--- /dev/null
+/** @file RNAparconv_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 RNAPARCONV_CMDL_H
+#define RNAPARCONV_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 RNAPARCONV_CMDLINE_PARSER_PACKAGE
+/** @brief the program name (used for printing errors) */
+#define RNAPARCONV_CMDLINE_PARSER_PACKAGE "RNAparconv"
+#endif
+
+#ifndef RNAPARCONV_CMDLINE_PARSER_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define RNAPARCONV_CMDLINE_PARSER_PACKAGE_NAME "RNAparconv"
+#endif
+
+#ifndef RNAPARCONV_CMDLINE_PARSER_VERSION
+/** @brief the program version */
+#define RNAPARCONV_CMDLINE_PARSER_VERSION VERSION
+#endif
+
+/** @brief Where the command line options are stored */
+struct RNAparconv_args_info
+{
+ const char *help_help; /**< @brief Print help 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. */
+ char * output_arg; /**< @brief Specify an output file name. If argument is missing the converted energy parameters are printed to 'stdout'.
+
+. */
+ char * output_orig; /**< @brief Specify an output file name. If argument is missing the converted energy parameters are printed to 'stdout'.
+
+ original value given at command line. */
+ const char *output_help; /**< @brief Specify an output file name. If argument is missing the converted energy parameters are printed to 'stdout'.
+
+ help description. */
+ char * input_arg; /**< @brief Specify an input file name. If argument is missing the energy parameter input can be supplied via 'stdin'.
+
+. */
+ char * input_orig; /**< @brief Specify an input file name. If argument is missing the energy parameter input can be supplied via 'stdin'.
+
+ original value given at command line. */
+ const char *input_help; /**< @brief Specify an input file name. If argument is missing the energy parameter input can be supplied via 'stdin'.
+
+ help description. */
+ int vanilla_flag; /**< @brief Print just as much as needed to represent the given energy parameters data set.
+ This option overrides all other output settings!
+
+ (default=off). */
+ const char *vanilla_help; /**< @brief Print just as much as needed to represent the given energy parameters data set.
+ This option overrides all other output settings!
+
+ help description. */
+ int dump_flag; /**< @brief Just dump Vienna 1.8.4 energy parameters in format used since 2.0.
+ This option skips any energy parameter input!
+
+ (default=off). */
+ const char *dump_help; /**< @brief Just dump Vienna 1.8.4 energy parameters in format used since 2.0.
+ This option skips any energy parameter input!
+
+ help description. */
+ int silent_flag; /**< @brief Print just energy parameters and appropriate comment lines but suppress all other output
+
+ (default=off). */
+ const char *silent_help; /**< @brief Print just energy parameters and appropriate comment lines but suppress all other output
+
+ help description. */
+ int without_HairpinE_flag; /**< @brief Do not print converted hairpin energies and enthalpies
+
+ (default=off). */
+ const char *without_HairpinE_help; /**< @brief Do not print converted hairpin energies and enthalpies
+
+ help description. */
+ int without_StackE_flag; /**< @brief Do not print converted stacking energies and enthalpies
+
+ (default=off). */
+ const char *without_StackE_help; /**< @brief Do not print converted stacking energies and enthalpies
+
+ help description. */
+ int without_IntE_flag; /**< @brief Do not print converted interior loop energies, enthalpies and asymetry factors
+
+ (default=off). */
+ const char *without_IntE_help; /**< @brief Do not print converted interior loop energies, enthalpies and asymetry factors
+
+ help description. */
+ int without_BulgeE_flag; /**< @brief Do not print converted bulge loop energies and enthalpies
+
+ (default=off). */
+ const char *without_BulgeE_help; /**< @brief Do not print converted bulge loop energies and enthalpies
+
+ help description. */
+ int without_MultiE_flag; /**< @brief Do not print converted multi loop energies and enthalpies
+
+ (default=off). */
+ const char *without_MultiE_help; /**< @brief Do not print converted multi loop energies and enthalpies
+
+ help description. */
+ int without_MismatchE_flag; /**< @brief Do not print converted exterior loop mismatch energies and enthalpies
+
+ (default=off). */
+ const char *without_MismatchE_help; /**< @brief Do not print converted exterior loop mismatch energies and enthalpies
+
+ help description. */
+ int without_MismatchH_flag; /**< @brief Do not print converted hairpin mismatch energies and enthalpies
+
+ (default=off). */
+ const char *without_MismatchH_help; /**< @brief Do not print converted hairpin mismatch energies and enthalpies
+
+ help description. */
+ int without_MismatchI_flag; /**< @brief Do not print converted interior loop mismatch energies and enthalpies
+
+ (default=off). */
+ const char *without_MismatchI_help; /**< @brief Do not print converted interior loop mismatch energies and enthalpies
+
+ help description. */
+ int without_MismatchM_flag; /**< @brief Do not print converted multi loop mismatch energies and enthalpies
+
+ (default=off). */
+ const char *without_MismatchM_help; /**< @brief Do not print converted multi loop mismatch energies and enthalpies
+
+ help description. */
+ int without_Dangle5_flag; /**< @brief Do not print converted 5' dangle energies and enthalpies
+
+ (default=off). */
+ const char *without_Dangle5_help; /**< @brief Do not print converted 5' dangle energies and enthalpies
+
+ help description. */
+ int without_Dangle3_flag; /**< @brief Do not print converted 3' dangle energies and enthalpies
+
+ (default=off). */
+ const char *without_Dangle3_help; /**< @brief Do not print converted 3' dangle energies and enthalpies
+
+ help description. */
+ int without_Misc_flag; /**< @brief Do not print converted Misc energies and enthalpies (TerminalAU, DuplexInit, lxc)
+
+ (default=off). */
+ const char *without_Misc_help; /**< @brief Do not print converted Misc energies and enthalpies (TerminalAU, DuplexInit, lxc)
+
+ help description. */
+
+ unsigned int help_given ; /**< @brief Whether 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 output_given ; /**< @brief Whether output was given. */
+ unsigned int input_given ; /**< @brief Whether input was given. */
+ unsigned int vanilla_given ; /**< @brief Whether vanilla was given. */
+ unsigned int dump_given ; /**< @brief Whether dump was given. */
+ unsigned int silent_given ; /**< @brief Whether silent was given. */
+ unsigned int without_HairpinE_given ; /**< @brief Whether without-HairpinE was given. */
+ unsigned int without_StackE_given ; /**< @brief Whether without-StackE was given. */
+ unsigned int without_IntE_given ; /**< @brief Whether without-IntE was given. */
+ unsigned int without_BulgeE_given ; /**< @brief Whether without-BulgeE was given. */
+ unsigned int without_MultiE_given ; /**< @brief Whether without-MultiE was given. */
+ unsigned int without_MismatchE_given ; /**< @brief Whether without-MismatchE was given. */
+ unsigned int without_MismatchH_given ; /**< @brief Whether without-MismatchH was given. */
+ unsigned int without_MismatchI_given ; /**< @brief Whether without-MismatchI was given. */
+ unsigned int without_MismatchM_given ; /**< @brief Whether without-MismatchM was given. */
+ unsigned int without_Dangle5_given ; /**< @brief Whether without-Dangle5 was given. */
+ unsigned int without_Dangle3_given ; /**< @brief Whether without-Dangle3 was given. */
+ unsigned int without_Misc_given ; /**< @brief Whether without-Misc 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 RNAparconv_cmdline_parser_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure RNAparconv_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 RNAparconv_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 *RNAparconv_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *RNAparconv_args_info_usage;
+/** @brief all the lines making the help output */
+extern const char *RNAparconv_args_info_help[];
+/** @brief all the lines making the full help output (including hidden options) */
+extern const char *RNAparconv_args_info_full_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 RNAparconv_cmdline_parser (int argc, char **argv,
+ struct RNAparconv_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 RNAparconv_cmdline_parser_ext() instead
+ */
+int RNAparconv_cmdline_parser2 (int argc, char **argv,
+ struct RNAparconv_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 RNAparconv_cmdline_parser_ext (int argc, char **argv,
+ struct RNAparconv_args_info *args_info,
+ struct RNAparconv_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 RNAparconv_cmdline_parser_dump(FILE *outfile,
+ struct RNAparconv_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 RNAparconv_cmdline_parser_file_save(const char *filename,
+ struct RNAparconv_args_info *args_info);
+
+/**
+ * Print the help
+ */
+void RNAparconv_cmdline_parser_print_help(void);
+/**
+ * Print the full help (including hidden options)
+ */
+void RNAparconv_cmdline_parser_print_full_help(void);
+/**
+ * Print the version
+ */
+void RNAparconv_cmdline_parser_print_version(void);
+
+/**
+ * Initializes all the fields a RNAparconv_cmdline_parser_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void RNAparconv_cmdline_parser_params_init(struct RNAparconv_cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a RNAparconv_cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized RNAparconv_cmdline_parser_params structure
+ */
+struct RNAparconv_cmdline_parser_params *RNAparconv_cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed RNAparconv_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void RNAparconv_cmdline_parser_init (struct RNAparconv_args_info *args_info);
+/**
+ * Deallocates the string fields of the RNAparconv_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void RNAparconv_cmdline_parser_free (struct RNAparconv_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 RNAparconv_cmdline_parser_required (struct RNAparconv_args_info *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* RNAPARCONV_CMDL_H */
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