Sequence::marginal Struct Reference
[Classes and functions related to simulating data under coalescent models]

The genealogy of a portion of a chromosome on which no recombination has occurred. More...

#include <Sequence/Coalescent/SimTypes.hpp>

List of all members.

Public Types
typedef std::vector< node > ::iterator	iterator
typedef std::vector< node > ::const_iterator	const_iterator
typedef std::vector< node > ::size_type	size_type
typedef std::vector< node > ::reference	reference
typedef std::vector< node > ::const_reference	const_reference
Public Member Functions
iterator	begin ()
iterator	end ()
const_iterator	begin () const
const_iterator	end () const
reference	operator[] (const std::vector< node >::size_type &i)
const_reference	operator[] (const std::vector< node >::size_type &i) const
	marginal (const int &b, const int &ns, const int &nn, const std::vector< node > &tree)
bool	operator< (const marginal &rhs) const
Public Attributes
int	beg
int	nsam
int	nnodes
std::vector< node >	tree

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Detailed Description

The genealogy of a portion of a chromosome on which no recombination has occurred.

A marginal history is a coalscent tree for a region in which no recombination has occured in the history of a sample. A sorted list of marginal trees is the ancstral recombination graph for a recombining region, and the typedef std::list<marginal> arg is used in this library

Examples:

bottleneck.cc, fragments.cc, freerec.cc, ms--.cc, and msbeta.cc.

Definition at line 164 of file SimTypes.hpp.

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Constructor & Destructor Documentation

Sequence::marginal::marginal	(	const int &	b,
		const int &	ns,
		const int &	nn,
		const std::vector< node > &	t
	)

Parameters:

	b	beg
	ns	nsam
	nn	nnodes
	t	tree

Definition at line 194 of file CoalescentSimTypes.cc.

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Member Function Documentation

marginal::const_iterator Sequence::marginal::begin

(

)

const

Returns:

this->tree.begin();

Definition at line 223 of file CoalescentSimTypes.cc.

marginal::iterator Sequence::marginal::begin

(

)

Returns:

this->tree.begin();

Definition at line 207 of file CoalescentSimTypes.cc.

marginal::const_iterator Sequence::marginal::end

(

)

const

Returns:

this->tree.end();

Definition at line 231 of file CoalescentSimTypes.cc.

marginal::iterator Sequence::marginal::end

(

)

Returns:

this->tree.end();

Definition at line 215 of file CoalescentSimTypes.cc.

bool Sequence::marginal::operator<

(

const marginal &

rhs

)

const

return this->beg < rhs.beg;

Definition at line 259 of file CoalescentSimTypes.cc.

marginal::const_reference Sequence::marginal::operator[]

(

const std::vector< node >::size_type &

i

)

const

Returns:

this->tree[i]

Warning:

Range checking by assert only!

Definition at line 249 of file CoalescentSimTypes.cc.

marginal::reference Sequence::marginal::operator[]

(

const std::vector< node >::size_type &

i

)

Returns:

this->tree[i]

Warning:

Range checking by assert only!

Definition at line 239 of file CoalescentSimTypes.cc.

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Member Data Documentation

int Sequence::marginal::beg

The (mutational) site at which the current marginal tree begins

Definition at line 169 of file SimTypes.hpp.

int Sequence::marginal::nnodes

The current number of nodes in the tree. By current, it is meant the current time in the simulation. At the start of a simulation of a sample size of k chromosomes, this should be initialized to k. This value is manipulated as nodes are added into the marginal history by the coalesce function.

Definition at line 182 of file SimTypes.hpp.

int Sequence::marginal::nsam [mutable]

The sample size being simulated. The 2*nsam-1 nodes in the tree are therefore indexed from 0 to 2*nsam-2

Definition at line 174 of file SimTypes.hpp.

std::vector<node> Sequence::marginal::tree

tree is the coalescent history of this marginal tree

Definition at line 186 of file SimTypes.hpp.

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

• SimTypes.hpp
• CoalescentSimTypes.cc