--- /dev/null
+/** @file RNAdistance_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 RNADISTANCE_CMDL_H
+#define RNADISTANCE_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 RNADISTANCE_CMDLINE_PARSER_PACKAGE
+/** @brief the program name (used for printing errors) */
+#define RNADISTANCE_CMDLINE_PARSER_PACKAGE "RNAdistance"
+#endif
+
+#ifndef RNADISTANCE_CMDLINE_PARSER_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define RNADISTANCE_CMDLINE_PARSER_PACKAGE_NAME "RNAdistance"
+#endif
+
+#ifndef RNADISTANCE_CMDLINE_PARSER_VERSION
+/** @brief the program version */
+#define RNADISTANCE_CMDLINE_PARSER_VERSION VERSION
+#endif
+
+/** @brief Where the command line options are stored */
+struct RNAdistance_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 *version_help; /**< @brief Print version and exit help description. */
+ char * distance_arg; /**< @brief Specify the distance representation to be used in calculations.
+ (default='f'). */
+ char * distance_orig; /**< @brief Specify the distance representation to be used in calculations.
+ original value given at command line. */
+ const char *distance_help; /**< @brief Specify the distance representation to be used in calculations.
+ help description. */
+ char * compare_arg; /**< @brief Specify the comparison directive.
+ (default='p'). */
+ char * compare_orig; /**< @brief Specify the comparison directive.
+ original value given at command line. */
+ const char *compare_help; /**< @brief Specify the comparison directive.
+ help description. */
+ int shapiro_flag; /**< @brief Use the Bruce Shapiro's cost matrix for comparing coarse structures.
+
+ (default=off). */
+ const char *shapiro_help; /**< @brief Use the Bruce Shapiro's cost matrix for comparing coarse structures.
+
+ help description. */
+ char * backtrack_arg; /**< @brief Print an \"alignment\" with gaps of the structures, to show matching substructures. The aligned structures are written to <filename>, if specified.
+ (default='none'). */
+ char * backtrack_orig; /**< @brief Print an \"alignment\" with gaps of the structures, to show matching substructures. The aligned structures are written to <filename>, if specified.
+ original value given at command line. */
+ const char *backtrack_help; /**< @brief Print an \"alignment\" with gaps of the structures, to show matching substructures. The aligned structures are written to <filename>, if specified.
+ help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int detailed_help_given ; /**< @brief Whether detailed-help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int distance_given ; /**< @brief Whether distance was given. */
+ unsigned int compare_given ; /**< @brief Whether compare was given. */
+ unsigned int shapiro_given ; /**< @brief Whether shapiro was given. */
+ unsigned int backtrack_given ; /**< @brief Whether backtrack was given. */
+
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct RNAdistance_cmdline_parser_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure RNAdistance_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 RNAdistance_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 *RNAdistance_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *RNAdistance_args_info_usage;
+/** @brief all the lines making the help output */
+extern const char *RNAdistance_args_info_help[];
+/** @brief all the lines making the detailed help output (including hidden options and details) */
+extern const char *RNAdistance_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 RNAdistance_cmdline_parser (int argc, char **argv,
+ struct RNAdistance_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 RNAdistance_cmdline_parser_ext() instead
+ */
+int RNAdistance_cmdline_parser2 (int argc, char **argv,
+ struct RNAdistance_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 RNAdistance_cmdline_parser_ext (int argc, char **argv,
+ struct RNAdistance_args_info *args_info,
+ struct RNAdistance_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 RNAdistance_cmdline_parser_dump(FILE *outfile,
+ struct RNAdistance_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 RNAdistance_cmdline_parser_file_save(const char *filename,
+ struct RNAdistance_args_info *args_info);
+
+/**
+ * Print the help
+ */
+void RNAdistance_cmdline_parser_print_help(void);
+/**
+ * Print the detailed help (including hidden options and details)
+ */
+void RNAdistance_cmdline_parser_print_detailed_help(void);
+/**
+ * Print the version
+ */
+void RNAdistance_cmdline_parser_print_version(void);
+
+/**
+ * Initializes all the fields a RNAdistance_cmdline_parser_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void RNAdistance_cmdline_parser_params_init(struct RNAdistance_cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a RNAdistance_cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized RNAdistance_cmdline_parser_params structure
+ */
+struct RNAdistance_cmdline_parser_params *RNAdistance_cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed RNAdistance_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void RNAdistance_cmdline_parser_init (struct RNAdistance_args_info *args_info);
+/**
+ * Deallocates the string fields of the RNAdistance_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void RNAdistance_cmdline_parser_free (struct RNAdistance_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 RNAdistance_cmdline_parser_required (struct RNAdistance_args_info *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* RNADISTANCE_CMDL_H */
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