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sleipnir / tools / SeekServer / cmdline.h

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/** @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 "SeekServer"
#endif

#ifndef CMDLINE_PARSER_PACKAGE_NAME
/** @brief the complete program name (used for help and version) */
#define CMDLINE_PARSER_PACKAGE_NAME "SeekServer"
#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 * port_arg;	/**< @brief Port (default='9000').  */
  char * port_orig;	/**< @brief Port original value given at command line.  */
  const char *port_help; /**< @brief Port help description.  */
  char * dset_arg;	/**< @brief Input a set of datasets.  */
  char * dset_orig;	/**< @brief Input a set of datasets original value given at command line.  */
  const char *dset_help; /**< @brief Input a set of datasets help description.  */
  char * input_arg;	/**< @brief Input gene mapping.  */
  char * input_orig;	/**< @brief Input gene mapping original value given at command line.  */
  const char *input_help; /**< @brief Input gene mapping help description.  */
  char * dir_in_arg;	/**< @brief Database directory.  */
  char * dir_in_orig;	/**< @brief Database directory original value given at command line.  */
  const char *dir_in_help; /**< @brief Database directory help description.  */
  char * dir_prep_in_arg;	/**< @brief Prep directory (containing .gavg, .gpres files).  */
  char * dir_prep_in_orig;	/**< @brief Prep directory (containing .gavg, .gpres files) original value given at command line.  */
  const char *dir_prep_in_help; /**< @brief Prep directory (containing .gavg, .gpres files) help description.  */
  char * dir_platform_arg;	/**< @brief Platform directory (containing .gplatavg, .gplatstdev, .gplatorder files).  */
  char * dir_platform_orig;	/**< @brief Platform directory (containing .gplatavg, .gplatstdev, .gplatorder files) original value given at command line.  */
  const char *dir_platform_help; /**< @brief Platform directory (containing .gplatavg, .gplatstdev, .gplatorder files) help description.  */
  char * dir_sinfo_arg;	/**< @brief Sinfo Directory (containing .sinfo files) (default='NA').  */
  char * dir_sinfo_orig;	/**< @brief Sinfo Directory (containing .sinfo files) original value given at command line.  */
  const char *dir_sinfo_help; /**< @brief Sinfo Directory (containing .sinfo files) help description.  */
  char * dir_gvar_arg;	/**< @brief Gene variance directory (containing .gexpvar files) (default='NA').  */
  char * dir_gvar_orig;	/**< @brief Gene variance directory (containing .gexpvar files) original value given at command line.  */
  const char *dir_gvar_help; /**< @brief Gene variance directory (containing .gexpvar files) help description.  */
  char * quant_arg;	/**< @brief quant file (assuming all datasets use the same quantization).  */
  char * quant_orig;	/**< @brief quant file (assuming all datasets use the same quantization) original value given at command line.  */
  const char *quant_help; /**< @brief quant file (assuming all datasets use the same quantization) help description.  */
  int num_db_arg;	/**< @brief Number of databaselets in database (default='1000').  */
  char * num_db_orig;	/**< @brief Number of databaselets in database original value given at command line.  */
  const char *num_db_help; /**< @brief Number of databaselets in database help description.  */
  float score_cutoff_arg;	/**< @brief Cutoff on the gene-gene score before adding, default: no cutoff (default='-9999').  */
  char * score_cutoff_orig;	/**< @brief Cutoff on the gene-gene score before adding, default: no cutoff original value given at command line.  */
  const char *score_cutoff_help; /**< @brief Cutoff on the gene-gene score before adding, default: no cutoff help description.  */
  int square_z_flag;	/**< @brief If using z-score, square-transform z-scores. Usually used in conjunction with --score-cutoff (default=off).  */
  const char *square_z_help; /**< @brief If using z-score, square-transform z-scores. Usually used in conjunction with --score-cutoff help description.  */
  int is_nibble_flag;	/**< @brief If true, the input DB is nibble type (default=off).  */
  const char *is_nibble_help; /**< @brief If true, the input DB is nibble type help description.  */
  int buffer_arg;	/**< @brief Number of Databaselets to store in memory (default='20').  */
  char * buffer_orig;	/**< @brief Number of Databaselets to store in memory original value given at command line.  */
  const char *buffer_help; /**< @brief Number of Databaselets to store in memory help description.  */
  int output_text_flag;	/**< @brief Output results (gene list and dataset weights) as text (default=off).  */
  const char *output_text_help; /**< @brief Output results (gene list and dataset weights) as text help description.  */
  char * additional_db_arg;	/**< @brief Utilize a second CDatabase collection. Path to the second CDatabase's setting file. (default='NA').  */
  char * additional_db_orig;	/**< @brief Utilize a second CDatabase collection. Path to the second CDatabase's setting file. original value given at command line.  */
  const char *additional_db_help; /**< @brief Utilize a second CDatabase collection. Path to the second CDatabase's setting file. help description.  */
  
  unsigned int help_given ;	/**< @brief Whether help was given.  */
  unsigned int version_given ;	/**< @brief Whether version was given.  */
  unsigned int port_given ;	/**< @brief Whether port was given.  */
  unsigned int dset_given ;	/**< @brief Whether dset was given.  */
  unsigned int input_given ;	/**< @brief Whether input was given.  */
  unsigned int dir_in_given ;	/**< @brief Whether dir_in was given.  */
  unsigned int dir_prep_in_given ;	/**< @brief Whether dir_prep_in was given.  */
  unsigned int dir_platform_given ;	/**< @brief Whether dir_platform was given.  */
  unsigned int dir_sinfo_given ;	/**< @brief Whether dir_sinfo was given.  */
  unsigned int dir_gvar_given ;	/**< @brief Whether dir_gvar was given.  */
  unsigned int quant_given ;	/**< @brief Whether quant was given.  */
  unsigned int num_db_given ;	/**< @brief Whether num_db was given.  */
  unsigned int score_cutoff_given ;	/**< @brief Whether score_cutoff was given.  */
  unsigned int square_z_given ;	/**< @brief Whether square_z was given.  */
  unsigned int is_nibble_given ;	/**< @brief Whether is_nibble was given.  */
  unsigned int buffer_given ;	/**< @brief Whether buffer was given.  */
  unsigned int output_text_given ;	/**< @brief Whether output_text was given.  */
  unsigned int additional_db_given ;	/**< @brief Whether additional_db 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 */