bpp::PhyloStatistics Class Reference

Compute several quantities on a tree simulateously, optimizing the recursions on the tree. More...

#include <Bpp/Phyl/PhyloStatistics.h>

Inheritance diagram for bpp::PhyloStatistics:

Collaboration diagram for bpp::PhyloStatistics:

Public Member Functions
	PhyloStatistics ()
virtual	~PhyloStatistics ()
PhyloStatistics *	clone () const
void	setTree (const Tree &tree)
	Compute statistics for a given input tree. More...
size_t	getNumberOfLeaves () const
size_t	getNumberOfAncestors () const
const std::vector< double > &	getBranchLengths () const
const std::vector< double > &	getNodeHeights () const
const std::vector< size_t > &	getNodeDepths () const
const std::vector< size_t > &	getNodeNumberOfSons () const
const std::vector< int > &	getNodeIds () const

Private Member Functions
void	computeForSubtree_ (const Node *node, double &height, size_t &depth)

Private Attributes
size_t	numberOfLeaves_
size_t	numberOfAncestors_
std::vector< double >	branchLengths_
std::vector< double >	nodeHeights_
std::vector< size_t >	nodeDepths_
std::vector< size_t >	nodeNumberOfSons_
std::vector< int >	nodeIds_

Detailed Description

Compute several quantities on a tree simulateously, optimizing the recursions on the tree.

This class uses a TreeTemplate. If the input tree is not a TreeTemplate, then a copy is performed before any computation.

See also

TreeTools, TreeTemplateTools.

Definition at line 25 of file PhyloStatistics.h.

Constructor & Destructor Documentation

PhyloStatistics()

bpp::PhyloStatistics::PhyloStatistics ( )

inline

Definition at line 38 of file PhyloStatistics.h.

Referenced by clone().

~PhyloStatistics()

virtual bpp::PhyloStatistics::~PhyloStatistics ( )

inlinevirtual

Definition at line 42 of file PhyloStatistics.h.

Member Function Documentation

clone()

PhyloStatistics * bpp::PhyloStatistics::clone ( ) const

inlinevirtual

Implements bpp::Clonable.

Definition at line 44 of file PhyloStatistics.h.

References PhyloStatistics().

computeForSubtree_()

void PhyloStatistics::computeForSubtree_ ( const Node *  node, double &  height, size_t &  depth  )

private

Definition at line 39 of file PhyloStatistics.cpp.

References branchLengths_, computeForSubtree_(), bpp::Node::getDistanceToFather(), bpp::Node::getNumberOfSons(), bpp::Node::hasDistanceToFather(), bpp::Node::isLeaf(), bpp::log(), nodeDepths_, nodeHeights_, nodeNumberOfSons_, numberOfAncestors_, and numberOfLeaves_.

Referenced by computeForSubtree_(), and setTree().

getBranchLengths()

const std::vector< double > & bpp::PhyloStatistics::getBranchLengths ( ) const

inline

Definition at line 55 of file PhyloStatistics.h.

References branchLengths_.

getNodeDepths()

const std::vector< size_t > & bpp::PhyloStatistics::getNodeDepths ( ) const

inline

Definition at line 57 of file PhyloStatistics.h.

References nodeDepths_.

getNodeHeights()

const std::vector< double > & bpp::PhyloStatistics::getNodeHeights ( ) const

inline

Definition at line 56 of file PhyloStatistics.h.

References nodeHeights_.

getNodeIds()

const std::vector< int > & bpp::PhyloStatistics::getNodeIds ( ) const

inline

Definition at line 59 of file PhyloStatistics.h.

References nodeIds_.

getNodeNumberOfSons()

const std::vector< size_t > & bpp::PhyloStatistics::getNodeNumberOfSons ( ) const

inline

Definition at line 58 of file PhyloStatistics.h.

References nodeNumberOfSons_.

getNumberOfAncestors()

size_t bpp::PhyloStatistics::getNumberOfAncestors ( ) const

inline

Definition at line 54 of file PhyloStatistics.h.

References numberOfAncestors_.

getNumberOfLeaves()

size_t bpp::PhyloStatistics::getNumberOfLeaves ( ) const

inline

Definition at line 53 of file PhyloStatistics.h.

References numberOfLeaves_.

setTree()

void PhyloStatistics::setTree

(

const Tree &

tree

)

Compute statistics for a given input tree.

Parameters

tree	The tree for which the statistics should be computed.

Definition at line 12 of file PhyloStatistics.cpp.

References branchLengths_, computeForSubtree_(), bpp::TreeTemplate< N >::getRootNode(), nodeDepths_, nodeHeights_, nodeIds_, nodeNumberOfSons_, numberOfAncestors_, and numberOfLeaves_.

Member Data Documentation

branchLengths_

std::vector<double> bpp::PhyloStatistics::branchLengths_

private

Definition at line 31 of file PhyloStatistics.h.

Referenced by computeForSubtree_(), getBranchLengths(), and setTree().

nodeDepths_

std::vector<size_t> bpp::PhyloStatistics::nodeDepths_

private

Definition at line 33 of file PhyloStatistics.h.

Referenced by computeForSubtree_(), getNodeDepths(), and setTree().

nodeHeights_

std::vector<double> bpp::PhyloStatistics::nodeHeights_

private

Definition at line 32 of file PhyloStatistics.h.

Referenced by computeForSubtree_(), getNodeHeights(), and setTree().

nodeIds_

std::vector<int> bpp::PhyloStatistics::nodeIds_

private

Definition at line 35 of file PhyloStatistics.h.

Referenced by getNodeIds(), and setTree().

nodeNumberOfSons_

std::vector<size_t> bpp::PhyloStatistics::nodeNumberOfSons_

private

Definition at line 34 of file PhyloStatistics.h.

Referenced by computeForSubtree_(), getNodeNumberOfSons(), and setTree().

numberOfAncestors_

size_t bpp::PhyloStatistics::numberOfAncestors_

private

Definition at line 30 of file PhyloStatistics.h.

Referenced by computeForSubtree_(), getNumberOfAncestors(), and setTree().

numberOfLeaves_

size_t bpp::PhyloStatistics::numberOfLeaves_

private

Definition at line 29 of file PhyloStatistics.h.

Referenced by computeForSubtree_(), getNumberOfLeaves(), and setTree().

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

• Bpp/Phyl/PhyloStatistics.h
• Bpp/Phyl/PhyloStatistics.cpp