reports.h File Reference

#include <vector>
#include <string>
#include "cafe_shell.h"
#include "family.h"
#include "viterbi.h"

Go to the source code of this file.

Data Structures
struct	family_line_item
class	tree_visualization
class	newick_visualization
struct	coord
class	svg_visualization
class	ascii_visualization
struct	Report
struct	report_parameters

Functions
void	update_depths (pTreeNode node, std::map< int, double > &depths, double curr_depth)
report_parameters	get_report_parameters (std::vector< std::string > tokens)
int	cafe_cmd_report (Globals &globals, std::vector< std::string > tokens)
	Report: Generates reports in various formats of the calculations completed More...
void	write_viterbi (std::ostream &ost, const Report &viterbi)
void	write_families_header (std::ostream &ost, bool cutPvalues, bool likelihoodRatios)
void	cafe_do_report (Globals &globals, viterbi_parameters &viterbi, report_parameters *params)
int	cafe_report_retrieve_data (const char *file, pCafeParam param, viterbi_parameters &viterbi)
std::ostream &	operator<< (std::ostream &ost, const family_line_item &item)
std::ostream &	operator<< (std::ostream &ost, const Report &report)
std::ios_base &	json (std::ios_base &os)
	These I/O manipulators allow selecting the report format. More...
std::ios_base &	html (std::ios_base &os)

Function Documentation

void cafe_do_report	(	Globals &	globals,
		viterbi_parameters &	viterbi,
		report_parameters *	params
	)

int cafe_report_retrieve_data	(	const char *	file,
		pCafeParam	param,
		viterbi_parameters &	viterbi
	)

report_parameters get_report_parameters

(

std::vector< std::string >

tokens

)

std::ios_base& html

(

std::ios_base &

os

)

std::ios_base& json

(

std::ios_base &

os

)

These I/O manipulators allow selecting the report format.

std::ostream& operator<<	(	std::ostream &	ost,
		const family_line_item &	item
	)

std::ostream& operator<<	(	std::ostream &	ost,
		const Report &	report
	)

void update_depths	(	pTreeNode	node,
		std::map< int, double > &	depths,
		double	curr_depth
	)

void write_families_header	(	std::ostream &	ost,
		bool	cutPvalues,
		bool	likelihoodRatios
	)

void write_viterbi	(	std::ostream &	ost,
		const Report &	viterbi
	)