cafe_main.c File Reference

#include "cafe.h"
#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include <pthread.h>
#include <mathfunc.h>
#include <memalloc.h>
#include <utils.h>

Data Structures
struct	LRTParam

Typedefs
typedef LRTParam *	pLRTParam

Functions
void	cafe_log (pCafeParam param, const char *msg,...)
	Logs the message and parameters in a standard way. More...
void	cafe_free_birthdeath_cache (pCafeTree pcafe)
void	copy_range_to_tree (pCafeTree tree, family_size_range *range)
void	thread_run (int numthreads, void *(*run)(void *), void *param, int size)
void	thread_run_with_arraylist (int numthreads, void *(*run)(void *), pArrayList pal)
void	cafe_lambda_set_default (pCafeParam param, double *lambda)
void	show_sizes (FILE *f, pCafeTree pcafe, family_size_range *range, pCafeFamilyItem pitem, int i)
void	input_values_randomize (input_values *vals, int lambda_len, int mu_len, int k, int kfix, double max_branch_length, double *k_weights)
double	cafe_get_clustered_posterior (pCafeParam param, double *ML, double *MAP, double *prior_rfsize)
double	__lnLGamma (double *palphabeta, void *data)
double	__cafe_cluster_lambda_search (double *parameters, void *args)
void	reset_birthdeath_cache (pCafeTree tree, int k_value, family_size_range *range)
double	__cafe_each_best_lambda_search (double *plambda, void *args)
double *	cafe_each_best_lambda_by_fminsearch (pCafeParam param, int lambda_len)
void *	__cafe_likelihood_ratio_test_thread_func (pLRTParam plrt)
void	cafe_likelihood_ratio_test (pCafeParam param, double *maximumPvalues)

Variables
pBirthDeathCacheArray	probability_cache = NULL
struct chooseln_cache	cache
	A cache of values of chooseln. More...
int	chooseln_cache_size
pthread_mutex_t	mutex_cafe_likelihood = PTHREAD_MUTEX_INITIALIZER

Typedef Documentation

typedef LRTParam* pLRTParam

Function Documentation

double __cafe_cluster_lambda_search	(	double *	parameters,
		void *	args
	)

double __cafe_each_best_lambda_search	(	double *	plambda,
		void *	args
	)

void* __cafe_likelihood_ratio_test_thread_func

(

pLRTParam

plrt

)

double __lnLGamma	(	double *	palphabeta,
		void *	data
	)

double* cafe_each_best_lambda_by_fminsearch	(	pCafeParam	param,
		int	lambda_len
	)

void cafe_free_birthdeath_cache

(

pCafeTree

pcafe

)

double cafe_get_clustered_posterior	(	pCafeParam	param,
		double *	ML,
		double *	MAP,
		double *	prior_rfsize
	)

void cafe_lambda_set_default	(	pCafeParam	param,
		double *	lambda
	)

void cafe_likelihood_ratio_test	(	pCafeParam	param,
		double *	maximumPvalues
	)

void cafe_log	(	pCafeParam	param,
		const char *	msg,
			...
	)

Logs the message and parameters in a standard way.

If the user has assigned a file for logging, message is written to the file and also to stdout. The stdout write will be suppressed if the param "quiet" flag is set.

void copy_range_to_tree	(	pCafeTree	tree,
		family_size_range *	range
	)

void input_values_randomize	(	input_values *	vals,
		int	lambda_len,
		int	mu_len,
		int	k,
		int	kfix,
		double	max_branch_length,
		double *	k_weights
	)

void reset_birthdeath_cache	(	pCafeTree	tree,
		int	k_value,
		family_size_range *	range
	)

void show_sizes	(	FILE *	f,
		pCafeTree	pcafe,
		family_size_range *	range,
		pCafeFamilyItem	pitem,
		int	i
	)

void thread_run	(	int	numthreads,
		void *(*)(void *)	run,
		void *	param,
		int	size
	)

void thread_run_with_arraylist	(	int	numthreads,
		void *(*)(void *)	run,
		pArrayList	pal
	)

Variable Documentation

struct chooseln_cache cache

A cache of values of chooseln.

Chooseln evaluates the natural logarithm of Gamma(n+1)/(Gamma(k+1)*Gamma(n-k+1)) The cache holds values for integer values of n and k. It does not appear to be threadsafe.

P(X(t) = c | X(0) = s) = {j=0}^{(s,c)} {s}{j}{s+c-j-1}{s-1} ^{s+c-2j}(1-2)^j

int chooseln_cache_size

pthread_mutex_t mutex_cafe_likelihood = PTHREAD_MUTEX_INITIALIZER

pBirthDeathCacheArray probability_cache = NULL

The variable cafe_param is a global singleton that holds general program state. cafe_param holds pcafe, a CafeTree, and pfamily, a CafeFamily . These are set by the user via the commands "tree" and "load" respectively. When the user calls the command "lambda" calculations are performed on the pcafe and pfamily variables.