cafe_shell.c File Reference

Functions corresponding to the commands available in Cafe. More...

#include <mathfunc.h>
#include <ctype.h>
#include <assert.h>
#include <float.h>
#include <stdarg.h>
#include <stdio.h>
#include "cafe.h"
#include "cafe_shell.h"

Macros
#define	STDERR_IF(a, b)   if ( a ) { fprintf(stderr,b); return -1; }

Functions
void	cafe_shell_set_lambda (pCafeParam param, double *lambda)
void	cafe_shell_set_lambda_mu (pCafeParam param, double *parameters)
void	cafe_shell_set_lambdas (pCafeParam param, double *lambda)
void	reset_k_likelihoods (pCafeNode pcnode, int k, int num_factors)
void	set_birth_death_probabilities (struct probabilities *probs, int num_lambdas, int first_mu, int fix_cluster, double *parameters)
void	set_birth_death_probabilities2 (struct probabilities *probs, int num_lambdas, int first_mu, int fix_cluster, int taxa_id, int eqbg, double *parameters)
void	set_birth_death_probabilities4 (struct probabilities *probs, int num_lambdas, int fix_cluster, int taxa_id, double *parameters)
void	initialize_z_membership (pCafeParam param)
void	initialize_k_bd (pCafeTree pcafe, pTree lambda_tree, int num_values, int fixcluster, double *parameters)
void	initialize_k_bd2 (pCafeParam param, double *parameters)
void	cafe_shell_set_branchlength (pCafeParam param, int max_family_size)
void	phylogeny_lambda_parse_func (pTree ptree, pTreeNode ptnode)
int	__cafe_cmd_lambda_tree (pCafeParam param, char *arg1, char *arg2)
void	set_range_from_family (family_size_range *range, pCafeFamily family)
void	__cafe_tree_string_gainloss (pString pstr, pPhylogenyNode ptnode)
void	__cafe_tree_string_sum_gainloss (pString pstr, pPhylogenyNode ptnode)
double	__cafe_tree_gainloss_mp_annotation (pString pstr, pTreeNode pnode, pMetapostConfig pmc, va_list ap)
double	cafe_tree_mp_remark (pString pstr, pTree ptree, pMetapostConfig pmc, va_list ap1)
int	__cafe_cmd_extinct_count_zero (pTree pcafe)
double	__hg_norm_cdf_func (double p, double *args)
void	__hg_print_sim_extinct (pHistogram **phist_sim_n, pHistogram *phist_sim, int r, pHistogram phist_tmp, double *cnt, int num_trials)
void	cafe_shell_free_errorstruct (pErrorStruct errormodel)
int	cafe_shell_read_error_true_measure (const char *errorfile, const char *truefile, int **observed_pairs, int maxFamilySize)
int	__check_error_model_columnsums (pErrorStruct errormodel)
pErrorStruct	cafe_shell_create_error_matrix_from_estimate (pErrorMeasure errormeasure)
double	__loglikelihood_pairs_from_true_measure (double *parameters, void *args)

Variables
pCafeParam	cafe_param
	Holds the global program state that user commands act on. More...
pTree	tmp_lambda_tree

Detailed Description

Functions corresponding to the commands available in Cafe.

Command list is found in the #cafe_cmd function

Macro Definition Documentation

#define STDERR_IF	(		a,
			b
	)		if ( a ) { fprintf(stderr,b); return -1; }

Function Documentation

int __cafe_cmd_extinct_count_zero

(

pTree

pcafe

)

int __cafe_cmd_lambda_tree	(	pCafeParam	param,
		char *	arg1,
		char *	arg2
	)

double __cafe_tree_gainloss_mp_annotation	(	pString	pstr,
		pTreeNode	pnode,
		pMetapostConfig	pmc,
		va_list	ap
	)

void __cafe_tree_string_gainloss	(	pString	pstr,
		pPhylogenyNode	ptnode
	)

void __cafe_tree_string_sum_gainloss	(	pString	pstr,
		pPhylogenyNode	ptnode
	)

int __check_error_model_columnsums

(

pErrorStruct

errormodel

)

double __hg_norm_cdf_func	(	double	p,
		double *	args
	)

void __hg_print_sim_extinct	(	pHistogram **	phist_sim_n,
		pHistogram *	phist_sim,
		int	r,
		pHistogram	phist_tmp,
		double *	cnt,
		int	num_trials
	)

double __loglikelihood_pairs_from_true_measure	(	double *	parameters,
		void *	args
	)

pErrorStruct cafe_shell_create_error_matrix_from_estimate

(

pErrorMeasure

errormeasure

)

void cafe_shell_free_errorstruct

(

pErrorStruct

errormodel

)

int cafe_shell_read_error_true_measure	(	const char *	errorfile,
		const char *	truefile,
		int **	observed_pairs,
		int	maxFamilySize
	)

void cafe_shell_set_branchlength	(	pCafeParam	param,
		int	max_family_size
	)

void cafe_shell_set_lambda	(	pCafeParam	param,
		double *	lambda
	)

void cafe_shell_set_lambda_mu	(	pCafeParam	param,
		double *	parameters
	)

void cafe_shell_set_lambdas	(	pCafeParam	param,
		double *	lambda
	)

double cafe_tree_mp_remark	(	pString	pstr,
		pTree	ptree,
		pMetapostConfig	pmc,
		va_list	ap1
	)

void initialize_k_bd	(	pCafeTree	pcafe,
		pTree	lambda_tree,
		int	num_values,
		int	fixcluster,
		double *	parameters
	)

void initialize_k_bd2	(	pCafeParam	param,
		double *	parameters
	)

void initialize_z_membership

(

pCafeParam

param

)

void phylogeny_lambda_parse_func	(	pTree	ptree,
		pTreeNode	ptnode
	)

void reset_k_likelihoods	(	pCafeNode	pcnode,
		int	k,
		int	num_factors
	)

void set_birth_death_probabilities	(	struct probabilities *	probs,
		int	num_lambdas,
		int	first_mu,
		int	fix_cluster,
		double *	parameters
	)

void set_birth_death_probabilities2	(	struct probabilities *	probs,
		int	num_lambdas,
		int	first_mu,
		int	fix_cluster,
		int	taxa_id,
		int	eqbg,
		double *	parameters
	)

void set_birth_death_probabilities4	(	struct probabilities *	probs,
		int	num_lambdas,
		int	fix_cluster,
		int	taxa_id,
		double *	parameters
	)

void set_range_from_family	(	family_size_range *	range,
		pCafeFamily	family
	)

Variable Documentation

pCafeParam cafe_param

Holds the global program state that user commands act on.

pTree tmp_lambda_tree