old property, consider using the removeProperty function before.

Parameters

name	The name of the property to set.
property	The property object (will be cloned).

Definition at line 128 of file PhyloBranch.h.

References bpp::PhyloBranch::hasProperty(), and bpp::PhyloBranch::properties_.

◆ setSiteTypeCount()

void bpp::PhyloBranchMapping::setSiteTypeCount	(	size_t	site,
		size_t	type,
		double	value
	)

inline

Sets the counts at a given site on a given type.

Definition at line 170 of file PhyloBranchMapping.h.

References counts_, getNumberOfSites(), and getNumberOfTypes().

Member Data Documentation

◆ counts_

VVdouble bpp::PhyloBranchMapping::counts_

protected

Definition at line 34 of file PhyloBranchMapping.h.

Referenced by getCounts(), getNumberOfSites(), getNumberOfTypes(), getSiteCount(), getSiteTypeCount(), operator()(), operator=(), setNumberOfSites(), setNumberOfSitesAndTypes(), setNumberOfTypes(), and setSiteTypeCount().

◆ isLengthDefined_

bool bpp::PhyloBranch::isLengthDefined_

protectedinherited

Definition at line 23 of file PhyloBranch.h.

Referenced by bpp::PhyloBranch::deleteLength(), bpp::PhyloBranch::getLength(), bpp::PhyloBranch::hasLength(), bpp::PhyloBranch::operator=(), and bpp::PhyloBranch::setLength().

◆ length_

double bpp::PhyloBranch::length_

protectedinherited

Definition at line 24 of file PhyloBranch.h.

Referenced by bpp::PhyloBranch::getLength(), bpp::PhyloBranch::operator=(), and bpp::PhyloBranch::setLength().

◆ properties_

std::map<std::string, Clonable*> bpp::PhyloBranch::properties_

mutableprotectedinherited

Definition at line 25 of file PhyloBranch.h.

Referenced by bpp::PhyloBranch::deleteProperties(), bpp::PhyloBranch::deleteProperty(), bpp::PhyloBranch::getBootstrapValue(), bpp::PhyloBranch::getProperty(), bpp::PhyloBranch::getPropertyNames(), bpp::PhyloBranch::hasBootstrapValue(), bpp::PhyloBranch::hasProperty(), bpp::PhyloBranch::operator=(), bpp::PhyloBranch::PhyloBranch(), bpp::PhyloBranch::removeProperties(), bpp::PhyloBranch::removeProperty(), and bpp::PhyloBranch::setProperty().

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

Bpp/Phyl/Mapping/PhyloBranchMapping.h

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PhyloBranchMapping() [1/4]

◆ PhyloBranchMapping() [2/4]

◆ PhyloBranchMapping() [3/4]

◆ PhyloBranchMapping() [4/4]

◆ ~PhyloBranchMapping()

Member Function Documentation

◆ clone()

◆ deleteLength()

◆ deleteProperties()

◆ deleteProperty()

◆ getBootstrapValue()

◆ getCounts() [1/2]

◆ getCounts() [2/2]

◆ getLength()

◆ getNumberOfSites()

◆ getNumberOfTypes()

◆ getProperty() [1/2]

◆ getProperty() [2/2]

◆ getPropertyNames()

◆ getSiteCount() [1/2]

◆ getSiteCount() [2/2]

◆ getSiteTypeCount()

◆ hasBootstrapValue()

◆ hasLength()

◆ hasProperty()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=()

◆ removeProperties()

◆ removeProperty()

◆ setLength()

◆ setNumberOfSites()

◆ setNumberOfSitesAndTypes()

◆ setNumberOfTypes()

◆ setProperty()

◆ setSiteTypeCount()

Member Data Documentation

◆ counts_

◆ isLengthDefined_

◆ length_

◆ properties_