bpp::PhyloBranch Class Reference

#include <Bpp/Phyl/Tree/PhyloBranch.h>

Inheritance diagram for bpp::PhyloBranch:

Collaboration diagram for bpp::PhyloBranch:

Public Member Functions
	PhyloBranch ()
	Constructors. More...
	PhyloBranch (double length)
	PhyloBranch (const PhyloBranchParam &branch)
	PhyloBranch (const PhyloBranch &branch)
	Copy constructor. More...
PhyloBranch &	operator= (const PhyloBranch &branch)
	Assignation operator. More...
PhyloBranch *	clone () const
virtual	~PhyloBranch ()
	destructor. In Graph, nothing is changed. More...
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
bool	isLengthDefined_
double	length_
std::map< std::string, Clonable * >	properties_

Detailed Description

Definition at line 20 of file PhyloBranch.h.

Constructor & Destructor Documentation

PhyloBranch() [1/4]

bpp::PhyloBranch::PhyloBranch ( )

inline

Constructors.

Warning

phyloTree_ does not know the edge exists.

Definition at line 35 of file PhyloBranch.h.

Referenced by clone().

PhyloBranch() [2/4]

bpp::PhyloBranch::PhyloBranch ( double  length )

inline

Definition at line 41 of file PhyloBranch.h.

PhyloBranch() [3/4]

PhyloBranch::PhyloBranch

(

const PhyloBranchParam &

branch

)

Definition at line 25 of file PhyloBranch.cpp.

PhyloBranch() [4/4]

PhyloBranch::PhyloBranch

(

const PhyloBranch &

branch

)

Copy constructor.

Parameters

branch

The branch to copy.

Copy constructor:

Definition at line 13 of file PhyloBranch.cpp.

References properties_.

~PhyloBranch()

virtual bpp::PhyloBranch::~PhyloBranch ( )

inlinevirtual

destructor. In Graph, nothing is changed.

Definition at line 70 of file PhyloBranch.h.

References deleteProperties().

Member Function Documentation

clone()

PhyloBranch * bpp::PhyloBranch::clone ( ) const

inline

Definition at line 64 of file PhyloBranch.h.

References PhyloBranch().

deleteLength()

void bpp::PhyloBranch::deleteLength ( )

inline

Delete length.

Definition at line 88 of file PhyloBranch.h.

References isLengthDefined_.

deleteProperties()

void bpp::PhyloBranch::deleteProperties ( )

inline

Delete all branch properties.

Definition at line 187 of file PhyloBranch.h.

References properties_.

Referenced by ~PhyloBranch().

deleteProperty()

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

inline

Definition at line 163 of file PhyloBranch.h.

References hasProperty(), and properties_.

getBootstrapValue()

double bpp::PhyloBranch::getBootstrapValue ( ) const

inline

Definition at line 205 of file PhyloBranch.h.

References hasBootstrapValue(), and properties_.

getLength()

double bpp::PhyloBranch::getLength ( ) const

inline

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 isLengthDefined_, and length_.

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

getProperty() [1/2]

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

inline

Definition at line 135 of file PhyloBranch.h.

References hasProperty(), and properties_.

getProperty() [2/2]

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

inline

Definition at line 143 of file PhyloBranch.h.

References hasProperty(), and properties_.

getPropertyNames()

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

inline

Definition at line 198 of file PhyloBranch.h.

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

hasBootstrapValue()

bool bpp::PhyloBranch::hasBootstrapValue ( ) const

inline

Definition at line 200 of file PhyloBranch.h.

References properties_.

Referenced by getBootstrapValue().

hasLength()

bool bpp::PhyloBranch::hasLength ( ) const

inline

Has the length been set?

Returns

true if a length has been defined

Definition at line 79 of file PhyloBranch.h.

References isLengthDefined_.

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

hasProperty()

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

inline

Definition at line 196 of file PhyloBranch.h.

References properties_.

Referenced by deleteProperty(), getProperty(), removeProperty(), and setProperty().

operator=()

PhyloBranch & PhyloBranch::operator=

(

const PhyloBranch &

branch

)

Assignation operator.

Parameters

branch

the branch to copy.

Returns

A reference toward this branch.

Assignation operator:

Definition at line 33 of file PhyloBranch.cpp.

References isLengthDefined_, length_, and properties_.

Referenced by bpp::PhyloBranchMapping::operator=(), and bpp::PhyloBranchReward::operator=().

removeProperties()

void bpp::PhyloBranch::removeProperties ( )

inline

Remove all branch properties.

Attached objects will not be deleted.

Definition at line 179 of file PhyloBranch.h.

References properties_.

removeProperty()

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

inline

Definition at line 151 of file PhyloBranch.h.

References hasProperty(), and properties_.

setLength()

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

inline

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 isLengthDefined_, and length_.

setProperty()

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

inline

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 hasProperty(), and properties_.

Member Data Documentation

isLengthDefined_

bool bpp::PhyloBranch::isLengthDefined_

protected

Definition at line 23 of file PhyloBranch.h.

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

length_

double bpp::PhyloBranch::length_

protected

Definition at line 24 of file PhyloBranch.h.

Referenced by getLength(), operator=(), and setLength().

properties_

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

mutableprotected

Definition at line 25 of file PhyloBranch.h.

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

---

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

• Bpp/Phyl/Tree/PhyloBranch.h
• Bpp/Phyl/Tree/PhyloBranch.cpp