Edge Class Reference

Edge of the ancestral recombination graph. More...

#include <Edge.hpp>

Public Member Functions
virtual	~Edge ()
	Destructor.
	Edge (unsigned int numberOfSegments)
	Constructor. More...
void	reset ()
	Restore object to factory state.
void	coalescence (double date, Edge *son1, Edge *son2, unsigned int *edgesPerSegments, Edge **MRCA, double &totalLength, double *segmentLengths)
	Builds for internal node. More...
void	recombination (double date, Edge *dest1, Edge *dest2, Random *random, double &totalLength, double *segmentLengths)
	Generates a recombination event. More...
void	set_terminal (unsigned int leaf_index)
	Define this edge to be terminal. More...
bool	segment (unsigned int segmentIndex) const
	Checks if a given segment is covered.
unsigned int	label () const
	leaf index (0 for internal nodes)
void	set_actualNumberOfSites (unsigned int actualNumberOfSites)
	Sets the actual number of sites.

Public Attributes
double	length
	Branch's raw length (doesn't take account segment coverage)
unsigned int	coverage
	Number of covered segments.
double	bottom
	Time position of the branch's bottom.
double	top
	Time position of the branch's top.
Edge *	son1
	Address of the first son.
Edge *	son2
	Address of the second son.
unsigned int	numberOfSons
	Number of sons (0, 1 or 2)
unsigned int *	numberOfMutationsPerActualSite
	Number of mutations per segment.

Detailed Description

Edge of the ancestral recombination graph.

Each Edge instance provides access to its 0, 1 or 2 descendants (the former holds for a terminal node, the middle for the parent of a recombined node and the latter for the parent of a coalesced node (most classical node in the coalescent).The Edge also provides to the edge length. Note that the Edge instance must be understood as an ARG node and the branch above it (latter in the coalescence process). Edge instances also keep track of the list of descendants descending from this node (which may differ along recombining segment). Edge instances must be created through one of the "default" and "coalescence" constructors or through the recombination method. Edge instances should never be copied but manipulated by references.

Constructor & Destructor Documentation

Edge

(

unsigned int

numberOfSegments

)

Constructor.

Parameters

numberOfSegments

the number of recombining segments (one for a non-recombining region).

Use the Pool, instead. Objects are delivered with a complete coverage.

Member Function Documentation

void coalescence	(	double	date,
		Edge *	son1,
		Edge *	son2,
		unsigned int *	edgesPerSegments,
		Edge **	MRCA,
		double &	totalLength,
		double *	segmentLengths
	)

Builds for internal node.

Parameters

date	the date of creation of the edge.
son1	first edge descending from this edge.
son2	second edge descending from this edge.
edgesPerSegments	counts the current number of (non-coalesced lineages for each lineages); must have the appropriate size and will be updated.
MRCA	the list where to place the address of segment MRCA, if it occurs.
totalLength	the total length of the tree.
segmentLengths	the table of tree lengths per segment.

Assumes the current object has the correct number of segments.

void recombination	(	double	date,
		Edge *	dest1,
		Edge *	dest2,
		Random *	random,
		double &	totalLength,
		double *	segmentLengths
	)

Generates a recombination event.

Parameters

date	the date of the event.
dest1	destination for the first resulting edge.
dest2	destination for the second resulting edge.
random	pointer to the Random instance used by the simulator.
totalLength	the total length of the tree.
segmentLengths	the table of tree lengths per segment.

dest1 and dest2 must be Edge address initialized with the appropriate number of segments.

void set_terminal

(

unsigned int

leaf_index

)

Define this edge to be terminal.

The edge have only non-covered segments

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

• /home/stephane/Documents/devel/egglib2/egglib-cpp/Edge.hpp
• /home/stephane/Documents/devel/egglib2/egglib-cpp/Edge.cpp