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sleipnir / tools / SparseNetCombiner / 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
 *  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 "NetworkCombiner"
#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 * output_arg;	/**< @brief Output file.  */
  char * output_orig;	/**< @brief Output file original value given at command line.  */
  const char *output_help; /**< @brief Output file 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.  */
  char * directory_arg;	/**< @brief input directory (must only contain input files).  */
  char * directory_orig;	/**< @brief input directory (must only contain input files) original value given at command line.  */
  const char *directory_help; /**< @brief input directory (must only contain input files) help description.  */
  int map_flag;	/**< @brief Map gene index among the network dabs to combine. (Should be used when the gene intex are not identical among network dabs) (default=off).  */
  const char *map_help; /**< @brief Map gene index among the network dabs to combine. (Should be used when the gene intex are not identical among network dabs) help description.  */
  char * method_arg;	/**< @brief Combination method, (selectmean computes the mea of the upper quartile values) (default='mean').  */
  char * method_orig;	/**< @brief Combination method, (selectmean computes the mea of the upper quartile values) original value given at command line.  */
  const char *method_help; /**< @brief Combination method, (selectmean computes the mea of the upper quartile values) help description.  */
  float quantile_arg;	/**< @brief If combine method is Quantile, set the returning quantile (default is median qunatile 0.5) (default='0.5').  */
  char * quantile_orig;	/**< @brief If combine method is Quantile, set the returning quantile (default is median qunatile 0.5) original value given at command line.  */
  const char *quantile_help; /**< @brief If combine method is Quantile, set the returning quantile (default is median qunatile 0.5) help description.  */
  char * weight_arg;	/**< @brief File with dataset weights, if given each dataset values if weighted by the dataset weight. Skips datasets with no-entry or with zero weights. File format: dataset name<tab>weight.  */
  char * weight_orig;	/**< @brief File with dataset weights, if given each dataset values if weighted by the dataset weight. Skips datasets with no-entry or with zero weights. File format: dataset name<tab>weight original value given at command line.  */
  const char *weight_help; /**< @brief File with dataset weights, if given each dataset values if weighted by the dataset weight. Skips datasets with no-entry or with zero weights. File format: dataset name<tab>weight help description.  */
  int zscore_flag;	/**< @brief Convert values to z-scores before combine (default=off).  */
  const char *zscore_help; /**< @brief Convert values to z-scores before combine help description.  */
  int rank_flag;	/**< @brief Rank transform data before combine (default=off).  */
  const char *rank_help; /**< @brief Rank transform data before combine help description.  */
  char * genes_arg;	/**< @brief Process only genes from the given set.  */
  char * genes_orig;	/**< @brief Process only genes from the given set original value given at command line.  */
  const char *genes_help; /**< @brief Process only genes from the given set help description.  */
  char * genee_arg;	/**< @brief Process only edges including a gene from the given set.  */
  char * genee_orig;	/**< @brief Process only edges including a gene from the given set original value given at command line.  */
  const char *genee_help; /**< @brief Process only edges including a gene from the given set help description.  */
  
  unsigned int help_given ;	/**< @brief Whether help was given.  */
  unsigned int version_given ;	/**< @brief Whether version was given.  */
  unsigned int output_given ;	/**< @brief Whether output was given.  */
  unsigned int verbosity_given ;	/**< @brief Whether verbosity was given.  */
  unsigned int directory_given ;	/**< @brief Whether directory was given.  */
  unsigned int map_given ;	/**< @brief Whether map was given.  */
  unsigned int method_given ;	/**< @brief Whether method was given.  */
  unsigned int quantile_given ;	/**< @brief Whether quantile was given.  */
  unsigned int weight_given ;	/**< @brief Whether weight was given.  */
  unsigned int zscore_given ;	/**< @brief Whether zscore was given.  */
  unsigned int rank_given ;	/**< @brief Whether rank was given.  */
  unsigned int genes_given ;	/**< @brief Whether genes was given.  */
  unsigned int genee_given ;	/**< @brief Whether genee 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 * 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);

extern char *cmdline_parser_method_values[] ;	/**< @brief Possible values for method.  */


#ifdef __cplusplus
}
#endif /* __cplusplus */
#endif /* CMDLINE_H */