text: /** @file RNAheat_cmdl.h
   *  @brief The header file for the command line option parser
   *  generated by GNU Gengetopt version 2.23
   *  http://www.gnu.org/software/gengetopt.
   *  DO NOT modify this file, since it can be overwritten
   *  @author GNU Gengetopt */
  
  #ifndef RNAHEAT_CMDL_H
  #define RNAHEAT_CMDL_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 RNAHEAT_CMDLINE_PARSER_PACKAGE
  /** @brief the program name (used for printing errors) */
  #define RNAHEAT_CMDLINE_PARSER_PACKAGE "RNAheat"
  #endif
  
  #ifndef RNAHEAT_CMDLINE_PARSER_PACKAGE_NAME
  /** @brief the complete program name (used for help and version) */
  #define RNAHEAT_CMDLINE_PARSER_PACKAGE_NAME "RNAheat"
  #endif
  
  #ifndef RNAHEAT_CMDLINE_PARSER_VERSION
  /** @brief the program version */
  #define RNAHEAT_CMDLINE_PARSER_VERSION VERSION
  #endif
  
  /** @brief Where the command line options are stored */
  struct RNAheat_args_info
  {
    const char *help_help; /**< @brief Print help and exit help description.  */
    const char *detailed_help_help; /**< @brief Print help, including all details and hidden options, and exit help description.  */
    const char *full_help_help; /**< @brief Print help, including hidden options, and exit help description.  */
    const char *version_help; /**< @brief Print version and exit help description.  */
    float Tmin_arg;	/**< @brief Lowest temperature
    
   (default='0').  */
    char * Tmin_orig;	/**< @brief Lowest temperature
    
   original value given at command line.  */
    const char *Tmin_help; /**< @brief Lowest temperature
    
   help description.  */
    float Tmax_arg;	/**< @brief Highest temperature
    
   (default='100').  */
    char * Tmax_orig;	/**< @brief Highest temperature
    
   original value given at command line.  */
    const char *Tmax_help; /**< @brief Highest temperature
    
   help description.  */
    float stepsize_arg;	/**< @brief Calculate partition function every stepsize degrees C
    
   (default='1.').  */
    char * stepsize_orig;	/**< @brief Calculate partition function every stepsize degrees C
    
   original value given at command line.  */
    const char *stepsize_help; /**< @brief Calculate partition function every stepsize degrees C
    
   help description.  */
    int ipoints_arg;	/**< @brief The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve
    
   (default='2').  */
    char * ipoints_orig;	/**< @brief The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve
    
   original value given at command line.  */
    const char *ipoints_help; /**< @brief The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve
    
   help description.  */
    int noconv_flag;	/**< @brief Do not automatically substitude nucleotide \"T\" with \"U\"
    
   (default=off).  */
    const char *noconv_help; /**< @brief Do not automatically substitude nucleotide \"T\" with \"U\"
    
   help description.  */
    int jobs_arg;	/**< @brief Split batch input into jobs and start processing in parallel using multiple threads. A value of 0 indicates to use as many parallel threads as computation cores are available.
   (default='0').  */
    char * jobs_orig;	/**< @brief Split batch input into jobs and start processing in parallel using multiple threads. A value of 0 indicates to use as many parallel threads as computation cores are available.
   original value given at command line.  */
    const char *jobs_help; /**< @brief Split batch input into jobs and start processing in parallel using multiple threads. A value of 0 indicates to use as many parallel threads as computation cores are available.
   help description.  */
    int unordered_flag;	/**< @brief Do not try to keep output in order with input while parallel processing is in place.
   (default=off).  */
    const char *unordered_help; /**< @brief Do not try to keep output in order with input while parallel processing is in place.
   help description.  */
    char ** infile_arg;	/**< @brief Read a file instead of reading from stdin
  .  */
    char ** infile_orig;	/**< @brief Read a file instead of reading from stdin
   original value given at command line.  */
    unsigned int infile_min; /**< @brief Read a file instead of reading from stdin
  's minimum occurreces */
    unsigned int infile_max; /**< @brief Read a file instead of reading from stdin
  's maximum occurreces */
    const char *infile_help; /**< @brief Read a file instead of reading from stdin
   help description.  */
    int auto_id_flag;	/**< @brief Automatically generate an ID for each sequence.
   (default=off).  */
    const char *auto_id_help; /**< @brief Automatically generate an ID for each sequence.
   help description.  */
    char * id_prefix_arg;	/**< @brief Prefix for automatically generated IDs (as used in output file names)
    
   (default='sequence').  */
    char * id_prefix_orig;	/**< @brief Prefix for automatically generated IDs (as used in output file names)
    
   original value given at command line.  */
    const char *id_prefix_help; /**< @brief Prefix for automatically generated IDs (as used in output file names)
    
   help description.  */
    char * id_delim_arg;	/**< @brief Change the delimiter between prefix and increasing number for automatically generated IDs (as used in output file names)
    
   (default='_').  */
    char * id_delim_orig;	/**< @brief Change the delimiter between prefix and increasing number for automatically generated IDs (as used in output file names)
    
   original value given at command line.  */
    const char *id_delim_help; /**< @brief Change the delimiter between prefix and increasing number for automatically generated IDs (as used in output file names)
    
   help description.  */
    int id_digits_arg;	/**< @brief Specify the number of digits of the counter in automatically generated alignment IDs.
   (default='4').  */
    char * id_digits_orig;	/**< @brief Specify the number of digits of the counter in automatically generated alignment IDs.
   original value given at command line.  */
    const char *id_digits_help; /**< @brief Specify the number of digits of the counter in automatically generated alignment IDs.
   help description.  */
    long id_start_arg;	/**< @brief Specify the first number in automatically generated alignment IDs.
   (default='1').  */
    char * id_start_orig;	/**< @brief Specify the first number in automatically generated alignment IDs.
   original value given at command line.  */
    const char *id_start_help; /**< @brief Specify the first number in automatically generated alignment IDs.
   help description.  */
    int maxBPspan_arg;	/**< @brief Set the maximum base pair span
    
   (default='-1').  */
    char * maxBPspan_orig;	/**< @brief Set the maximum base pair span
    
   original value given at command line.  */
    const char *maxBPspan_help; /**< @brief Set the maximum base pair span
    
   help description.  */
    int noTetra_flag;	/**< @brief Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.
    
   (default=off).  */
    const char *noTetra_help; /**< @brief Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.
    
   help description.  */
    int dangles_arg;	/**< @brief How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops
   (default='2').  */
    char * dangles_orig;	/**< @brief How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops
   original value given at command line.  */
    const char *dangles_help; /**< @brief How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops
   help description.  */
    int noLP_flag;	/**< @brief Produce structures without lonely pairs (helices of length 1).
   (default=off).  */
    const char *noLP_help; /**< @brief Produce structures without lonely pairs (helices of length 1).
   help description.  */
    int noGU_flag;	/**< @brief Do not allow GU pairs
    
   (default=off).  */
    const char *noGU_help; /**< @brief Do not allow GU pairs
    
   help description.  */
    int noClosingGU_flag;	/**< @brief Do not allow GU pairs at the end of helices
    
   (default=off).  */
    const char *noClosingGU_help; /**< @brief Do not allow GU pairs at the end of helices
    
   help description.  */
    char * paramFile_arg;	/**< @brief Read energy parameters from paramfile, instead of using the default parameter set.
  .  */
    char * paramFile_orig;	/**< @brief Read energy parameters from paramfile, instead of using the default parameter set.
   original value given at command line.  */
    const char *paramFile_help; /**< @brief Read energy parameters from paramfile, instead of using the default parameter set.
   help description.  */
    char * nsp_arg;	/**< @brief Allow other pairs in addition to the usual AU,GC,and GU pairs.
  .  */
    char * nsp_orig;	/**< @brief Allow other pairs in addition to the usual AU,GC,and GU pairs.
   original value given at command line.  */
    const char *nsp_help; /**< @brief Allow other pairs in addition to the usual AU,GC,and GU pairs.
   help description.  */
    int energyModel_arg;	/**< @brief Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc.  Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.
    
  .  */
    char * energyModel_orig;	/**< @brief Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc.  Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.
    
   original value given at command line.  */
    const char *energyModel_help; /**< @brief Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc.  Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.
    
   help description.  */
    int gquad_flag;	/**< @brief Incoorporate G-Quadruplex formation into the structure prediction algorithm.
    
   (default=off).  */
    const char *gquad_help; /**< @brief Incoorporate G-Quadruplex formation into the structure prediction algorithm.
    
   help description.  */
    int circ_flag;	/**< @brief Assume a circular (instead of linear) RNA molecule.
    
   (default=off).  */
    const char *circ_help; /**< @brief Assume a circular (instead of linear) RNA molecule.
    
   help description.  */
    
    unsigned int help_given ;	/**< @brief Whether help was given.  */
    unsigned int detailed_help_given ;	/**< @brief Whether detailed-help was given.  */
    unsigned int full_help_given ;	/**< @brief Whether full-help was given.  */
    unsigned int version_given ;	/**< @brief Whether version was given.  */
    unsigned int Tmin_given ;	/**< @brief Whether Tmin was given.  */
    unsigned int Tmax_given ;	/**< @brief Whether Tmax was given.  */
    unsigned int stepsize_given ;	/**< @brief Whether stepsize was given.  */
    unsigned int ipoints_given ;	/**< @brief Whether ipoints was given.  */
    unsigned int noconv_given ;	/**< @brief Whether noconv was given.  */
    unsigned int jobs_given ;	/**< @brief Whether jobs was given.  */
    unsigned int unordered_given ;	/**< @brief Whether unordered was given.  */
    unsigned int infile_given ;	/**< @brief Whether infile was given.  */
    unsigned int auto_id_given ;	/**< @brief Whether auto-id was given.  */
    unsigned int id_prefix_given ;	/**< @brief Whether id-prefix was given.  */
    unsigned int id_delim_given ;	/**< @brief Whether id-delim was given.  */
    unsigned int id_digits_given ;	/**< @brief Whether id-digits was given.  */
    unsigned int id_start_given ;	/**< @brief Whether id-start was given.  */
    unsigned int maxBPspan_given ;	/**< @brief Whether maxBPspan was given.  */
    unsigned int noTetra_given ;	/**< @brief Whether noTetra was given.  */
    unsigned int dangles_given ;	/**< @brief Whether dangles was given.  */
    unsigned int noLP_given ;	/**< @brief Whether noLP was given.  */
    unsigned int noGU_given ;	/**< @brief Whether noGU was given.  */
    unsigned int noClosingGU_given ;	/**< @brief Whether noClosingGU was given.  */
    unsigned int paramFile_given ;	/**< @brief Whether paramFile was given.  */
    unsigned int nsp_given ;	/**< @brief Whether nsp was given.  */
    unsigned int energyModel_given ;	/**< @brief Whether energyModel was given.  */
    unsigned int gquad_given ;	/**< @brief Whether gquad was given.  */
    unsigned int circ_given ;	/**< @brief Whether circ was given.  */
  
    char **inputs ; /**< @brief unnamed options (options without names) */
    unsigned inputs_num ; /**< @brief unnamed options number */
  } ;
  
  /** @brief The additional parameters to pass to parser functions */
  struct RNAheat_cmdline_parser_params
  {
    int override; /**< @brief whether to override possibly already present options (default 0) */
    int initialize; /**< @brief whether to initialize the option structure RNAheat_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 RNAheat_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 *RNAheat_args_info_purpose;
  /** @brief the usage string of the program */
  extern const char *RNAheat_args_info_usage;
  /** @brief the description string of the program */
  extern const char *RNAheat_args_info_description;
  /** @brief all the lines making the help output */
  extern const char *RNAheat_args_info_help[];
  /** @brief all the lines making the full help output (including hidden options) */
  extern const char *RNAheat_args_info_full_help[];
  /** @brief all the lines making the detailed help output (including hidden options and details) */
  extern const char *RNAheat_args_info_detailed_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 RNAheat_cmdline_parser (int argc, char **argv,
    struct RNAheat_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 RNAheat_cmdline_parser_ext() instead
   */
  int RNAheat_cmdline_parser2 (int argc, char **argv,
    struct RNAheat_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 RNAheat_cmdline_parser_ext (int argc, char **argv,
    struct RNAheat_args_info *args_info,
    struct RNAheat_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 RNAheat_cmdline_parser_dump(FILE *outfile,
    struct RNAheat_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 RNAheat_cmdline_parser_file_save(const char *filename,
    struct RNAheat_args_info *args_info);
  
  /**
   * Print the help
   */
  void RNAheat_cmdline_parser_print_help(void);
  /**
   * Print the full help (including hidden options)
   */
  void RNAheat_cmdline_parser_print_full_help(void);
  /**
   * Print the detailed help (including hidden options and details)
   */
  void RNAheat_cmdline_parser_print_detailed_help(void);
  /**
   * Print the version
   */
  void RNAheat_cmdline_parser_print_version(void);
  
  /**
   * Initializes all the fields a RNAheat_cmdline_parser_params structure 
   * to their default values
   * @param params the structure to initialize
   */
  void RNAheat_cmdline_parser_params_init(struct RNAheat_cmdline_parser_params *params);
  
  /**
   * Allocates dynamically a RNAheat_cmdline_parser_params structure and initializes
   * all its fields to their default values
   * @return the created and initialized RNAheat_cmdline_parser_params structure
   */
  struct RNAheat_cmdline_parser_params *RNAheat_cmdline_parser_params_create(void);
  
  /**
   * Initializes the passed RNAheat_args_info structure's fields
   * (also set default values for options that have a default)
   * @param args_info the structure to initialize
   */
  void RNAheat_cmdline_parser_init (struct RNAheat_args_info *args_info);
  /**
   * Deallocates the string fields of the RNAheat_args_info structure
   * (but does not deallocate the structure itself)
   * @param args_info the structure to deallocate
   */
  void RNAheat_cmdline_parser_free (struct RNAheat_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 RNAheat_cmdline_parser_required (struct RNAheat_args_info *args_info,
    const char *prog_name);
  
  
  #ifdef __cplusplus
  }
  #endif /* __cplusplus */
  #endif /* RNAHEAT_CMDL_H */
  