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.


Define Documentation

#define CHUNK_SIZE   4096
 


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  ) 
 


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