--- /dev/null
+/** @file RNAplex_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 RNAPLEX_CMDL_H
+#define RNAPLEX_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 RNAPLEX_CMDLINE_PARSER_PACKAGE
+/** @brief the program name (used for printing errors) */
+#define RNAPLEX_CMDLINE_PARSER_PACKAGE "RNAplex"
+#endif
+
+#ifndef RNAPLEX_CMDLINE_PARSER_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define RNAPLEX_CMDLINE_PARSER_PACKAGE_NAME "RNAplex"
+#endif
+
+#ifndef RNAPLEX_CMDLINE_PARSER_VERSION
+/** @brief the program version */
+#define RNAPLEX_CMDLINE_PARSER_VERSION VERSION
+#endif
+
+/** @brief Where the command line options are stored */
+struct RNAplex_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 * query_arg; /**< @brief File containing the query sequence.
+. */
+ char * query_orig; /**< @brief File containing the query sequence.
+ original value given at command line. */
+ const char *query_help; /**< @brief File containing the query sequence.
+ help description. */
+ char * target_arg; /**< @brief File containing the target sequence.
+. */
+ char * target_orig; /**< @brief File containing the target sequence.
+ original value given at command line. */
+ const char *target_help; /**< @brief File containing the target sequence.
+ help description. */
+ char * accessibility_dir_arg; /**< @brief Location of the accessibility profiles.
+. */
+ char * accessibility_dir_orig; /**< @brief Location of the accessibility profiles.
+ original value given at command line. */
+ const char *accessibility_dir_help; /**< @brief Location of the accessibility profiles.
+ help description. */
+ int binary_flag; /**< @brief Allow the reading and parsing of memory dumped opening energy file
+ (default=off). */
+ const char *binary_help; /**< @brief Allow the reading and parsing of memory dumped opening energy file
+ 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. */
+ double temp_arg; /**< @brief Rescale energy parameters to a temperature T. Default is 37C.
+
+. */
+ char * temp_orig; /**< @brief Rescale energy parameters to a temperature T. Default is 37C.
+
+ original value given at command line. */
+ const char *temp_help; /**< @brief Rescale energy parameters to a temperature T. Default is 37C.
+
+ help description. */
+ int interaction_length_arg; /**< @brief Maximal length of an interaction
+ (default='40'). */
+ char * interaction_length_orig; /**< @brief Maximal length of an interaction
+ original value given at command line. */
+ const char *interaction_length_help; /**< @brief Maximal length of an interaction
+ help description. */
+ int extension_cost_arg; /**< @brief Cost to add to each nucleotide in a duplex
+ (default='0'). */
+ char * extension_cost_orig; /**< @brief Cost to add to each nucleotide in a duplex
+ original value given at command line. */
+ const char *extension_cost_help; /**< @brief Cost to add to each nucleotide in a duplex
+ help description. */
+ int probe_mode_flag; /**< @brief Compute Tm for probes (default=off). */
+ const char *probe_mode_help; /**< @brief Compute Tm for probes help description. */
+ double probe_concentration_arg; /**< @brief Set the probe concentration for the Tm computation
+
+ (default='0.1'). */
+ char * probe_concentration_orig; /**< @brief Set the probe concentration for the Tm computation
+
+ original value given at command line. */
+ const char *probe_concentration_help; /**< @brief Set the probe concentration for the Tm computation
+
+ help description. */
+ double na_concentration_arg; /**< @brief Set the Na+ concentration for the Tm computation
+
+ (default='1.0'). */
+ char * na_concentration_orig; /**< @brief Set the Na+ concentration for the Tm computation
+
+ original value given at command line. */
+ const char *na_concentration_help; /**< @brief Set the Na+ concentration for the Tm computation
+
+ help description. */
+ double mg_concentration_arg; /**< @brief Set the Mg2+ concentration for the Tm computation
+
+ (default='1.0'). */
+ char * mg_concentration_orig; /**< @brief Set the Mg2+ concentration for the Tm computation
+
+ original value given at command line. */
+ const char *mg_concentration_help; /**< @brief Set the Mg2+ concentration for the Tm computation
+
+ help description. */
+ double k_concentration_arg; /**< @brief Set the K+ concentration for the Tm computation
+
+ (default='1.0'). */
+ char * k_concentration_orig; /**< @brief Set the K+ concentration for the Tm computation
+
+ original value given at command line. */
+ const char *k_concentration_help; /**< @brief Set the K+ concentration for the Tm computation
+
+ help description. */
+ double tris_concentration_arg; /**< @brief Set the tris+ concentration for the Tm computation
+
+ (default='1.0'). */
+ char * tris_concentration_orig; /**< @brief Set the tris+ concentration for the Tm computation
+
+ original value given at command line. */
+ const char *tris_concentration_help; /**< @brief Set the tris+ concentration for the Tm computation
+
+ help description. */
+ int fast_folding_arg; /**< @brief Speedup of the target search
+ (default='0'). */
+ char * fast_folding_orig; /**< @brief Speedup of the target search
+ original value given at command line. */
+ const char *fast_folding_help; /**< @brief Speedup of the target search
+ help description. */
+ double scale_accessibility_arg; /**< @brief Rescale all opening energy by a factor V
+ (default='1.0'). */
+ char * scale_accessibility_orig; /**< @brief Rescale all opening energy by a factor V
+ original value given at command line. */
+ const char *scale_accessibility_help; /**< @brief Rescale all opening energy by a factor V
+ 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 alignment_mode_flag; /**< @brief Tells RNAplex to compute interactions based on alignments
+ (default=off). */
+ const char *alignment_mode_help; /**< @brief Tells RNAplex to compute interactions based on alignments
+ help description. */
+ int convert_to_bin_flag; /**< @brief If set, RNAplex will convert all opening energy file in a directory set by the -a option into binary opening energy files
+ (default=off). */
+ const char *convert_to_bin_help; /**< @brief If set, RNAplex will convert all opening energy file in a directory set by the -a option into binary opening energy files
+ help description. */
+ int duplex_distance_arg; /**< @brief Distance between target 3' ends of two consecutive duplexes
+ (default='0'). */
+ char * duplex_distance_orig; /**< @brief Distance between target 3' ends of two consecutive duplexes
+ original value given at command line. */
+ const char *duplex_distance_help; /**< @brief Distance between target 3' ends of two consecutive duplexes
+ help description. */
+ double energy_threshold_arg; /**< @brief Minimal energy for a duplex to be returned
+ (default='-100000'). */
+ char * energy_threshold_orig; /**< @brief Minimal energy for a duplex to be returned
+ original value given at command line. */
+ const char *energy_threshold_help; /**< @brief Minimal energy for a duplex to be returned
+ help description. */
+ char * produce_ps_arg; /**< @brief Draw an alignment annotated interaction from RNAplex
+. */
+ char * produce_ps_orig; /**< @brief Draw an alignment annotated interaction from RNAplex
+ original value given at command line. */
+ const char *produce_ps_help; /**< @brief Draw an alignment annotated interaction from RNAplex
+ help description. */
+ int WindowLength_arg; /**< @brief Tells how large the region around the target site should be for redrawing the alignment interaction
+ (default='1'). */
+ char * WindowLength_orig; /**< @brief Tells how large the region around the target site should be for redrawing the alignment interaction
+ original value given at command line. */
+ const char *WindowLength_help; /**< @brief Tells how large the region around the target site should be for redrawing the alignment interaction
+ 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 query_given ; /**< @brief Whether query was given. */
+ unsigned int target_given ; /**< @brief Whether target was given. */
+ unsigned int accessibility_dir_given ; /**< @brief Whether accessibility-dir was given. */
+ unsigned int binary_given ; /**< @brief Whether binary was given. */
+ unsigned int paramFile_given ; /**< @brief Whether paramFile was given. */
+ unsigned int temp_given ; /**< @brief Whether temp was given. */
+ unsigned int interaction_length_given ; /**< @brief Whether interaction-length was given. */
+ unsigned int extension_cost_given ; /**< @brief Whether extension-cost was given. */
+ unsigned int probe_mode_given ; /**< @brief Whether probe-mode was given. */
+ unsigned int probe_concentration_given ; /**< @brief Whether probe-concentration was given. */
+ unsigned int na_concentration_given ; /**< @brief Whether na-concentration was given. */
+ unsigned int mg_concentration_given ; /**< @brief Whether mg-concentration was given. */
+ unsigned int k_concentration_given ; /**< @brief Whether k-concentration was given. */
+ unsigned int tris_concentration_given ; /**< @brief Whether tris-concentration was given. */
+ unsigned int fast_folding_given ; /**< @brief Whether fast-folding was given. */
+ unsigned int scale_accessibility_given ; /**< @brief Whether scale-accessibility was given. */
+ unsigned int constraint_given ; /**< @brief Whether constraint was given. */
+ unsigned int alignment_mode_given ; /**< @brief Whether alignment-mode was given. */
+ unsigned int convert_to_bin_given ; /**< @brief Whether convert-to-bin was given. */
+ unsigned int duplex_distance_given ; /**< @brief Whether duplex-distance was given. */
+ unsigned int energy_threshold_given ; /**< @brief Whether energy-threshold was given. */
+ unsigned int produce_ps_given ; /**< @brief Whether produce-ps was given. */
+ unsigned int WindowLength_given ; /**< @brief Whether WindowLength was given. */
+
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct RNAplex_cmdline_parser_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure RNAplex_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 RNAplex_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 *RNAplex_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *RNAplex_args_info_usage;
+/** @brief all the lines making the help output */
+extern const char *RNAplex_args_info_help[];
+/** @brief all the lines making the detailed help output (including hidden options and details) */
+extern const char *RNAplex_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 RNAplex_cmdline_parser (int argc, char **argv,
+ struct RNAplex_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 RNAplex_cmdline_parser_ext() instead
+ */
+int RNAplex_cmdline_parser2 (int argc, char **argv,
+ struct RNAplex_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 RNAplex_cmdline_parser_ext (int argc, char **argv,
+ struct RNAplex_args_info *args_info,
+ struct RNAplex_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 RNAplex_cmdline_parser_dump(FILE *outfile,
+ struct RNAplex_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 RNAplex_cmdline_parser_file_save(const char *filename,
+ struct RNAplex_args_info *args_info);
+
+/**
+ * Print the help
+ */
+void RNAplex_cmdline_parser_print_help(void);
+/**
+ * Print the detailed help (including hidden options and details)
+ */
+void RNAplex_cmdline_parser_print_detailed_help(void);
+/**
+ * Print the version
+ */
+void RNAplex_cmdline_parser_print_version(void);
+
+/**
+ * Initializes all the fields a RNAplex_cmdline_parser_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void RNAplex_cmdline_parser_params_init(struct RNAplex_cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a RNAplex_cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized RNAplex_cmdline_parser_params structure
+ */
+struct RNAplex_cmdline_parser_params *RNAplex_cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed RNAplex_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void RNAplex_cmdline_parser_init (struct RNAplex_args_info *args_info);
+/**
+ * Deallocates the string fields of the RNAplex_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void RNAplex_cmdline_parser_free (struct RNAplex_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 RNAplex_cmdline_parser_required (struct RNAplex_args_info *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* RNAPLEX_CMDL_H */
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