SimTypes.hpp File Reference

declaration of types for coalescent simulation More...

#include <vector>
#include <list>
#include <iosfwd>
#include <cassert>
#include <memory>

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Classes
struct	Sequence::coalsim::segment
	A portion of a recombining chromosome. More...
struct	Sequence::coalsim::chromosome
	A chromosome is a container of segments. More...
struct	Sequence::coalsim::node
	A point on a marginal tree at which a coalescent event occurs. More...
struct	Sequence::coalsim::marginal
	The genealogy of a portion of a chromosome on which no recombination has occurred. More...
class	Sequence::coalsim::newick_stream_marginal_tree
	Class that provides a typecast-on-output of a marginal tree to a newick tree Example use: More...

Namespaces
	Sequence
	The namespace in which this library resides.
	Sequence::coalsim
	Routines for coalescent simulation.

Typedefs
typedef std::list< marginal >	Sequence::coalsim::arg
	Ancestral Recombination Graph. More...

Functions
std::ostream &	Sequence::coalsim::operator<< (std::ostream &s, const chromosome &c)
	output operator for chromosome types in coalescent simulation Outputs the segments contained by the chromosome
std::ostream &	Sequence::coalsim::operator<< (std::ostream &s, const marginal &m)
	Write a marginal tree to an ostream.
std::ostream &	Sequence::coalsim::operator<< (std::ostream &o, const newick_stream_marginal_tree &n)
std::istream &	Sequence::coalsim::operator>> (std::istream &i, newick_stream_marginal_tree &n)

Detailed Description

declaration of types for coalescent simulation

Definition in file SimTypes.hpp.