/** @file RNAup_cmdl.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 RNAUP_CMDL_H
#define RNAUP_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 RNAUP_CMDLINE_PARSER_PACKAGE
/** @brief the program name (used for printing errors) */
#define RNAUP_CMDLINE_PARSER_PACKAGE "RNAup"
#endif

#ifndef RNAUP_CMDLINE_PARSER_PACKAGE_NAME
/** @brief the complete program name (used for help and version) */
#define RNAUP_CMDLINE_PARSER_PACKAGE_NAME "RNAup"
#endif

#ifndef RNAUP_CMDLINE_PARSER_VERSION
/** @brief the program version */
#define RNAUP_CMDLINE_PARSER_VERSION VERSION
#endif

/** @brief Where the command line options are stored */
struct RNAup_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.  */
  int constraint_flag;	/**< @brief Calculate structures subject to constraints.
 (default=off).  */
  const char *constraint_help; /**< @brief Calculate structures subject to constraints.
 help description.  */
  int no_output_file_flag;	/**< @brief Do not produce an output file
  
 (default=off).  */
  const char *no_output_file_help; /**< @brief Do not produce an output file
  
 help description.  */
  int no_header_flag;	/**< @brief Do not produce a header with the command line parameters used in the outputfile
  
 (default=off).  */
  const char *no_header_help; /**< @brief Do not produce a header with the command line parameters used in the outputfile
  
 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.  */
  char ** ulength_arg;	/**< @brief specifies the length of the unstructured region in the output.
 (default='4').  */
  char ** ulength_orig;	/**< @brief specifies the length of the unstructured region in the output.
 original value given at command line.  */
  unsigned int ulength_min; /**< @brief specifies the length of the unstructured region in the output.
's minimum occurreces */
  unsigned int ulength_max; /**< @brief specifies the length of the unstructured region in the output.
's maximum occurreces */
  const char *ulength_help; /**< @brief specifies the length of the unstructured region in the output.
 help description.  */
  char * contributions_arg;	/**< @brief Specify the contributions listed in the output
 (default='S').  */
  char * contributions_orig;	/**< @brief Specify the contributions listed in the output
 original value given at command line.  */
  const char *contributions_help; /**< @brief Specify the contributions listed in the output
 help description.  */
  int window_arg;	/**< @brief Determine the maximal length of the region of interaction
  
 (default='25').  */
  char * window_orig;	/**< @brief Determine the maximal length of the region of interaction
  
 original value given at command line.  */
  const char *window_help; /**< @brief Determine the maximal length of the region of interaction
  
 help description.  */
  int include_both_flag;	/**< @brief Include the probability of unpaired regions in both (b) RNAs. By default
  only the probability of being unpaired in the longer RNA (target) is used.
  
 (default=off).  */
  const char *include_both_help; /**< @brief Include the probability of unpaired regions in both (b) RNAs. By default
  only the probability of being unpaired in the longer RNA (target) is used.
  
 help description.  */
  int extend5_arg;	/**< @brief Extend the region of interaction in the target to some residues on the 5' side
.  */
  char * extend5_orig;	/**< @brief Extend the region of interaction in the target to some residues on the 5' side
 original value given at command line.  */
  const char *extend5_help; /**< @brief Extend the region of interaction in the target to some residues on the 5' side
 help description.  */
  int extend3_arg;	/**< @brief Extend the region of interaction in the target to some residues on the 3' side
.  */
  char * extend3_orig;	/**< @brief Extend the region of interaction in the target to some residues on the 3' side
 original value given at command line.  */
  const char *extend3_help; /**< @brief Extend the region of interaction in the target to some residues on the 3' side
 help description.  */
  int interaction_pairwise_flag;	/**< @brief Activate pairwise interaction mode
 (default=off).  */
  const char *interaction_pairwise_help; /**< @brief Activate pairwise interaction mode
 help description.  */
  int interaction_first_flag;	/**< @brief Activate interaction mode using first sequence only
 (default=off).  */
  const char *interaction_first_help; /**< @brief Activate interaction mode using first sequence only
 help description.  */
  double pfScale_arg;	/**< @brief In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences.
  You can also recompile the program to use double precision (see the README file).
  
.  */
  char * pfScale_orig;	/**< @brief In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences.
  You can also recompile the program to use double precision (see the README file).
  
 original value given at command line.  */
  const char *pfScale_help; /**< @brief In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences.
  You can also recompile the program to use double precision (see the README file).
  
 help description.  */
  double temp_arg;	/**< @brief Rescale energy parameters to a temperature of temp C. Default is 37C.
  
.  */
  char * temp_orig;	/**< @brief Rescale energy parameters to a temperature of temp C. Default is 37C.
  
 original value given at command line.  */
  const char *temp_help; /**< @brief Rescale energy parameters to a temperature of temp C. Default is 37C.
  
 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.  */
  
  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 constraint_given ;	/**< @brief Whether constraint was given.  */
  unsigned int no_output_file_given ;	/**< @brief Whether no_output_file was given.  */
  unsigned int no_header_given ;	/**< @brief Whether no_header was given.  */
  unsigned int noconv_given ;	/**< @brief Whether noconv was given.  */
  unsigned int ulength_given ;	/**< @brief Whether ulength was given.  */
  unsigned int contributions_given ;	/**< @brief Whether contributions was given.  */
  unsigned int window_given ;	/**< @brief Whether window was given.  */
  unsigned int include_both_given ;	/**< @brief Whether include_both was given.  */
  unsigned int extend5_given ;	/**< @brief Whether extend5 was given.  */
  unsigned int extend3_given ;	/**< @brief Whether extend3 was given.  */
  unsigned int interaction_pairwise_given ;	/**< @brief Whether interaction_pairwise was given.  */
  unsigned int interaction_first_given ;	/**< @brief Whether interaction_first was given.  */
  unsigned int pfScale_given ;	/**< @brief Whether pfScale was given.  */
  unsigned int temp_given ;	/**< @brief Whether temp 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.  */

} ;

/** @brief The additional parameters to pass to parser functions */
struct RNAup_cmdline_parser_params
{
  int override; /**< @brief whether to override possibly already present options (default 0) */
  int initialize; /**< @brief whether to initialize the option structure RNAup_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 RNAup_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 *RNAup_args_info_purpose;
/** @brief the usage string of the program */
extern const char *RNAup_args_info_usage;
/** @brief all the lines making the help output */
extern const char *RNAup_args_info_help[];
/** @brief all the lines making the full help output (including hidden options) */
extern const char *RNAup_args_info_full_help[];
/** @brief all the lines making the detailed help output (including hidden options and details) */
extern const char *RNAup_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 RNAup_cmdline_parser (int argc, char **argv,
  struct RNAup_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 RNAup_cmdline_parser_ext() instead
 */
int RNAup_cmdline_parser2 (int argc, char **argv,
  struct RNAup_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 RNAup_cmdline_parser_ext (int argc, char **argv,
  struct RNAup_args_info *args_info,
  struct RNAup_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 RNAup_cmdline_parser_dump(FILE *outfile,
  struct RNAup_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 RNAup_cmdline_parser_file_save(const char *filename,
  struct RNAup_args_info *args_info);

/**
 * Print the help
 */
void RNAup_cmdline_parser_print_help(void);
/**
 * Print the full help (including hidden options)
 */
void RNAup_cmdline_parser_print_full_help(void);
/**
 * Print the detailed help (including hidden options and details)
 */
void RNAup_cmdline_parser_print_detailed_help(void);
/**
 * Print the version
 */
void RNAup_cmdline_parser_print_version(void);

/**
 * Initializes all the fields a RNAup_cmdline_parser_params structure 
 * to their default values
 * @param params the structure to initialize
 */
void RNAup_cmdline_parser_params_init(struct RNAup_cmdline_parser_params *params);

/**
 * Allocates dynamically a RNAup_cmdline_parser_params structure and initializes
 * all its fields to their default values
 * @return the created and initialized RNAup_cmdline_parser_params structure
 */
struct RNAup_cmdline_parser_params *RNAup_cmdline_parser_params_create(void);

/**
 * Initializes the passed RNAup_args_info structure's fields
 * (also set default values for options that have a default)
 * @param args_info the structure to initialize
 */
void RNAup_cmdline_parser_init (struct RNAup_args_info *args_info);
/**
 * Deallocates the string fields of the RNAup_args_info structure
 * (but does not deallocate the structure itself)
 * @param args_info the structure to deallocate
 */
void RNAup_cmdline_parser_free (struct RNAup_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 RNAup_cmdline_parser_required (struct RNAup_args_info *args_info,
  const char *prog_name);


#ifdef __cplusplus
}
#endif /* __cplusplus */
#endif /* RNAUP_CMDL_H */