patprob.c File Reference

Calculate site pattern probabilities. More...

#include "patprob.h"
#include "misc.h"
#include "network.h"
#include "branchtab.h"
#include "parse.h"
#include "parstore.h"
#include "binary.h"
#include <stdlib.h>
#include <string.h>
#include <sys/types.h>
#include <time.h>
#include <unistd.h>
#include <limits.h>
#include <gsl/gsl_rng.h>

Data Structures
struct	ThreadArg
	Data structure used by each thread. More...

Functions
static ThreadArg *	ThreadArg_new (const void *network, unsigned nreps, int doSing)
	Construct a new ThreadArg by copying a template.
static void	ThreadArg_free (ThreadArg *self)
	ThreadArg destructor.
static int	tfunc (void *varg, void *tdata)
	function run by each thread
BranchTab *	get_brlen (const void *network, long nreps, int doSing, double min_brlen, gsl_rng *rng)
	Estimate branch lengths. More...

Detailed Description

Calculate site pattern probabilities.

Author

Alan R. Rogers

Copyright

Copyright (c) 2016, Alan R. Rogers roger.nosp@m.s@an.nosp@m.thro..nosp@m.utah.nosp@m..edu. This file is released under the Internet Systems Consortium License, which can be found in file "LICENSE".

Function Documentation

get_brlen()

BranchTab * get_brlen	(	const void *	network,
		long	nreps,
		int	doSing,
		double	min_brlen,
		gsl_rng *	rng
	)

Estimate branch lengths.

Function returns a pointer to a newly-allocated object of type BranchTab, which contains all the observed site patterns and their mean branch lengths.

References BranchTab_add(), BranchTab_size(), tfunc(), and ThreadArg_new().

Referenced by costFun().