bpp::DRTreeParsimonyNodeData Class Reference

Parsimony data structure for a node. More...

#include <Bpp/Phyl/Parsimony/DRTreeParsimonyData.h>

Inheritance diagram for bpp::DRTreeParsimonyNodeData:

Collaboration diagram for bpp::DRTreeParsimonyNodeData:

Public Member Functions
	DRTreeParsimonyNodeData ()
	DRTreeParsimonyNodeData (const DRTreeParsimonyNodeData &tpnd)
DRTreeParsimonyNodeData &	operator= (const DRTreeParsimonyNodeData &tpnd)
DRTreeParsimonyNodeData *	clone () const
const Node *	getNode () const
	Get the node associated to this data structure. More...
void	setNode (const Node *node)
	Set the node associated to this data. More...
std::vector< Bitset > &	getBitsetsArrayForNeighbor (int neighborId)
const std::vector< Bitset > &	getBitsetsArrayForNeighbor (int neighborId) const
std::vector< unsigned int > &	getScoresArrayForNeighbor (int neighborId)
const std::vector< unsigned int > &	getScoresArrayForNeighbor (int neighborId) const
bool	isNeighbor (int neighborId) const
void	eraseNeighborArrays ()

Private Attributes
std::map< int, std::vector< Bitset > >	nodeBitsets_
std::map< int, std::vector< unsigned int > >	nodeScores_
const Node *	node_

Detailed Description

Parsimony data structure for a node.

This class is for use with the DRTreeParsimonyData class.

Store for each neighbor node

• a vector of bitsets,
• a vector of score for the corresponding subtree.

See also

DRTreeParsimonyData

Definition at line 68 of file DRTreeParsimonyData.h.

Constructor & Destructor Documentation

DRTreeParsimonyNodeData() [1/2]

bpp::DRTreeParsimonyNodeData::DRTreeParsimonyNodeData ( )

inline

Definition at line 77 of file DRTreeParsimonyData.h.

Referenced by clone().

DRTreeParsimonyNodeData() [2/2]

bpp::DRTreeParsimonyNodeData::DRTreeParsimonyNodeData ( const DRTreeParsimonyNodeData &  tpnd )

inline

Definition at line 83 of file DRTreeParsimonyData.h.

Member Function Documentation

clone()

DRTreeParsimonyNodeData* bpp::DRTreeParsimonyNodeData::clone ( ) const

inlinevirtual

Implements bpp::TreeParsimonyNodeData.

Definition at line 97 of file DRTreeParsimonyData.h.

References DRTreeParsimonyNodeData().

eraseNeighborArrays()

void bpp::DRTreeParsimonyNodeData::eraseNeighborArrays ( )

inline

Definition at line 126 of file DRTreeParsimonyData.h.

References nodeBitsets_, and nodeScores_.

Referenced by bpp::DRTreeParsimonyData::init(), and bpp::DRTreeParsimonyData::reInit().

getBitsetsArrayForNeighbor() [1/2]

std::vector<Bitset>& bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor ( int  neighborId )

inline

Definition at line 104 of file DRTreeParsimonyData.h.

References nodeBitsets_.

Referenced by bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorderForNode(), bpp::DRTreeParsimonyData::init(), bpp::DRTreeParsimonyData::reInit(), and bpp::DRTreeParsimonyScore::testNNI().

getBitsetsArrayForNeighbor() [2/2]

const std::vector<Bitset>& bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor ( int  neighborId ) const

inline

Definition at line 108 of file DRTreeParsimonyData.h.

References nodeBitsets_.

getNode()

const Node* bpp::DRTreeParsimonyNodeData::getNode ( ) const

inlinevirtual

Get the node associated to this data structure.

Returns

The node associated to this structure.

Implements bpp::TreeParsimonyNodeData.

Definition at line 100 of file DRTreeParsimonyData.h.

References node_.

Referenced by bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), and bpp::DRTreeParsimonyScore::computeScoresPreorderForNode().

getScoresArrayForNeighbor() [1/2]

std::vector<unsigned int>& bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor ( int  neighborId )

inline

Definition at line 112 of file DRTreeParsimonyData.h.

References nodeScores_.

Referenced by bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorderForNode(), bpp::DRTreeParsimonyData::init(), bpp::DRTreeParsimonyData::reInit(), and bpp::DRTreeParsimonyScore::testNNI().

getScoresArrayForNeighbor() [2/2]

const std::vector<unsigned int>& bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor ( int  neighborId ) const

inline

Definition at line 116 of file DRTreeParsimonyData.h.

References nodeScores_.

isNeighbor()

bool bpp::DRTreeParsimonyNodeData::isNeighbor ( int  neighborId ) const

inline

Definition at line 121 of file DRTreeParsimonyData.h.

References nodeBitsets_.

operator=()

DRTreeParsimonyNodeData& bpp::DRTreeParsimonyNodeData::operator= ( const DRTreeParsimonyNodeData &  tpnd )

inline

Definition at line 89 of file DRTreeParsimonyData.h.

References node_, nodeBitsets_, and nodeScores_.

setNode()

void bpp::DRTreeParsimonyNodeData::setNode ( const Node *  node )

inlinevirtual

Set the node associated to this data.

Parameters

node	A pointer toward the node to be associated to this data.

Implements bpp::TreeParsimonyNodeData.

Definition at line 102 of file DRTreeParsimonyData.h.

References node_.

Referenced by bpp::DRTreeParsimonyData::init(), and bpp::DRTreeParsimonyData::reInit().

Member Data Documentation

node_

const Node* bpp::DRTreeParsimonyNodeData::node_

private

Definition at line 74 of file DRTreeParsimonyData.h.

Referenced by getNode(), operator=(), and setNode().

nodeBitsets_

std::map<int, std::vector<Bitset> > bpp::DRTreeParsimonyNodeData::nodeBitsets_

mutableprivate

Definition at line 72 of file DRTreeParsimonyData.h.

Referenced by eraseNeighborArrays(), getBitsetsArrayForNeighbor(), isNeighbor(), and operator=().

nodeScores_

std::map<int, std::vector<unsigned int> > bpp::DRTreeParsimonyNodeData::nodeScores_

mutableprivate

Definition at line 73 of file DRTreeParsimonyData.h.

Referenced by eraseNeighborArrays(), getScoresArrayForNeighbor(), and operator=().

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

• Bpp/Phyl/Parsimony/DRTreeParsimonyData.h