bpp::PhyloBranchParam Class Reference

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

Inheritance diagram for bpp::PhyloBranchParam:

Collaboration diagram for bpp::PhyloBranchParam:

Public Member Functions
	PhyloBranchParam (const std::string &prefix="")
	Constructors. More...
	PhyloBranchParam (const PhyloBranch &branch)
	PhyloBranchParam (const PhyloBranchParam &branch)
	Copy constructor. More...
PhyloBranchParam &	operator= (const PhyloBranchParam &branch)
	Assignation operator. More...
PhyloBranchParam *	clone () const
double	getLength () const
	What is the branch length? More...
void	setLength (double newLength)
bool	hasParameter (const std::string &name) const override
const ParameterList &	getParameters () const override
const Parameter &	parameter (const std::string &name) const override
const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const
double	getParameterValue (const std::string &name) const override
void	setAllParametersValues (const ParameterList &parameters) override
void	setParameterValue (const std::string &name, double value) override
void	setParametersValues (const ParameterList &parameters) override
bool	matchParametersValues (const ParameterList &parameters) override
void	removeConstraint (const std::string &name) override
void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
size_t	getNumberOfParameters () const override
void	setNamespace (const std::string &prefix) override
std::string	getNamespace () const override
std::string	getParameterNameWithoutNamespace (const std::string &name) const override
virtual void	fireParameterChanged (const ParameterList &parameters)

Protected Member Functions
const std::shared_ptr< Parameter > &	getParameter (size_t i) const
std::shared_ptr< Parameter > &	getParameter (size_t i)
virtual void	addParameter_ (Parameter *parameter)
virtual void	addParameters_ (const ParameterList &parameters)
virtual void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)
virtual void	shareParameters_ (const ParameterList &parameters)
virtual void	includeParameters_ (const ParameterList &parameters)
virtual void	deleteParameter_ (size_t index)
virtual void	deleteParameter_ (std::string &name)
virtual void	deleteParameters_ (const std::vector< std::string > &names)
void	resetParameters_ ()
Parameter &	getParameter_ (const std::string &name)
Parameter &	getParameter_ (size_t index)
const Parameter &	getParameter_ (size_t index) const
Parameter &	getParameterWithNamespace_ (const std::string &name)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const
ParameterList &	getParameters_ () override

Private Attributes
ParameterList	parameters_
std::string	prefix_

Friends
class	ParametrizablePhyloTree

Detailed Description

Basic branch in which length is parameterized.

Note : Branch Length must be the first parameter (index 0).

Definition at line 23 of file PhyloBranchParam.h.

Constructor & Destructor Documentation

PhyloBranchParam() [1/3]

bpp::PhyloBranchParam::PhyloBranchParam ( const std::string &  prefix = "" )

inline

Constructors.

Warning

phyloTree_ does not know the edge exists.

Definition at line 34 of file PhyloBranchParam.h.

References bpp::AbstractParametrizable::addParameter_(), bpp::Parameter::R_PLUS_STAR, and bpp::NumConstants::SMALL().

Referenced by clone().

PhyloBranchParam() [2/3]

PhyloBranchParam::PhyloBranchParam

(

const PhyloBranch &

branch

)

Definition at line 11 of file PhyloBranchParam.cpp.

References bpp::AbstractParametrizable::addParameter_(), bpp::PhyloBranch::getLength(), bpp::PhyloBranch::hasLength(), bpp::Parameter::R_PLUS_STAR, and bpp::NumConstants::SMALL().

PhyloBranchParam() [3/3]

bpp::PhyloBranchParam::PhyloBranchParam ( const PhyloBranchParam &  branch )

inline

Copy constructor.

Parameters

branch

The branch to copy.

Definition at line 47 of file PhyloBranchParam.h.

Member Function Documentation

clone()

PhyloBranchParam * bpp::PhyloBranchParam::clone ( ) const

inlinevirtual

Implements bpp::AbstractParametrizable.

Definition at line 69 of file PhyloBranchParam.h.

References PhyloBranchParam().

getLength()

double bpp::PhyloBranchParam::getLength ( ) const

inline

What is the branch length?

Returns

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

Definition at line 78 of file PhyloBranchParam.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::getValue().

operator=()

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

inline

Assignation operator.

Warning

This operator copies all fields, excepted father and son branch pointers. Without specific id, the PhyloTree does not know the existence of the new edge.

Parameters

branch

the branch to copy.

Returns

A reference toward this branch.

Definition at line 62 of file PhyloBranchParam.h.

setLength()

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

inline

Define a new branch length

Parameters

newLength

a double repserenting the new length of the branch

Definition at line 88 of file PhyloBranchParam.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::setValue().

Friends And Related Function Documentation

ParametrizablePhyloTree

friend class ParametrizablePhyloTree

friend

Definition at line 94 of file PhyloBranchParam.h.

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

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