bpp::MixedSubstitutionModelSet::HyperNode Class Reference

#include <Bpp/Phyl/Model/MixedSubstitutionModelSet.h>

Collaboration diagram for bpp::MixedSubstitutionModelSet::HyperNode:

Classes
class	Node

Public Member Functions
	HyperNode (const MixedSubstitutionModelSet *)
	HyperNode (const HyperNode &)
HyperNode &	operator= (const HyperNode &)
	~HyperNode ()
void	setModel (size_t nM, const Vint &vnS)
	sets submodel numbers in the nMth mixed model. Checks if all the numbers are valid. More...
void	addToModel (size_t nM, const Vint &vnS)
	adds submodel numbers to the nMth mixed model. Checks if all the numbers are valid. More...
HyperNode &	operator+= (const HyperNode &)
	Cumulates the Nodes of the given HyperNode into this one. More...
bool	operator<= (const HyperNode &) const
	checks if this HyperNode is included in another one. More...
bool	isComplete () const
	checks if this HyperNode includes at least a submodel of each mixed model More...
bool	operator>= (const HyperNode &) const
	checks if this HyperNode includes another one. More...
bool	intersects (const HyperNode &) const
	checks if this HyperNode intersects another one. More...
double	getProbability () const
	returns the probability More...
void	setProbability (double x)
	sets the probability More...
const Node &	getNode (size_t i) const

Private Attributes
std::vector< Node >	vNumbers_
Vint	vUnused_
	the coordinates of the Nodes that are not used. More...
double	proba_
	probability of this HyperNode. More...

Detailed Description

Definition at line 125 of file MixedSubstitutionModelSet.h.

Constructor & Destructor Documentation

HyperNode() [1/2]

MixedSubstitutionModelSet::HyperNode::HyperNode

(

const MixedSubstitutionModelSet *

pMSMS

)

Definition at line 305 of file MixedSubstitutionModelSet.cpp.

References bpp::SubstitutionModelSet::getModel(), bpp::SubstitutionModelSet::getNumberOfModels(), and vUnused_.

HyperNode() [2/2]

MixedSubstitutionModelSet::HyperNode::HyperNode

(

const HyperNode &

hn

)

Definition at line 317 of file MixedSubstitutionModelSet.cpp.

~HyperNode()

bpp::MixedSubstitutionModelSet::HyperNode::~HyperNode ( )

inline

Definition at line 212 of file MixedSubstitutionModelSet.h.

Member Function Documentation

addToModel()

void MixedSubstitutionModelSet::HyperNode::addToModel	(	size_t	nM,
		const Vint &	vnS
	)

adds submodel numbers to the nMth mixed model. Checks if all the numbers are valid.

Parameters

nM	number of the mixed model
vnS	vector of numbers of the submodel

Definition at line 343 of file MixedSubstitutionModelSet.cpp.

getNode()

const Node& bpp::MixedSubstitutionModelSet::HyperNode::getNode ( size_t  i ) const

inline

Definition at line 274 of file MixedSubstitutionModelSet.h.

References vNumbers_.

Referenced by bpp::MixedSubstitutionModelSet::complete(), bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::MixedSubstitutionModelSet::getHyperNodeProbability(), and bpp::RNonHomogeneousMixedTreeLikelihood::init().

getProbability()

double bpp::MixedSubstitutionModelSet::HyperNode::getProbability ( ) const

inline

returns the probability

Definition at line 266 of file MixedSubstitutionModelSet.h.

References proba_.

Referenced by bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), and bpp::RNonHomogeneousMixedTreeLikelihood::getProbability().

intersects()

bool MixedSubstitutionModelSet::HyperNode::intersects

(

const HyperNode &

hn

)

const

checks if this HyperNode intersects another one.

Definition at line 387 of file MixedSubstitutionModelSet.cpp.

References vNumbers_.

Referenced by bpp::MixedSubstitutionModelSet::hasExclusivePaths().

isComplete()

bool MixedSubstitutionModelSet::HyperNode::isComplete

(

)

const

checks if this HyperNode includes at least a submodel of each mixed model

Definition at line 359 of file MixedSubstitutionModelSet.cpp.

operator+=()

MixedSubstitutionModelSet::HyperNode & MixedSubstitutionModelSet::HyperNode::operator+=

(

const HyperNode &

hn

)

Cumulates the Nodes of the given HyperNode into this one.

Definition at line 403 of file MixedSubstitutionModelSet.cpp.

References vNumbers_.

operator<=()

bool MixedSubstitutionModelSet::HyperNode::operator<=

(

const HyperNode &

hn

)

const

checks if this HyperNode is included in another one.

Definition at line 376 of file MixedSubstitutionModelSet.cpp.

References vNumbers_.

operator=()

MixedSubstitutionModelSet::HyperNode & MixedSubstitutionModelSet::HyperNode::operator=

(

const HyperNode &

hn

)

Definition at line 323 of file MixedSubstitutionModelSet.cpp.

References proba_, vNumbers_, and vUnused_.

operator>=()

bool MixedSubstitutionModelSet::HyperNode::operator>=

(

const HyperNode &

hn

)

const

checks if this HyperNode includes another one.

Definition at line 398 of file MixedSubstitutionModelSet.cpp.

setModel()

void MixedSubstitutionModelSet::HyperNode::setModel	(	size_t	nM,
		const Vint &	vnS
	)

sets submodel numbers in the nMth mixed model. Checks if all the numbers are valid.

Parameters

nM	number of the mixed model
vnS	vector of numbers of the submodel

Definition at line 351 of file MixedSubstitutionModelSet.cpp.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::init().

setProbability()

void bpp::MixedSubstitutionModelSet::HyperNode::setProbability ( double  x )

inline

sets the probability

Definition at line 272 of file MixedSubstitutionModelSet.h.

References proba_.

Referenced by bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), and bpp::RNonHomogeneousMixedTreeLikelihood::setProbability().

Member Data Documentation

proba_

double bpp::MixedSubstitutionModelSet::HyperNode::proba_

private

probability of this HyperNode.

Definition at line 206 of file MixedSubstitutionModelSet.h.

Referenced by getProbability(), operator=(), and setProbability().

vNumbers_

std::vector<Node> bpp::MixedSubstitutionModelSet::HyperNode::vNumbers_

private

Definition at line 192 of file MixedSubstitutionModelSet.h.

Referenced by getNode(), intersects(), operator+=(), operator<=(), and operator=().

vUnused_

Vint bpp::MixedSubstitutionModelSet::HyperNode::vUnused_

private

the coordinates of the Nodes that are not used.

Definition at line 199 of file MixedSubstitutionModelSet.h.

Referenced by HyperNode(), and operator=().

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

• Bpp/Phyl/Model/MixedSubstitutionModelSet.h
• Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp