reports.cpp File Reference

#include "../config.h"
#include <stdexcept>
#include <ostream>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <iterator>
#include <algorithm>
#include <strings.h>
#include "reports.h"
#include "likelihood_ratio.h"
#include "pvalue.h"
#include "branch_cutting.h"
#include "viterbi.h"
#include "Globals.h"
#include "cafe.h"

Functions
void	cafe_shell_set_lambda (pCafeParam param, double *lambda)
size_t	file_read_line (pString pstr, FILE *fp)
void	cafe_report_load_bc_or_lhr_list (char *data, double **pvalues, int i, int nnodes)
void	phylogeny_lambda_parse_func (pTree ptree, pTreeNode ptnode)
double *	cafe_report_load_data_double_list (char *data, int delimiter, int *num)
double *	cafe_report_load_data_double_pairs (char *data, int delimiter)
int *	cafe_report_load_data_int_pairs (char *data, int delimiter)
template<typename T , typename U >
std::ostream &	operator<< (ostream &ost, const std::pair< T, U > &pair)
template<typename T >
std::ostream &	operator<< (ostream &ost, const std::vector< T > &v)
	Writes a vector of arbitrary objects to a stream, separated by commas. More...
template<typename T >
std::vector< pair< T, T > >	to_pairs (const std::vector< T > &v)
	Converts a vector of objects to pairs of objects. More...
int	expanded (change c)
	Accepts a change structure and returns its expand value. More...
int	unchanged (change c)
	Accepts a change structure and returns its unchanged value. More...
int	decreased (change c)
	Accepts a change structure and returns its decrease value. More...
template<typename func >
std::vector< int >	get_change (const std::vector< change > &v, func f)
void	lambda_tree_string (pString pstr, pPhylogenyNode pnode)
void	cafe_report_set_viterbi (pCafeFamily family, pCafeTree pcafe, viterbi_parameters &viterbi, int i)
void	cafe_tree_string_id (pString pstr, pPhylogenyNode pnode)
string	quoted (string s)
void	write_viterbi (ostream &ost, const Report &viterbi)
void	write_families_header (ostream &ost, bool cutPvalues, bool likelihoodRatios)
void	write_doubles (ostream &ost, vector< double > items)
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)
std::ostream &	operator<< (std::ostream &ost, const family_line_item &item)
std::ostream &	operator<< (std::ostream &ost, const tree_visualization &viz)
std::ostream &	operator<< (ostream &ost, const Report &report)
report_parameters	get_report_parameters (std::vector< std::string > tokens)
string	extension (Report::Formats f)
void	set_format (ostream &ost, Report::Formats f)
void	cafe_do_report (Globals &globals, viterbi_parameters &viterbi, report_parameters *params)
void	cafe_report_load_viterbi_pvalue (char *data, viterbi_parameters &v, pCafeFamilyItem item, pCafeTree ptree)
int	cafe_report_retrieve_data (const char *file, pCafeParam param, viterbi_parameters &viterbi)
void	update_depths (pTreeNode node, std::map< int, double > &depths, double curr_depth)
void	calc_row (pTreeNode node, map< int, int > &positions)
map< int, int >	get_row_positions (pTree tree)
map< int, int >	get_col_positions (pTree tree, int drawing_width)
void	draw_clade (pTreeNode node, vector< string > &char_matrix, int startcol, map< int, int > &col_positions, map< int, int > &row_positions)

Variables
pTree	tmp_lambda_tree

Function Documentation

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

void cafe_report_load_bc_or_lhr_list	(	char *	data,
		double **	pvalues,
		int	i,
		int	nnodes
	)

double* cafe_report_load_data_double_list	(	char *	data,
		int	delimiter,
		int *	num
	)

double* cafe_report_load_data_double_pairs	(	char *	data,
		int	delimiter
	)

int* cafe_report_load_data_int_pairs	(	char *	data,
		int	delimiter
	)

void cafe_report_load_viterbi_pvalue	(	char *	data,
		viterbi_parameters &	v,
		pCafeFamilyItem	item,
		pCafeTree	ptree
	)

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

void cafe_report_set_viterbi	(	pCafeFamily	family,
		pCafeTree	pcafe,
		viterbi_parameters &	viterbi,
		int	i
	)

void cafe_shell_set_lambda	(	pCafeParam	param,
		double *	lambda
	)

void cafe_tree_string_id	(	pString	pstr,
		pPhylogenyNode	pnode
	)

void calc_row	(	pTreeNode	node,
		map< int, int > &	positions
	)

int decreased

(

change

c

)

Accepts a change structure and returns its decrease value.

void draw_clade	(	pTreeNode	node,
		vector< string > &	char_matrix,
		int	startcol,
		map< int, int > &	col_positions,
		map< int, int > &	row_positions
	)

int expanded

(

change

c

)

Accepts a change structure and returns its expand value.

string extension

(

Report::Formats

f

)

size_t file_read_line	(	pString	pstr,
		FILE *	fp
	)

template<typename func >

std::vector<int> get_change	(	const std::vector< change > &	v,
		func	f
	)

map<int, int> get_col_positions	(	pTree	tree,
		int	drawing_width
	)

report_parameters get_report_parameters

(

std::vector< std::string >

tokens

)

map<int, int> get_row_positions

(

pTree

tree

)

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.

void lambda_tree_string	(	pString	pstr,
		pPhylogenyNode	pnode
	)

template<typename T , typename U >

std::ostream& operator<<	(	ostream &	ost,
		const std::pair< T, U > &	pair
	)

Writes a pair of arbitrary objects to a stream, surrounded by brackets in JSON mode or parenthesis otherwise, and separated by a comma

template<typename T >

std::ostream& operator<<	(	ostream &	ost,
		const std::vector< T > &	v
	)

Writes a vector of arbitrary objects to a stream, separated by commas.

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

std::ostream& operator<<	(	std::ostream &	ost,
		const tree_visualization &	viz
	)

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

void phylogeny_lambda_parse_func	(	pTree	ptree,
		pTreeNode	ptnode
	)

string quoted

(

string

s

)

void set_format	(	ostream &	ost,
		Report::Formats	f
	)

template<typename T >

std::vector<pair<T, T> > to_pairs

(

const std::vector< T > &

v

)

Converts a vector of objects to pairs of objects.

int unchanged

(

change

c

)

Accepts a change structure and returns its unchanged value.

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

void write_doubles	(	ostream &	ost,
		vector< double >	items
	)

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

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

Variable Documentation

pTree tmp_lambda_tree