1. libsleipnir
  2. sleipnir

Source

sleipnir / tools / SVMperfer / cmdline.h

/** @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 "SVMperfer"
#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 * labels_arg;	/**< @brief Labels file.  */
  char * labels_orig;	/**< @brief Labels file original value given at command line.  */
  const char *labels_help; /**< @brief Labels file 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.  */
  char * input_arg;	/**< @brief Input PCL file .  */
  char * input_orig;	/**< @brief Input PCL file  original value given at command line.  */
  const char *input_help; /**< @brief Input PCL file  help description.  */
  char * model_arg;	/**< @brief Model file.  */
  char * model_orig;	/**< @brief Model file original value given at command line.  */
  const char *model_help; /**< @brief Model file help description.  */
  char * test_labels_arg;	/**< @brief Test Labels file.  */
  char * test_labels_orig;	/**< @brief Test Labels file original value given at command line.  */
  const char *test_labels_help; /**< @brief Test Labels file help description.  */
  int all_flag;	/**< @brief Always classify all genes in PCLs (default=off).  */
  const char *all_help; /**< @brief Always classify all genes in PCLs help description.  */
  int slack_flag;	/**< @brief Use slack rescaling (not implemented for ROC loss) (default=off).  */
  const char *slack_help; /**< @brief Use slack rescaling (not implemented for ROC loss) help description.  */
  int verbosity_arg;	/**< @brief Sets the svm_struct verbosity (default='0').  */
  char * verbosity_orig;	/**< @brief Sets the svm_struct verbosity original value given at command line.  */
  const char *verbosity_help; /**< @brief Sets the svm_struct verbosity help description.  */
  int skip_arg;	/**< @brief Number of columns to skip in input pcls (default='2').  */
  char * skip_orig;	/**< @brief Number of columns to skip in input pcls original value given at command line.  */
  const char *skip_help; /**< @brief Number of columns to skip in input pcls help description.  */
  int normalize_flag;	/**< @brief Normalize PCLS to 0 mean 1 variance (default=off).  */
  const char *normalize_help; /**< @brief Normalize PCLS to 0 mean 1 variance help description.  */
  int cross_validation_arg;	/**< @brief Number of cross-validation sets ( arg of 1 will turn off cross-validation ) (default='5').  */
  char * cross_validation_orig;	/**< @brief Number of cross-validation sets ( arg of 1 will turn off cross-validation ) original value given at command line.  */
  const char *cross_validation_help; /**< @brief Number of cross-validation sets ( arg of 1 will turn off cross-validation ) help description.  */
  int error_function_arg;	/**< @brief Sets the loss function for SVM learning: Choice of:
  0\tZero/one loss: 1 if vector of predictions contains error, 0 otherwise.
  1\tF1: 100 minus the F1-score in percent.
  2\tErrorrate: Percentage of errors in prediction vector.
  3\tPrec/Rec Breakeven: 100 minus PRBEP in percent.
  4\tPrec@k: 100 minus precision at k in percent.
  5\tRec@k: 100 minus recall at k in percent.
  10\tROCArea: Percentage of swapped pos/neg pairs (i.e. 100 - ROCArea).\n (default='10').  */
  char * error_function_orig;	/**< @brief Sets the loss function for SVM learning: Choice of:
  0\tZero/one loss: 1 if vector of predictions contains error, 0 otherwise.
  1\tF1: 100 minus the F1-score in percent.
  2\tErrorrate: Percentage of errors in prediction vector.
  3\tPrec/Rec Breakeven: 100 minus PRBEP in percent.
  4\tPrec@k: 100 minus precision at k in percent.
  5\tRec@k: 100 minus recall at k in percent.
  10\tROCArea: Percentage of swapped pos/neg pairs (i.e. 100 - ROCArea).\n original value given at command line.  */
  const char *error_function_help; /**< @brief Sets the loss function for SVM learning: Choice of:
  0\tZero/one loss: 1 if vector of predictions contains error, 0 otherwise.
  1\tF1: 100 minus the F1-score in percent.
  2\tErrorrate: Percentage of errors in prediction vector.
  3\tPrec/Rec Breakeven: 100 minus PRBEP in percent.
  4\tPrec@k: 100 minus precision at k in percent.
  5\tRec@k: 100 minus recall at k in percent.
  10\tROCArea: Percentage of swapped pos/neg pairs (i.e. 100 - ROCArea).\n help description.  */
  float k_value_arg;	/**< @brief Value of k parameter used for Prec@k and Rec@k in (0,1) (default='0.5').  */
  char * k_value_orig;	/**< @brief Value of k parameter used for Prec@k and Rec@k in (0,1) original value given at command line.  */
  const char *k_value_help; /**< @brief Value of k parameter used for Prec@k and Rec@k in (0,1) help description.  */
  float tradeoff_arg;	/**< @brief SVM tradeoff constant C (default='1').  */
  char * tradeoff_orig;	/**< @brief SVM tradeoff constant C original value given at command line.  */
  const char *tradeoff_help; /**< @brief SVM tradeoff constant C help description.  */
  int simple_model_flag;	/**< @brief Write model files with only linear weights (default=on).  */
  const char *simple_model_help; /**< @brief Write model files with only linear weights help description.  */
  char * params_arg;	/**< @brief Parameter file.  */
  char * params_orig;	/**< @brief Parameter file original value given at command line.  */
  const char *params_help; /**< @brief Parameter file help description.  */
  int mmap_flag;	/**< @brief Memory map binary input (default=off).  */
  const char *mmap_help; /**< @brief Memory map binary input help description.  */
  
  unsigned int help_given ;	/**< @brief Whether help was given.  */
  unsigned int version_given ;	/**< @brief Whether version was given.  */
  unsigned int labels_given ;	/**< @brief Whether labels was given.  */
  unsigned int output_given ;	/**< @brief Whether output was given.  */
  unsigned int input_given ;	/**< @brief Whether input was given.  */
  unsigned int model_given ;	/**< @brief Whether model was given.  */
  unsigned int test_labels_given ;	/**< @brief Whether test_labels was given.  */
  unsigned int all_given ;	/**< @brief Whether all was given.  */
  unsigned int slack_given ;	/**< @brief Whether slack was given.  */
  unsigned int verbosity_given ;	/**< @brief Whether verbosity was given.  */
  unsigned int skip_given ;	/**< @brief Whether skip was given.  */
  unsigned int normalize_given ;	/**< @brief Whether normalize was given.  */
  unsigned int cross_validation_given ;	/**< @brief Whether cross_validation was given.  */
  unsigned int error_function_given ;	/**< @brief Whether error_function was given.  */
  unsigned int k_value_given ;	/**< @brief Whether k_value was given.  */
  unsigned int tradeoff_given ;	/**< @brief Whether tradeoff was given.  */
  unsigned int simple_model_given ;	/**< @brief Whether simple_model was given.  */
  unsigned int params_given ;	/**< @brief Whether params was given.  */
  unsigned int mmap_given ;	/**< @brief Whether mmap 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);


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