error_model.cpp File Reference

#include <cctype>
#include <algorithm>
#include <vector>
#include <sstream>
#include <cfloat>
#include <iomanip>
#include <fstream>
#include <iostream>
#include <cmath>
#include "error_model.h"
#include "cafe_commands.h"
#include "gene_family.h"
#include "cafe_shell.h"

Data Structures
struct	to_lower

Functions
int	__check_error_model_columnsums (pErrorStruct errormodel)
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)
double	__loglikelihood_pairs_from_true_measure (double *parameters, void *args)
pErrorStruct	cafe_shell_create_error_matrix_from_estimate (pErrorMeasure errormeasure)
bool	case_insensitive_equal (std::string s1, std::string s2)
std::vector< std::string >	split (std::string str, char delimiter)
pErrorStruct	get_error_model (pCafeFamily family, std::string filename)
std::ostream &	operator<< (std::ostream &ost, ErrorStruct &errormodel)
std::istream &	operator>> (std::istream &ifst, ErrorStruct &errormodel)
void	init_error_ptr (pCafeFamily family, pCafeTree pTree, pErrorStruct errormodel, std::string speciesname)
int	set_error_matrix_from_file (pCafeFamily family, pCafeTree pTree, family_size_range &range, std::string filename, std::string speciesname)
int	remove_error_model (pCafeFamily family, pCafeTree pcafe, std::string species_name)
void	free_error_model (pCafeFamily family, pCafeTree pcafe)
void	read_freq_from_measures (std::istream *ist1, std::istream *ist2, int *sizeFreq, int &maxFamilySize)
void	read_error_double_measure (std::istream &ist1, std::istream &ist2, int **observed_pairs, int maxFamilySize)
double	get_marginal_error_probability_epsilon (pErrorMeasure errormeasure, double *parameters)
double	__loglikelihood_pairs_from_double_measure (double *parameters, void *args)
void	get_size_probability_distribution (int maxFamilySize, int *sizeFreq, double *sizeDist)
pErrorMeasure	estimate_error_double_measure (std::ostream &log, std::istream *ist1, std::istream *ist2, int b_symmetric, int max_diff, int b_peakzero, int max_FamilySize)
pErrorMeasure	estimate_error_true_measure (std::ostream &log, const char *errorfile, const char *truefile, int b_symmetric, int max_diff, int b_peakzero, int max_family_size)

Function Documentation

int __check_error_model_columnsums

(

pErrorStruct

errormodel

)

double __loglikelihood_pairs_from_double_measure	(	double *	parameters,
		void *	args
	)

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
	)

bool case_insensitive_equal	(	std::string	s1,
		std::string	s2
	)

pErrorMeasure estimate_error_double_measure	(	std::ostream &	log,
		std::istream *	ist1,
		std::istream *	ist2,
		int	b_symmetric,
		int	max_diff,
		int	b_peakzero,
		int	max_FamilySize
	)

pErrorMeasure estimate_error_true_measure	(	std::ostream &	log,
		const char *	errorfile,
		const char *	truefile,
		int	b_symmetric,
		int	max_diff,
		int	b_peakzero,
		int	max_family_size
	)

void free_error_model	(	pCafeFamily	family,
		pCafeTree	pcafe
	)

pErrorStruct get_error_model	(	pCafeFamily	family,
		std::string	filename
	)

double get_marginal_error_probability_epsilon	(	pErrorMeasure	errormeasure,
		double *	parameters
	)

void get_size_probability_distribution	(	int	maxFamilySize,
		int *	sizeFreq,
		double *	sizeDist
	)

void init_error_ptr	(	pCafeFamily	family,
		pCafeTree	pTree,
		pErrorStruct	errormodel,
		std::string	speciesname
	)

std::ostream& operator<<	(	std::ostream &	ost,
		ErrorStruct &	errormodel
	)

std::istream& operator>>	(	std::istream &	ifst,
		ErrorStruct &	errormodel
	)

void read_error_double_measure	(	std::istream &	ist1,
		std::istream &	ist2,
		int **	observed_pairs,
		int	maxFamilySize
	)

void read_freq_from_measures	(	std::istream *	ist1,
		std::istream *	ist2,
		int *	sizeFreq,
		int &	maxFamilySize
	)

int remove_error_model	(	pCafeFamily	family,
		pCafeTree	pcafe,
		std::string	species_name
	)

int set_error_matrix_from_file	(	pCafeFamily	family,
		pCafeTree	pTree,
		family_size_range &	range,
		std::string	filename,
		std::string	speciesname
	)

std::vector<std::string> split	(	std::string	str,
		char	delimiter
	)