bbq Implementation Documentation

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main.cpp File Reference

#include <ctype.h>
#include <iostream>
#include <fstream>
#include <list>
#include <stdio.h>
#include <map>
#include <string>
#include "footprint_detector.h"
#include "weighted_bitsets.h"
#include "weighted_footprint_detector.h"

Defines
#define	CHUNK_SIZE   4096
Functions
void	fill_reverse_segments ()
bool	read_genome (char *fname, int i)
	reads fname (in fasta format) into T[i].
void	skip (std::ifstream &ifs)
	read over all useless characters such as spaces, tabs and line breaks
bool	read_parameters (int argc, char **argv)
void	print_help_message ()
void	read_data (int argc, char **argv)
void	free_all ()
void	test_unweighted ()
int	main (int argc, char **argv)
	Use bbq as follows:.
Variables
char **	T
char **	s
char **	s_names
int *	n
int *	N
int *	m
int	L
int	k
int	K
std::set< std::string >	groups
std::map< std::string, std::list< std::string > >	group_members
bool	params_good
	Are the parameters passed to the program legal?
int	num_of_opts
	number of command-line options
int	num_of_hits
	number of hits to be computed
float	threshold
	for -t option; threshold <0.
bool	count_results
	if the threshold was specified by -tc rather than by -t , we only count solutions -- instead of printing every solution -- matching the threshold.
bool	reverse
	consider reverse complemented segments also?
bool	report_progress
	print progress report while algorithm is running?
int	algorithm
	choose algorithm (A1) (default) or (A2)
bool	weighted
	false if -u option (unweighted) is given.
int	weight_type
	see weighted_footprint_detector::weight_type for a description of different weight types available.
bool	grouped
	group fragments into classes based on the first four letters
bool	use_multisets
	true if multiple occurences within one cluster are to make a difference.
bool	ps_output
	true if postscript output (-P ) was specified.
std::string	ps_file_name
bool	stupid_user
	give more verbose output for stupid users
int	num_of_group_characters
	see documentation of weighted_footprint_detector::num_of_group_characters
bool	bounded_difference
	Use a fast algorithm that only takes into account matches where (set theoretic) difference between the sets involved in the match is bounded by delta.
int	delta
	bound for the number of non-matching fragments contined in a match.

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Define Documentation

#define CHUNK_SIZE   4096

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Function Documentation

void fill_reverse_segments (   )

void free_all (   )

int main (  int  argc, char **  argv )

Use bbq as follows:. bbq <footprint-file> ... , where is an integer indicating the cluster length to optimize for, <footprint-file> is a filename as well as ... .

void print_help_message (   )

void read_data (  int  argc, char **  argv )

bool read_genome (  char *  fname, int  i )

reads fname (in fasta format) into T[i].

bool read_parameters (  int  argc, char **  argv )

void skip (  std::ifstream &  ifs  )

read over all useless characters such as spaces, tabs and line breaks

void test_unweighted (   )

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Variable Documentation

int algorithm

choose algorithm (A1) (default) or (A2)

bool bounded_difference

Use a fast algorithm that only takes into account matches where (set theoretic) difference between the sets involved in the match is bounded by delta.

bool count_results

if the threshold was specified by -tc rather than by -t , we only count solutions -- instead of printing every solution -- matching the threshold. This feature can be very useful to find a suitable threshold that yields a reasonable number of matches.

int delta

bound for the number of non-matching fragments contined in a match. The bound delta is taken into account if bounded_difference=true (using command line option -D).

std::map< std::string,std::list<std::string> > group_members

bool grouped

group fragments into classes based on the first four letters

std::set<std::string> groups

int K

int k

int L

int* m

int* N

int* n

int num_of_group_characters

see documentation of weighted_footprint_detector::num_of_group_characters

int num_of_hits

number of hits to be computed

int num_of_opts

number of command-line options

bool params_good

Are the parameters passed to the program legal?

std::string ps_file_name

bool ps_output

true if postscript output (-P ) was specified.

bool report_progress

print progress report while algorithm is running?

bool reverse

consider reverse complemented segments also?

char** s

char** s_names

bool stupid_user

give more verbose output for stupid users

char** T

float threshold

for -t option; threshold <0. means that only an optimal solution is computed; threshold >=0 means that only all solutions >=threshold are computed.

bool use_multisets

true if multiple occurences within one cluster are to make a difference.

int weight_type

see weighted_footprint_detector::weight_type for a description of different weight types available.

bool weighted

false if -u option (unweighted) is given.

bbq Implementation Documentation
Axel Mosig, Bioinformatics, University of Leipzig