Ancestral recombination graph. More...

#include <Arg.hpp>

Public Member Functions
	Arg ()
	Default constructor. More...

void	set (Current *current, unsigned int numberOfSegments)
	Object initialization. More...

void	reset (Current *current)
	Object reset method. More...

	Arg (Current *current, unsigned int numberOfSegments)
	Standard constructor. More...

virtual	~Arg ()
	Destructor. More...

double	time () const
	Gets the current value of the time counter. More...

void	addTime (double increment)
	Increments the time counter. More...

void	coalescence (double incr, unsigned int pop, unsigned int index1, unsigned int index2)
	Performs a coalescence event. More...

void	coalescence (double incr, unsigned int pop, Random *random)
	Performs a coalescence event. More...

void	recombination (double incr, Random *random)
	Performs a recombination event. More...

Edge *	mute (unsigned int segment, double treePosition)
	Places a mutation. More...

double	ageUltimateMRCA () const
	Age of the uMRCA. More...

double	ageMRCA (unsigned int segmentIndex)
	Age of the MRCA for a given segment. More...

const Edge *	MRCA (unsigned int segmentIndex)
	MRCA for each segment. More...

const Edge *	uMRCA ()
	Ultimate MRCA.

std::string	newick (unsigned int segment)
	Formats the newick-formatted tree for a segment. More...

void	set_actualNumberOfSites (unsigned int actualNumberOfSites)
	Set the number of actual sites in all branches.

Public Attributes
unsigned int	numberOfSegments
	the number of recombining segments

unsigned int	numberOfSamples
	Number of initial lineages.

double	totalLength
	Total tree length (summed over all segments) More...

double *	segmentLengths
	Segment-specific tree length. More...

unsigned int	numberOfEdges
	Current number of Edges in the tree (including the MRCA node)

unsigned int	numberOfRecombinationEvents
	Total number of recombination events that occurred.

Detailed Description

Ancestral recombination graph.

This class stores the ARG (genealogical information). It is progressively built by appropriate (especially regarding to the timing) calls to coal() and recomb() methods. Then it can be used by a mutator class to generates data, or it can also generate newick trees (one tree by non-recombining segment).

Constructor & Destructor Documentation

Arg ( )

Default constructor.

Creates a null, useless, object.

Arg	(	Current *	current,
		unsigned int	numberOfSegments
	)

Standard constructor.

Parameters

current	address of the Current instance used by the simulator.
numberOfSegments	number of recombining segments

~Arg ( )

virtual

Destructor.

Clears all Edge instances referenced in the object.

Member Function Documentation

void addTime ( double increment )

Increments the time counter.

double ageMRCA ( unsigned int segmentIndex )

inline

Age of the MRCA for a given segment.

The MRCA is the Most Recent Common Ancestor, that is the point where the coalescent process is over (all lineages have coalesced). This member will have a meaningful value only if the coalescent process is completed.

Note that the value is cached; it is computed only one upon first call and no again, even if the Arg is modified<

double ageUltimateMRCA ( ) const

inline

Age of the uMRCA.

The uMRCA is the ultimate Most Recent Common Ancestor, that is the point where the last segment finds its most recent common ancestor. This member will have a meaningful value only if the coalescent process is completed.

void coalescence	(	double	incr,
		unsigned int	pop,
		unsigned int	index1,
		unsigned int	index2
	)

Performs a coalescence event.

For this version, the two lineages to coalesce are predefined.

Parameters

incr	increment of the time counter.
pop	index of the population.
index1	first lineage to coalesce.
index2	second lineage to coalesce.

void coalescence	(	double	incr,
		unsigned int	pop,
		Random *	random
	)

Performs a coalescence event.

For this version, the two lineages to coalesce are randomly picked in the given population

Parameters

incr	increment of the time counter.
pop	index of the population.
random	pointer to simulator's random generator instance.

const Edge* MRCA ( unsigned int segmentIndex )

inline

MRCA for each segment.

The MRCA is the Most Recent Common Ancestor, that is the point where the coalescent process is over (all lineages have coalesced). This member will have a meaningful value only if the coalescent process is completed.

Note that the value is cached; it is computed only one upon first call and no again, even if the Arg is modified

Edge * mute	(	unsigned int	segment,
		double	treePosition
	)

Places a mutation.

Parameters

segment	index of the segment affected.
treePosition	a random number placed on the interval defined by the tree length at this position.

Returns: the concerned Edge's address.

Another nerve-taking point: calling this method assume that all Edge of have previously undergone a call of branchLength(position) with intervalPosition - what should be done by the called (that is, Mutator) through my (Arg's) treeLength of something. BEWARE WHEN MODIFYING (enhancements should be directed to Edge in my view)

std::string newick ( unsigned int segment )

Formats the newick-formatted tree for a segment.

void recombination	(	double	incr,
		Random *	random
	)

Performs a recombination event.

Parameters

incr	increment of the time counter.
random	pointer to simulator's random generator instance.

void reset ( Current * current )

Object reset method.

This method doesn't reset all parameters (the number of segments and associated tables are retained, as well as the Edge object pool).

Parameters

current address of the Current instance used by the simulator.

void set	(	Current *	current,
		unsigned int	numberOfSegments
	)

Object initialization.

Parameters

current	address of the Current instance used by the simulator.
numberOfSegments	number of recombining segments.

double time ( ) const

Gets the current value of the time counter.

Member Data Documentation

double* segmentLengths

Segment-specific tree length.

double totalLength

Total tree length (summed over all segments)

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

/home/stephane/Documents/devel/egglib2/egglib-cpp/Arg.hpp
/home/stephane/Documents/devel/egglib2/egglib-cpp/Arg.cpp

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation