/tools/BNTester/cmdline.h
C Header | 216 lines | 107 code | 23 blank | 86 comment | 0 complexity | 31883f228e8dc0421918035d3e2928d7 MD5 | raw file
Possible License(s): CC-BY-3.0
- /** @file cmdline.h
- * @brief The header file for the command line option parser
- * generated by GNU Gengetopt version 2.22
- * http://www.gnu.org/software/gengetopt.
- * DO NOT modify this file, since it can be overwritten
- * @author GNU Gengetopt by Lorenzo Bettini */
- #ifndef CMDLINE_H
- #define CMDLINE_H
- /* If we use autoconf. */
- #ifdef HAVE_CONFIG_H
- #include "config.h"
- #endif
- #include <stdio.h> /* for FILE */
- #ifdef __cplusplus
- extern "C" {
- #endif /* __cplusplus */
- #ifndef CMDLINE_PARSER_PACKAGE
- /** @brief the program name */
- #define CMDLINE_PARSER_PACKAGE "BNTester"
- #endif
- #ifndef CMDLINE_PARSER_VERSION
- /** @brief the program version */
- #define CMDLINE_PARSER_VERSION "1.0"
- #endif
- /** @brief Where the command line options are stored */
- struct gengetopt_args_info
- {
- const char *help_help; /**< @brief Print help and exit help description. */
- const char *version_help; /**< @brief Print version and exit help description. */
- char * datadir_arg; /**< @brief Data directory. */
- char * datadir_orig; /**< @brief Data directory original value given at command line. */
- const char *datadir_help; /**< @brief Data directory help description. */
- char * dataset_arg; /**< @brief Dataset DAD file. */
- char * dataset_orig; /**< @brief Dataset DAD file original value given at command line. */
- const char *dataset_help; /**< @brief Dataset DAD file help description. */
- char * input_arg; /**< @brief Input (X)DSL file. */
- char * input_orig; /**< @brief Input (X)DSL file original value given at command line. */
- const char *input_help; /**< @brief Input (X)DSL file help description. */
- char * output_arg; /**< @brief Output DAB file. */
- char * output_orig; /**< @brief Output DAB file original value given at command line. */
- const char *output_help; /**< @brief Output DAB file help description. */
- int everything_flag; /**< @brief Evaluate pairs without an answer (default=off). */
- const char *everything_help; /**< @brief Evaluate pairs without an answer help description. */
- char * genes_arg; /**< @brief Gene inclusion file. */
- char * genes_orig; /**< @brief Gene inclusion file original value given at command line. */
- const char *genes_help; /**< @brief Gene inclusion file help description. */
- char * genex_arg; /**< @brief Gene exclusion file. */
- char * genex_orig; /**< @brief Gene exclusion file original value given at command line. */
- const char *genex_help; /**< @brief Gene exclusion file help description. */
- char * genee_arg; /**< @brief Term inclusion file. */
- char * genee_orig; /**< @brief Term inclusion file original value given at command line. */
- const char *genee_help; /**< @brief Term inclusion file help description. */
- int zero_flag; /**< @brief Zero missing values (default=off). */
- const char *zero_help; /**< @brief Zero missing values help description. */
- int pnl_flag; /**< @brief Use PNL library (default=off). */
- const char *pnl_help; /**< @brief Use PNL library help description. */
- int function_flag; /**< @brief Use function-fitting networks (default=off). */
- const char *function_help; /**< @brief Use function-fitting networks help description. */
- int group_flag; /**< @brief Group identical inputs (default=on). */
- const char *group_help; /**< @brief Group identical inputs help description. */
- int verbosity_arg; /**< @brief Message verbosity (default='5'). */
- char * verbosity_orig; /**< @brief Message verbosity original value given at command line. */
- const char *verbosity_help; /**< @brief Message verbosity help description. */
-
- unsigned int help_given ; /**< @brief Whether help was given. */
- unsigned int version_given ; /**< @brief Whether version was given. */
- unsigned int datadir_given ; /**< @brief Whether datadir was given. */
- unsigned int dataset_given ; /**< @brief Whether dataset was given. */
- unsigned int input_given ; /**< @brief Whether input was given. */
- unsigned int output_given ; /**< @brief Whether output was given. */
- unsigned int everything_given ; /**< @brief Whether everything was given. */
- unsigned int genes_given ; /**< @brief Whether genes was given. */
- unsigned int genex_given ; /**< @brief Whether genex was given. */
- unsigned int genee_given ; /**< @brief Whether genee was given. */
- unsigned int zero_given ; /**< @brief Whether zero was given. */
- unsigned int pnl_given ; /**< @brief Whether pnl was given. */
- unsigned int function_given ; /**< @brief Whether function was given. */
- unsigned int group_given ; /**< @brief Whether group was given. */
- unsigned int verbosity_given ; /**< @brief Whether verbosity was given. */
- char **inputs ; /**< @brief unamed options (options without names) */
- unsigned inputs_num ; /**< @brief unamed options number */
- int Data_group_counter; /**< @brief Counter for group Data */
- } ;
- /** @brief The additional parameters to pass to parser functions */
- struct cmdline_parser_params
- {
- int override; /**< @brief whether to override possibly already present options (default 0) */
- int initialize; /**< @brief whether to initialize the option structure gengetopt_args_info (default 1) */
- int check_required; /**< @brief whether to check that all required options were provided (default 1) */
- int check_ambiguity; /**< @brief whether to check for options already specified in the option structure gengetopt_args_info (default 0) */
- int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
- } ;
- /** @brief the purpose string of the program */
- extern const char *gengetopt_args_info_purpose;
- /** @brief the usage string of the program */
- extern const char *gengetopt_args_info_usage;
- /** @brief all the lines making the help output */
- extern const char *gengetopt_args_info_help[];
- /**
- * The command line parser
- * @param argc the number of command line options
- * @param argv the command line options
- * @param args_info the structure where option information will be stored
- * @return 0 if everything went fine, NON 0 if an error took place
- */
- int cmdline_parser (int argc, char * const *argv,
- struct gengetopt_args_info *args_info);
- /**
- * The command line parser (version with additional parameters - deprecated)
- * @param argc the number of command line options
- * @param argv the command line options
- * @param args_info the structure where option information will be stored
- * @param override whether to override possibly already present options
- * @param initialize whether to initialize the option structure my_args_info
- * @param check_required whether to check that all required options were provided
- * @return 0 if everything went fine, NON 0 if an error took place
- * @deprecated use cmdline_parser_ext() instead
- */
- int cmdline_parser2 (int argc, char * const *argv,
- struct gengetopt_args_info *args_info,
- int override, int initialize, int check_required);
- /**
- * The command line parser (version with additional parameters)
- * @param argc the number of command line options
- * @param argv the command line options
- * @param args_info the structure where option information will be stored
- * @param params additional parameters for the parser
- * @return 0 if everything went fine, NON 0 if an error took place
- */
- int cmdline_parser_ext (int argc, char * const *argv,
- struct gengetopt_args_info *args_info,
- struct cmdline_parser_params *params);
- /**
- * Save the contents of the option struct into an already open FILE stream.
- * @param outfile the stream where to dump options
- * @param args_info the option struct to dump
- * @return 0 if everything went fine, NON 0 if an error took place
- */
- int cmdline_parser_dump(FILE *outfile,
- struct gengetopt_args_info *args_info);
- /**
- * Save the contents of the option struct into a (text) file.
- * This file can be read by the config file parser (if generated by gengetopt)
- * @param filename the file where to save
- * @param args_info the option struct to save
- * @return 0 if everything went fine, NON 0 if an error took place
- */
- int cmdline_parser_file_save(const char *filename,
- struct gengetopt_args_info *args_info);
- /**
- * Print the help
- */
- void cmdline_parser_print_help(void);
- /**
- * Print the version
- */
- void cmdline_parser_print_version(void);
- /**
- * Initializes all the fields a cmdline_parser_params structure
- * to their default values
- * @param params the structure to initialize
- */
- void cmdline_parser_params_init(struct cmdline_parser_params *params);
- /**
- * Allocates dynamically a cmdline_parser_params structure and initializes
- * all its fields to their default values
- * @return the created and initialized cmdline_parser_params structure
- */
- struct cmdline_parser_params *cmdline_parser_params_create(void);
- /**
- * Initializes the passed gengetopt_args_info structure's fields
- * (also set default values for options that have a default)
- * @param args_info the structure to initialize
- */
- void cmdline_parser_init (struct gengetopt_args_info *args_info);
- /**
- * Deallocates the string fields of the gengetopt_args_info structure
- * (but does not deallocate the structure itself)
- * @param args_info the structure to deallocate
- */
- void cmdline_parser_free (struct gengetopt_args_info *args_info);
- /**
- * Checks that all the required options were specified
- * @param args_info the structure to check
- * @param prog_name the name of the program that will be used to print
- * possible errors
- * @return
- */
- int cmdline_parser_required (struct gengetopt_args_info *args_info,
- const char *prog_name);
- #ifdef __cplusplus
- }
- #endif /* __cplusplus */
- #endif /* CMDLINE_H */