Source

sleipnir / tools / SeekTest / cmdline.h

/** @file cmdline.h
 *  @brief The header file for the command line option parser
 *  generated by GNU Gengetopt version 2.22.5
 *  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 (used for printing errors) */
#define CMDLINE_PARSER_PACKAGE "SeekTest"
#endif

#ifndef CMDLINE_PARSER_PACKAGE_NAME
/** @brief the complete program name (used for help and version) */
#define CMDLINE_PARSER_PACKAGE_NAME "SeekTest"
#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.  */
  int dab_flag;	/**< @brief DAB mode (default=off).  */
  const char *dab_help; /**< @brief DAB mode help description.  */
  int bin_flag;	/**< @brief PCL Bin mode (default=off).  */
  const char *bin_help; /**< @brief PCL Bin mode help description.  */
  int db_flag;	/**< @brief DB mode (default=off).  */
  const char *db_help; /**< @brief DB mode help description.  */
  char * db_dir_arg;	/**< @brief DB directory.  */
  char * db_dir_orig;	/**< @brief DB directory original value given at command line.  */
  const char *db_dir_help; /**< @brief DB directory help description.  */
  int db_num_arg;	/**< @brief Number of files in DB directory (default='1000').  */
  char * db_num_orig;	/**< @brief Number of files in DB directory original value given at command line.  */
  const char *db_num_help; /**< @brief Number of files in DB directory help description.  */
  char * prep_arg;	/**< @brief Prep directory (containing .gavg and .gpres files).  */
  char * prep_orig;	/**< @brief Prep directory (containing .gavg and .gpres files) original value given at command line.  */
  const char *prep_help; /**< @brief Prep directory (containing .gavg and .gpres files) help description.  */
  char * sinfo_arg;	/**< @brief Sinfo directory (containing .sinfo files).  */
  char * sinfo_orig;	/**< @brief Sinfo directory (containing .sinfo files) original value given at command line.  */
  const char *sinfo_help; /**< @brief Sinfo directory (containing .sinfo files) help description.  */
  char * dataset_list_arg;	/**< @brief Dataset list.  */
  char * dataset_list_orig;	/**< @brief Dataset list original value given at command line.  */
  const char *dataset_list_help; /**< @brief Dataset list help description.  */
  char * query_arg;	/**< @brief List of genes separated by spaces in one line.  */
  char * query_orig;	/**< @brief List of genes separated by spaces in one line original value given at command line.  */
  const char *query_help; /**< @brief List of genes separated by spaces in one line help description.  */
  char * quant_arg;	/**< @brief Quant file.  */
  char * quant_orig;	/**< @brief Quant file original value given at command line.  */
  const char *quant_help; /**< @brief Quant file help description.  */
  int count_pair_flag;	/**< @brief Count number of z-scores exceeding a threshold (default=off).  */
  const char *count_pair_help; /**< @brief Count number of z-scores exceeding a threshold help description.  */
  int histogram_flag;	/**< @brief Get distribution of z-scores of given genes (default=off).  */
  const char *histogram_help; /**< @brief Get distribution of z-scores of given genes help description.  */
  char * gene_set_list_arg;	/**< @brief List of gene-set files.  */
  char * gene_set_list_orig;	/**< @brief List of gene-set files original value given at command line.  */
  const char *gene_set_list_help; /**< @brief List of gene-set files help description.  */
  char * input_arg;	/**< @brief Gene mapping file.  */
  char * input_orig;	/**< @brief Gene mapping file original value given at command line.  */
  const char *input_help; /**< @brief Gene mapping file help description.  */
  char * dabinput_arg;	/**< @brief DAB dataset file.  */
  char * dabinput_orig;	/**< @brief DAB dataset file original value given at command line.  */
  const char *dabinput_help; /**< @brief DAB dataset file help description.  */
  char * gavg_input_arg;	/**< @brief Gene average (.gavg) input file.  */
  char * gavg_input_orig;	/**< @brief Gene average (.gavg) input file original value given at command line.  */
  const char *gavg_input_help; /**< @brief Gene average (.gavg) input file help description.  */
  char * gpres_input_arg;	/**< @brief Gene presence (.gpres) input file.  */
  char * gpres_input_orig;	/**< @brief Gene presence (.gpres) input file original value given at command line.  */
  const char *gpres_input_help; /**< @brief Gene presence (.gpres) input file help description.  */
  
  unsigned int help_given ;	/**< @brief Whether help was given.  */
  unsigned int version_given ;	/**< @brief Whether version was given.  */
  unsigned int dab_given ;	/**< @brief Whether dab was given.  */
  unsigned int bin_given ;	/**< @brief Whether bin was given.  */
  unsigned int db_given ;	/**< @brief Whether db was given.  */
  unsigned int db_dir_given ;	/**< @brief Whether db_dir was given.  */
  unsigned int db_num_given ;	/**< @brief Whether db_num was given.  */
  unsigned int prep_given ;	/**< @brief Whether prep was given.  */
  unsigned int sinfo_given ;	/**< @brief Whether sinfo was given.  */
  unsigned int dataset_list_given ;	/**< @brief Whether dataset_list was given.  */
  unsigned int query_given ;	/**< @brief Whether query was given.  */
  unsigned int quant_given ;	/**< @brief Whether quant was given.  */
  unsigned int count_pair_given ;	/**< @brief Whether count_pair was given.  */
  unsigned int histogram_given ;	/**< @brief Whether histogram was given.  */
  unsigned int gene_set_list_given ;	/**< @brief Whether gene_set_list was given.  */
  unsigned int input_given ;	/**< @brief Whether input was given.  */
  unsigned int dabinput_given ;	/**< @brief Whether dabinput was given.  */
  unsigned int gavg_input_given ;	/**< @brief Whether gavg_input was given.  */
  unsigned int gpres_input_given ;	/**< @brief Whether gpres_input was given.  */

  char **inputs ; /**< @brief unamed options (options without names) */
  unsigned inputs_num ; /**< @brief unamed options number */
} ;

/** @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 **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 **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 **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 */