--- /dev/null
+/** @file RNAPKplex_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 RNAPKPLEX_CMDL_H
+#define RNAPKPLEX_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 PKPLEX_CMDLINE_PARSER_PACKAGE
+/** @brief the program name (used for printing errors) */
+#define PKPLEX_CMDLINE_PARSER_PACKAGE "RNAPKplex"
+#endif
+
+#ifndef PKPLEX_CMDLINE_PARSER_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define PKPLEX_CMDLINE_PARSER_PACKAGE_NAME "RNAPKplex"
+#endif
+
+#ifndef PKPLEX_CMDLINE_PARSER_VERSION
+/** @brief the program version */
+#define PKPLEX_CMDLINE_PARSER_VERSION VERSION
+#endif
+
+/** @brief Where the command line options are stored */
+struct PKplex_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. */
+ float cutoff_arg; /**< @brief Report only base pairs with an average probability > cutoff in the dot plot
+
+ (default='0.01'). */
+ char * cutoff_orig; /**< @brief Report only base pairs with an average probability > cutoff in the dot plot
+
+ original value given at command line. */
+ const char *cutoff_help; /**< @brief Report only base pairs with an average probability > cutoff in the dot plot
+
+ 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 stabilizing energies for certain tetra-loops. Mostly for testing.
+
+ (default=off). */
+ const char *noTetra_help; /**< @brief Do not include special stabilizing energies for certain tetra-loops. Mostly for testing.
+
+ 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. */
+ 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 * nsp_arg; /**< @brief Allow other pairs in addition to the usual AU,GC,and GU pairs.
+ (default='empty'). */
+ 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. */
+ double energyCutoff_arg; /**< @brief Energy cutoff or pseudoknot initiation cost. Minimum energy gain of a pseudoknot interaction for it to be returned. Pseudoknots with smaller energy gains are rejected.
+
+ (default='-8.10'). */
+ char * energyCutoff_orig; /**< @brief Energy cutoff or pseudoknot initiation cost. Minimum energy gain of a pseudoknot interaction for it to be returned. Pseudoknots with smaller energy gains are rejected.
+
+ original value given at command line. */
+ const char *energyCutoff_help; /**< @brief Energy cutoff or pseudoknot initiation cost. Minimum energy gain of a pseudoknot interaction for it to be returned. Pseudoknots with smaller energy gains are rejected.
+
+ 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. */
+ int verbose_flag; /**< @brief print verbose output
+ (default=off). */
+ const char *verbose_help; /**< @brief print verbose output
+ help description. */
+ double subopts_arg; /**< @brief print suboptimal structures whose energy difference of the pseudoknot to the optimum pseudoknot is smaller than the given value.
+ (default='0.0'). */
+ char * subopts_orig; /**< @brief print suboptimal structures whose energy difference of the pseudoknot to the optimum pseudoknot is smaller than the given value.
+ original value given at command line. */
+ const char *subopts_help; /**< @brief print suboptimal structures whose energy difference of the pseudoknot to the optimum pseudoknot is smaller than the given value.
+ 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 cutoff_given ; /**< @brief Whether cutoff was given. */
+ unsigned int temp_given ; /**< @brief Whether temp was given. */
+ unsigned int noTetra_given ; /**< @brief Whether noTetra 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 noconv_given ; /**< @brief Whether noconv was given. */
+ unsigned int nsp_given ; /**< @brief Whether nsp was given. */
+ unsigned int energyCutoff_given ; /**< @brief Whether energyCutoff was given. */
+ unsigned int paramFile_given ; /**< @brief Whether paramFile was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int subopts_given ; /**< @brief Whether subopts was given. */
+
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct PKplex_cmdline_parser_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure PKplex_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 PKplex_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 *PKplex_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *PKplex_args_info_usage;
+/** @brief all the lines making the help output */
+extern const char *PKplex_args_info_help[];
+/** @brief all the lines making the detailed help output (including hidden options and details) */
+extern const char *PKplex_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 PKplex_cmdline_parser (int argc, char **argv,
+ struct PKplex_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 PKplex_cmdline_parser_ext() instead
+ */
+int PKplex_cmdline_parser2 (int argc, char **argv,
+ struct PKplex_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 PKplex_cmdline_parser_ext (int argc, char **argv,
+ struct PKplex_args_info *args_info,
+ struct PKplex_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 PKplex_cmdline_parser_dump(FILE *outfile,
+ struct PKplex_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 PKplex_cmdline_parser_file_save(const char *filename,
+ struct PKplex_args_info *args_info);
+
+/**
+ * Print the help
+ */
+void PKplex_cmdline_parser_print_help(void);
+/**
+ * Print the detailed help (including hidden options and details)
+ */
+void PKplex_cmdline_parser_print_detailed_help(void);
+/**
+ * Print the version
+ */
+void PKplex_cmdline_parser_print_version(void);
+
+/**
+ * Initializes all the fields a PKplex_cmdline_parser_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void PKplex_cmdline_parser_params_init(struct PKplex_cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a PKplex_cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized PKplex_cmdline_parser_params structure
+ */
+struct PKplex_cmdline_parser_params *PKplex_cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed PKplex_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void PKplex_cmdline_parser_init (struct PKplex_args_info *args_info);
+/**
+ * Deallocates the string fields of the PKplex_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void PKplex_cmdline_parser_free (struct PKplex_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 PKplex_cmdline_parser_required (struct PKplex_args_info *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* RNAPKPLEX_CMDL_H */
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