sleipnir / tools / SVMhierarchy / 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 "SVMhierarchy"
#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 * dab_input_arg;	/**< @brief Input Dat/Dab file .  */
  char * dab_input_orig;	/**< @brief Input Dat/Dab file  original value given at command line.  */
  const char *dab_input_help; /**< @brief Input Dat/Dab 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.  */
  char * ontoparam_arg;	/**< @brief Ontology file.  */
  char * ontoparam_orig;	/**< @brief Ontology file original value given at command line.  */
  const char *ontoparam_help; /**< @brief Ontology 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 Hierarchical Multilabel SVM) (default=off).  */
  const char *slack_help; /**< @brief Use slack rescaling (NOT implemented for Hierarchical Multilabel SVM) 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 loss_function_arg;	/**< @brief Sets the loss function for SVM learning: Choice of:
  0\tHamming distance loss: total number of differences in label vector.
  1\tHamming distance loss (modified): total number of differences in label vector; over-annotation not counted as difference. 
  2\tLikelihood distance loss. 
  3\tLikelihood distance loss (modified). 
  \n (default='0').  */
  char * loss_function_orig;	/**< @brief Sets the loss function for SVM learning: Choice of:
  0\tHamming distance loss: total number of differences in label vector.
  1\tHamming distance loss (modified): total number of differences in label vector; over-annotation not counted as difference. 
  2\tLikelihood distance loss. 
  3\tLikelihood distance loss (modified). 
  \n original value given at command line.  */
  const char *loss_function_help; /**< @brief Sets the loss function for SVM learning: Choice of:
  0\tHamming distance loss: total number of differences in label vector.
  1\tHamming distance loss (modified): total number of differences in label vector; over-annotation not counted as difference. 
  2\tLikelihood distance loss. 
  3\tLikelihood distance loss (modified). 
  \n 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.  */
  float epsilon_arg;	/**< @brief allow that tolerance for termination criterion (default='0.1').  */
  char * epsilon_orig;	/**< @brief allow that tolerance for termination criterion original value given at command line.  */
  const char *epsilon_help; /**< @brief allow that tolerance for termination criterion help description.  */
  int learning_algorithm_arg;	/**< @brief Choice of structural learning algorithm (default 4):
  0\tn-slack algorithm 
  1\tn-slack algorithm with shrinking heuristic
  2\t1-slack algorithm (primal) 
  3\t1-slack algorithm (dual)
  4\t1-slack algorithm (dual) with constraint cache\n (default='3').  */
  char * learning_algorithm_orig;	/**< @brief Choice of structural learning algorithm (default 4):
  0\tn-slack algorithm 
  1\tn-slack algorithm with shrinking heuristic
  2\t1-slack algorithm (primal) 
  3\t1-slack algorithm (dual)
  4\t1-slack algorithm (dual) with constraint cache\n original value given at command line.  */
  const char *learning_algorithm_help; /**< @brief Choice of structural learning algorithm (default 4):
  0\tn-slack algorithm 
  1\tn-slack algorithm with shrinking heuristic
  2\t1-slack algorithm (primal) 
  3\t1-slack algorithm (dual)
  4\t1-slack algorithm (dual) with constraint cache\n help description.  */
  int threads_arg;	/**< @brief number of threads (only apply to algorithm 3 currently) (default='4').  */
  char * threads_orig;	/**< @brief number of threads (only apply to algorithm 3 currently) original value given at command line.  */
  const char *threads_help; /**< @brief number of threads (only apply to algorithm 3 currently) 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 dab_input_given ;	/**< @brief Whether dab_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 ontoparam_given ;	/**< @brief Whether ontoparam 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 loss_function_given ;	/**< @brief Whether loss_function was given.  */
  unsigned int tradeoff_given ;	/**< @brief Whether tradeoff was given.  */
  unsigned int epsilon_given ;	/**< @brief Whether epsilon was given.  */
  unsigned int learning_algorithm_given ;	/**< @brief Whether learning_algorithm was given.  */
  unsigned int threads_given ;	/**< @brief Whether threads 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 */
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