A chromosome is a container of segments. More...

#include <Sequence/Coalescent/SimTypes.hpp>

Public Types
typedef segment *	iterator

typedef const segment *	const_iterator

Public Member Functions
	chromosome ()
	constructor sets segs to NULL, pop to 0, and nsegs to 0

	chromosome (const chromosome &ch)
	copy constructor

	chromosome (const std::vector< segment > &initial_segs, const int &population=0)
	constructor More...

	~chromosome ()

chromosome &	operator= (const chromosome &ch)
	assignment operator

void	swap_with (chromosome &ch)

void	assign_allocated_segs (segment *newsegs, const unsigned &new_nsegs)

int	first () const

int	last () const

int	links () const

iterator	begin ()

iterator	end ()

const_iterator	begin () const

const_iterator	end () const

Public Attributes
segment *	segs

int	pop

unsigned	nsegs

Detailed Description

A chromosome is a container of segments.

Note: this is a malloc-based container

Definition at line 92 of file SimTypes.hpp.

Constructor & Destructor Documentation

◆ chromosome()

Sequence::coalsim::chromosome::chromosome	(	const std::vector< segment > &	initial_segs,
		const int &	population = `0`
	)

constructor

Parameters

initial_segs	a vector of segments
population	used to set pop

Note: nsegs is set to initial_segs.size()

Definition at line 63 of file CoalescentSimTypes.cc.

◆ ~chromosome()

Sequence::coalsim::chromosome::~chromosome ( )

frees pointer to segments

Definition at line 79 of file CoalescentSimTypes.cc.

Member Function Documentation

◆ assign_allocated_segs()

void Sequence::coalsim::chromosome::assign_allocated_segs	(	segment *	newsegs,
		const unsigned &	new_nsegs
	)

Replaces the current segs with those pointed to by newsegs

Parameters

newsegs	an array of segments allocated with malloc
new_nsegs	the number of segs stored in newsegs

Definition at line 133 of file CoalescentSimTypes.cc.

◆ begin() [1/2]

chromosome::iterator Sequence::coalsim::chromosome::begin ( )

Returns: segs

Definition at line 146 of file CoalescentSimTypes.cc.

◆ begin() [2/2]

chromosome::const_iterator Sequence::coalsim::chromosome::begin ( ) const

Returns: segs

Definition at line 162 of file CoalescentSimTypes.cc.

◆ end() [1/2]

chromosome::iterator Sequence::coalsim::chromosome::end ( )

Returns: segs+nsegs

Definition at line 154 of file CoalescentSimTypes.cc.

◆ end() [2/2]

chromosome::const_iterator Sequence::coalsim::chromosome::end ( ) const

Returns: segs+nsegs

Definition at line 170 of file CoalescentSimTypes.cc.

◆ first()

int Sequence::coalsim::chromosome::first ( ) const

inline

Returns: the first position in the chromosome

Definition at line 125 of file SimTypes.hpp.

◆ last()

int Sequence::coalsim::chromosome::last ( ) const

inline

Returns: the last position in the chromosome

Definition at line 134 of file SimTypes.hpp.

◆ links()

int Sequence::coalsim::chromosome::links ( ) const

Computes and returns the number of positions at which recombination can occur in the chromosome

Returns: (segs+nsegs-1)->end - segs->beg

Definition at line 178 of file CoalescentSimTypes.cc.

◆ swap_with()

void Sequence::coalsim::chromosome::swap_with ( chromosome & ch )

Swaps the data members of the current chromosome with chromosome ch. Called by the coalesce routine, and is necessary to prevent nastiness such as multiple calls to free when vectors of chromosomes go out of scope. Implemented as: std::swap(this->segs,ch.segs); std::swap(this->nsegs,ch.nsegs); std::swap(this->pop,ch.pop);

Definition at line 117 of file CoalescentSimTypes.cc.

Member Data Documentation

◆ nsegs

unsigned Sequence::coalsim::chromosome::nsegs

The number of segments contained in the pointer segs

Definition at line 115 of file SimTypes.hpp.

◆ pop

int Sequence::coalsim::chromosome::pop

the population in which the chromosome is currently found

Definition at line 111 of file SimTypes.hpp.

◆ segs

segment* Sequence::coalsim::chromosome::segs

The list of segments making up the ancestral material of a chromosome at the current point in the simulation.

Note: Please be aware that allocation of this array is done via malloc, rather than operator new. As coalescent simulations are all about copying segments, the use of malloc is more efficient for simulation purposes, as it results in many fewer calls to the default constructor. But this means you cannot assign to this pointer something allocated with operator new, else bad things will happen.

Definition at line 105 of file SimTypes.hpp.

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

Public Types

Public Member Functions

Public Attributes