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

Inheritance diagram for bpp::PhyloBranchReward:

Collaboration diagram for bpp::PhyloBranchReward:

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

	PhyloBranchReward (double length)

	PhyloBranchReward (const PhyloBranch &branch)

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

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

PhyloBranchReward *	clone () const

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

void	setNumberOfSites (size_t nbSites)
	Sets a number of sites. More...

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

double	getSiteReward (size_t site) const

void	setSiteReward (size_t site, double rew)

double	operator() (size_t site) const
	Gets the rewards at a given site on a given type. More...

double &	operator() (size_t site)

const Vdouble &	getRewards () const
	return rewards More...

Vdouble &	getRewards ()

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
Vdouble	rewards_

bool	isLengthDefined_

double	length_

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

Detailed Description

Definition at line 25 of file PhyloBranchReward.h.

Constructor & Destructor Documentation

◆ PhyloBranchReward() [1/4]

bpp::PhyloBranchReward::PhyloBranchReward ( )

inline

Constructors.

Warning: phyloTree_ does not know the edge exists.

Definition at line 44 of file PhyloBranchReward.h.

Referenced by clone().

◆ PhyloBranchReward() [2/4]

bpp::PhyloBranchReward::PhyloBranchReward ( double length )

inline

Definition at line 49 of file PhyloBranchReward.h.

◆ PhyloBranchReward() [3/4]

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

inline

Definition at line 54 of file PhyloBranchReward.h.

◆ PhyloBranchReward() [4/4]

bpp::PhyloBranchReward::PhyloBranchReward ( const PhyloBranchReward & branch )

inline

Copy constructor.

Parameters

branch The branch to copy.

Definition at line 65 of file PhyloBranchReward.h.

◆ ~PhyloBranchReward()

bpp::PhyloBranchReward::~PhyloBranchReward ( )

inline

destructor. In Graph, nothing is changed.

Definition at line 89 of file PhyloBranchReward.h.

Member Function Documentation

◆ clone()

PhyloBranchReward* bpp::PhyloBranchReward::clone ( ) const

inline

Definition at line 83 of file PhyloBranchReward.h.

References PhyloBranchReward().

◆ deleteLength()

void bpp::PhyloBranch::deleteLength ( )

inlineinherited

Delete length.

Definition at line 90 of file PhyloBranch.h.

References bpp::PhyloBranch::isLengthDefined_.

◆ deleteProperties()

void bpp::PhyloBranch::deleteProperties ( )

inlineinherited

Delete all branch properties.

Definition at line 189 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 165 of file PhyloBranch.h.

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

◆ getBootstrapValue()

double bpp::PhyloBranch::getBootstrapValue ( ) const

inlineinherited

Definition at line 207 of file PhyloBranch.h.

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

◆ 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 101 of file PhyloBranch.h.

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

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

◆ getNumberOfSites()

size_t bpp::PhyloBranchReward::getNumberOfSites ( ) const

inline

Gets the number of sites.

Definition at line 103 of file PhyloBranchReward.h.

References rewards_.

Referenced by getSiteReward(), and setSiteReward().

◆ getProperty() [1/2]

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

inlineinherited

Definition at line 137 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 145 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 200 of file PhyloBranch.h.

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

◆ getRewards() [1/2]

Vdouble& bpp::PhyloBranchReward::getRewards ( )

inline

Definition at line 151 of file PhyloBranchReward.h.

References rewards_.

◆ getRewards() [2/2]

const Vdouble& bpp::PhyloBranchReward::getRewards ( ) const

inline

return rewards

Definition at line 146 of file PhyloBranchReward.h.

References rewards_.

◆ getSiteReward()

double bpp::PhyloBranchReward::getSiteReward ( size_t site ) const

inline

Definition at line 109 of file PhyloBranchReward.h.

References getNumberOfSites(), and rewards_.

◆ hasBootstrapValue()

bool bpp::PhyloBranch::hasBootstrapValue ( ) const

inlineinherited

Definition at line 202 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 81 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 198 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::PhyloBranchReward::operator() ( size_t site )

inline

Definition at line 137 of file PhyloBranchReward.h.

References rewards_.

◆ operator()() [2/2]

double bpp::PhyloBranchReward::operator() ( size_t site ) const

inline

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

Without check

Definition at line 132 of file PhyloBranchReward.h.

References rewards_.

◆ operator=()

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

inline

Assignation operator.

Parameters

branch the branch to copy.

Returns: A reference toward this branch.

Definition at line 76 of file PhyloBranchReward.h.

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

◆ removeProperties()

void bpp::PhyloBranch::removeProperties ( )

inlineinherited

Remove all branch properties.

Attached objects will not be deleted.

Definition at line 181 of file PhyloBranch.h.

References bpp::PhyloBranch::properties_.

◆ removeProperty()

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

inlineinherited

Definition at line 153 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 114 of file PhyloBranch.h.

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

◆ setNumberOfSites()

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

inline

Sets a number of sites.

Definition at line 95 of file PhyloBranchReward.h.

References rewards_.

◆ 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 130 of file PhyloBranch.h.

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

◆ setSiteReward()

void bpp::PhyloBranchReward::setSiteReward	(	size_t	site,
		double	rew
	)

inline

Definition at line 116 of file PhyloBranchReward.h.

References getNumberOfSites(), and rewards_.

Member Data Documentation

◆ 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().

◆ rewards_

Vdouble bpp::PhyloBranchReward::rewards_

protected

Definition at line 34 of file PhyloBranchReward.h.

Referenced by getNumberOfSites(), getRewards(), getSiteReward(), operator()(), operator=(), setNumberOfSites(), and setSiteReward().

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

Bpp/Phyl/Mapping/PhyloBranchReward.h

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PhyloBranchReward() [1/4]

◆ PhyloBranchReward() [2/4]

◆ PhyloBranchReward() [3/4]

◆ PhyloBranchReward() [4/4]

◆ ~PhyloBranchReward()

Member Function Documentation

◆ clone()

◆ deleteLength()

◆ deleteProperties()

◆ deleteProperty()

◆ getBootstrapValue()

◆ getLength()

◆ getNumberOfSites()

◆ getProperty() [1/2]

◆ getProperty() [2/2]

◆ getPropertyNames()

◆ getRewards() [1/2]

◆ getRewards() [2/2]

◆ getSiteReward()

◆ hasBootstrapValue()

◆ hasLength()

◆ hasProperty()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=()

◆ removeProperties()

◆ removeProperty()

◆ setLength()

◆ setNumberOfSites()

◆ setProperty()

◆ setSiteReward()

Member Data Documentation

◆ isLengthDefined_

◆ length_

◆ properties_

◆ rewards_