src/options.h File Reference

Header file that defines the software options. More...

#include "types.h"

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Functions

void usage ()
 Function that defines the software options.
int parse_params (int argc, char **argv)
 Function used to parse user parameters.
int check_parameters_validity ()
 Function used to check parameters entered by the user.
void destroy_options ()
 Function used to destroyed allocated options.

Variables

char * OPTS_ref_file
char * OPTS_file
char_arrayOPTS_file_array
char * OPTS_output_dir
int OPTS_output_format
int OPTS_verbose
int OPTS_lambda
char_arrayOPTS_alignments
int OPTS_min_length_region
int OPTS_max_length_region
int OPTS_filter_species
int OPTS_min_id
int OPTS_max_id
int OPTS_nb_seqs_set
int OPTS_selecting_mode
int OPTS_max_species_repet
int OPTS_carnac
char * PROG_CARNAC

Detailed Description

Header file that defines the software options.

Author:
Benjamin Grenier-Boley <benjamin.grenier-boley@inria.fr>
Version:
1.02
Date:
September 2008
This file will define all options that can be used in the software

Function Documentation

int check_parameters_validity (  ) 

Function used to check parameters entered by the user.

Returns:
an integer representing the validity :
1 -> exit success
0 -> an error occured
This function will check parameters validity and returns the result of the checking

References _ERROR, char_array::chars, DESTROY, ERROR_, char_array::nb_chars, NEW, OPTS_carnac, OPTS_file, OPTS_max_id, OPTS_max_length_region, OPTS_min_id, OPTS_min_length_region, OPTS_output_dir, OPTS_ref_file, and RENEW.

Referenced by main().

void destroy_options (  ) 

Function used to destroyed allocated options.

This function will destroy the allocated options : the reference name, the array of alignments files and the location of the file in fasta or in GFF3 format

References char_array::chars, DESTROY, char_array::nb_chars, OPTS_file, OPTS_output_dir, and OPTS_ref_file.

Referenced by main().

int parse_params ( int  argc,
char **  argv 
)

Function used to parse user parameters.

Parameters:
[in] argc : number of parameters
[in] argv : the parameters
Returns:
an integer representing the status :
1 -> exit success
0 -> an error occured
This function will parse all user parameters and will check for their validity

References _ERROR, char_array::chars, ERROR_, char_array::nb_chars, NEW, OPTS_carnac, OPTS_file, OPTS_filter_species, OPTS_lambda, OPTS_max_id, OPTS_max_length_region, OPTS_max_species_repet, OPTS_min_id, OPTS_min_length_region, OPTS_nb_seqs_set, OPTS_output_dir, OPTS_output_format, OPTS_ref_file, OPTS_selecting_mode, OPTS_verbose, and RENEW.

Referenced by main().

void usage (  ) 

Function that defines the software options.

This function will be printed on the screen to help users deal with options. It will be printed also when user's options are not correct

References DISPLAY_ERR.

Referenced by main().


Variable Documentation

Array of alignments file

Referenced by print_verbose_start_alignments(), and read_alignments_files().

char* OPTS_file

Other species file(s)

Referenced by check_parameters_validity(), destroy_options(), get_sequences(), and parse_params().

Array of file(s) containing sequences

Referenced by get_sequences().

Filter on species

Referenced by calculate_nb_al_function(), and parse_params().

Maximum number of repetitions by species

Referenced by check_species_repetitions(), main(), parse_params(), and print_verbose_start_check_repetitions().

Output format

Referenced by main(), and parse_params().

Selecting mode

Referenced by main(), parse_params(), write_GFF3(), and write_multifasta().

char* PROG_CARNAC

Which program to use : arnica or carnac


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