/** @file RNAsnoop_cmdl.h * @brief The header file for the command line option parser * generated by GNU Gengetopt version 2.22.3 * http://www.gnu.org/software/gengetopt. * DO NOT modify this file, since it can be overwritten * @author GNU Gengetopt by Lorenzo Bettini */ #ifndef RNASNOOP_CMDL_H #define RNASNOOP_CMDL_H /* If we use autoconf. */ #ifdef HAVE_CONFIG_H #include "config.h" #endif #include /* for FILE */ #ifdef __cplusplus extern "C" { #endif /* __cplusplus */ #ifndef RNASNOOP_CMDLINE_PARSER_PACKAGE /** @brief the program name (used for printing errors) */ #define RNASNOOP_CMDLINE_PARSER_PACKAGE "RNAsnoop" #endif #ifndef RNASNOOP_CMDLINE_PARSER_PACKAGE_NAME /** @brief the complete program name (used for help and version) */ #define RNASNOOP_CMDLINE_PARSER_PACKAGE_NAME "RNAsnoop" #endif #ifndef RNASNOOP_CMDLINE_PARSER_VERSION /** @brief the program version */ #define RNASNOOP_CMDLINE_PARSER_VERSION VERSION #endif /** @brief Where the command line options are stored */ struct RNAsnoop_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.\n. */ char * query_orig; /**< @brief File containing the query sequence.\n original value given at command line. */ const char *query_help; /**< @brief File containing the query sequence.\n help description. */ char * target_arg; /**< @brief File containing the target sequence.\n. */ char * target_orig; /**< @brief File containing the target sequence.\n original value given at command line. */ const char *target_help; /**< @brief File containing the target sequence.\n help description. */ char * suffix_arg; /**< @brief Specificy the suffix that was added by RNAup to the accessibility files\n\n (default='_u1_to_30.out'). */ char * suffix_orig; /**< @brief Specificy the suffix that was added by RNAup to the accessibility files\n\n original value given at command line. */ const char *suffix_help; /**< @brief Specificy the suffix that was added by RNAup to the accessibility files\n\n help description. */ char * from_RNAplfold_arg; /**< @brief Specify the directory where accessibility profile generated by RNAplfold are found\n\n. */ char * from_RNAplfold_orig; /**< @brief Specify the directory where accessibility profile generated by RNAplfold are found\n\n original value given at command line. */ const char *from_RNAplfold_help; /**< @brief Specify the directory where accessibility profile generated by RNAplfold are found\n\n help description. */ int alignment_mode_flag; /**< @brief Specify if RNAsnoop gets alignments or single sequences as input\n\n (default=off). */ const char *alignment_mode_help; /**< @brief Specify if RNAsnoop gets alignments or single sequences as input\n\n help description. */ int fast_folding_arg; /**< @brief Speedup of the target search (default='1'). */ 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. */ 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 minimal_right_duplex_arg; /**< @brief Minimal Right Duplex Energy\n\n (default='-270'). */ char * minimal_right_duplex_orig; /**< @brief Minimal Right Duplex Energy\n\n original value given at command line. */ const char *minimal_right_duplex_help; /**< @brief Minimal Right Duplex Energy\n\n help description. */ int minimal_loop_energy_arg; /**< @brief Minimal Right Duplex Energy\n (default='-280'). */ char * minimal_loop_energy_orig; /**< @brief Minimal Right Duplex Energy\n original value given at command line. */ const char *minimal_loop_energy_help; /**< @brief Minimal Right Duplex Energy\n help description. */ int minimal_left_duplex_arg; /**< @brief Minimal Left Duplex Energy\n\n (default='-170'). */ char * minimal_left_duplex_orig; /**< @brief Minimal Left Duplex Energy\n\n original value given at command line. */ const char *minimal_left_duplex_help; /**< @brief Minimal Left Duplex Energy\n\n help description. */ int minimal_duplex_arg; /**< @brief Minimal Duplex Energy\n\n (default='-1090'). */ char * minimal_duplex_orig; /**< @brief Minimal Duplex Energy\n\n original value given at command line. */ const char *minimal_duplex_help; /**< @brief Minimal Duplex Energy\n\n help description. */ int duplex_distance_arg; /**< @brief Distance between target 3' ends of two consecutive duplexes\n (default='1'). */ char * duplex_distance_orig; /**< @brief Distance between target 3' ends of two consecutive duplexes\n original value given at command line. */ const char *duplex_distance_help; /**< @brief Distance between target 3' ends of two consecutive duplexes\n help description. */ int minimal_stem_length_arg; /**< @brief Minimal snoRNA stem length\n\n (default='5'). */ char * minimal_stem_length_orig; /**< @brief Minimal snoRNA stem length\n\n original value given at command line. */ const char *minimal_stem_length_help; /**< @brief Minimal snoRNA stem length\n\n help description. */ int maximal_stem_length_arg; /**< @brief Maximal snoRNA stem length\n\n (default='120'). */ char * maximal_stem_length_orig; /**< @brief Maximal snoRNA stem length\n\n original value given at command line. */ const char *maximal_stem_length_help; /**< @brief Maximal snoRNA stem length\n\n help description. */ int minimal_duplex_box_length_arg; /**< @brief Minimal distance between the duplex end and the H/ACA box\n\n (default='11'). */ char * minimal_duplex_box_length_orig; /**< @brief Minimal distance between the duplex end and the H/ACA box\n\n original value given at command line. */ const char *minimal_duplex_box_length_help; /**< @brief Minimal distance between the duplex end and the H/ACA box\n\n help description. */ int maximal_duplex_box_length_arg; /**< @brief Maximal distance between the duplex end and the H/ACA box\n\n (default='16'). */ char * maximal_duplex_box_length_orig; /**< @brief Maximal distance between the duplex end and the H/ACA box\n\n original value given at command line. */ const char *maximal_duplex_box_length_help; /**< @brief Maximal distance between the duplex end and the H/ACA box\n\n help description. */ int minimal_snoRNA_stem_loop_length_arg; /**< @brief Minimal number of nucleotides between the beginning of stem loop and beginning of the snoRNA sequence\n\n (default='1'). */ char * minimal_snoRNA_stem_loop_length_orig; /**< @brief Minimal number of nucleotides between the beginning of stem loop and beginning of the snoRNA sequence\n\n original value given at command line. */ const char *minimal_snoRNA_stem_loop_length_help; /**< @brief Minimal number of nucleotides between the beginning of stem loop and beginning of the snoRNA sequence\n\n help description. */ int maximal_snoRNA_stem_loop_length_arg; /**< @brief Maximal number of nucleotides between the beginning of stem loop and beginning of the snoRNA sequence\n\n (default='100000'). */ char * maximal_snoRNA_stem_loop_length_orig; /**< @brief Maximal number of nucleotides between the beginning of stem loop and beginning of the snoRNA sequence\n\n original value given at command line. */ const char *maximal_snoRNA_stem_loop_length_help; /**< @brief Maximal number of nucleotides between the beginning of stem loop and beginning of the snoRNA sequence\n\n help description. */ int minimal_snoRNA_duplex_length_arg; /**< @brief Minimal distance between duplex start and snoRNA\n\n (default='0'). */ char * minimal_snoRNA_duplex_length_orig; /**< @brief Minimal distance between duplex start and snoRNA\n\n original value given at command line. */ const char *minimal_snoRNA_duplex_length_help; /**< @brief Minimal distance between duplex start and snoRNA\n\n help description. */ int maximal_snoRNA_duplex_length_arg; /**< @brief Maximal distance between duplex start and snoRNA\n\n (default='0'). */ char * maximal_snoRNA_duplex_length_orig; /**< @brief Maximal distance between duplex start and snoRNA\n\n original value given at command line. */ const char *maximal_snoRNA_duplex_length_help; /**< @brief Maximal distance between duplex start and snoRNA\n\n help description. */ int minimal_duplex_stem_energy_arg; /**< @brief Minimal duplex stem energy\n\n (default='-1370'). */ char * minimal_duplex_stem_energy_orig; /**< @brief Minimal duplex stem energy\n\n original value given at command line. */ const char *minimal_duplex_stem_energy_help; /**< @brief Minimal duplex stem energy\n\n help description. */ int minimal_total_energy_arg; /**< @brief Minimal total energy\n\n (default='100000'). */ char * minimal_total_energy_orig; /**< @brief Minimal total energy\n\n original value given at command line. */ const char *minimal_total_energy_help; /**< @brief Minimal total energy\n\n help description. */ int maximal_stem_asymmetry_arg; /**< @brief Maximal snoRNA stem asymmetry\n\n (default='30'). */ char * maximal_stem_asymmetry_orig; /**< @brief Maximal snoRNA stem asymmetry\n\n original value given at command line. */ const char *maximal_stem_asymmetry_help; /**< @brief Maximal snoRNA stem asymmetry\n\n help description. */ int minimal_lower_stem_energy_arg; /**< @brief Minimal lower stem energy\n\n (default='100000'). */ char * minimal_lower_stem_energy_orig; /**< @brief Minimal lower stem energy\n\n original value given at command line. */ const char *minimal_lower_stem_energy_help; /**< @brief Minimal lower stem energy\n\n help description. */ double energy_threshold_arg; /**< @brief Maximal energy difference between the mfe and the desired suboptimal\n (default='-1'). */ char * energy_threshold_orig; /**< @brief Maximal energy difference between the mfe and the desired suboptimal\n original value given at command line. */ const char *energy_threshold_help; /**< @brief Maximal energy difference between the mfe and the desired suboptimal\n help description. */ int produce_ps_flag; /**< @brief Draw annotated 2D structures for a list of dot-bracket structures\n (default=off). */ const char *produce_ps_help; /**< @brief Draw annotated 2D structures for a list of dot-bracket structures\n help description. */ char * output_directory_arg; /**< @brief Set where the generated figures should be stored\n\n (default='./'). */ char * output_directory_orig; /**< @brief Set where the generated figures should be stored\n\n original value given at command line. */ const char *output_directory_help; /**< @brief Set where the generated figures should be stored\n\n help description. */ int direct_redraw_flag; /**< @brief Outputs 2D interactions concurrently with the interaction calculation for each suboptimal interaction. The -I option should be preferred.\n\n (default=off). */ const char *direct_redraw_help; /**< @brief Outputs 2D interactions concurrently with the interaction calculation for each suboptimal interaction. The -I option should be preferred.\n\n help description. */ char * from_RNAup_arg; /**< @brief Specify the directory where accessibility profiles generated by RNAup are found\n\n. */ char * from_RNAup_orig; /**< @brief Specify the directory where accessibility profiles generated by RNAup are found\n\n original value given at command line. */ const char *from_RNAup_help; /**< @brief Specify the directory where accessibility profiles generated by RNAup are found\n\n 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 suffix_given ; /**< @brief Whether suffix was given. */ unsigned int from_RNAplfold_given ; /**< @brief Whether from-RNAplfold was given. */ unsigned int alignment_mode_given ; /**< @brief Whether alignment-mode was given. */ unsigned int fast_folding_given ; /**< @brief Whether fast-folding was given. */ unsigned int extension_cost_given ; /**< @brief Whether extension-cost was given. */ unsigned int minimal_right_duplex_given ; /**< @brief Whether minimal-right-duplex was given. */ unsigned int minimal_loop_energy_given ; /**< @brief Whether minimal-loop-energy was given. */ unsigned int minimal_left_duplex_given ; /**< @brief Whether minimal-left-duplex was given. */ unsigned int minimal_duplex_given ; /**< @brief Whether minimal-duplex was given. */ unsigned int duplex_distance_given ; /**< @brief Whether duplex-distance was given. */ unsigned int minimal_stem_length_given ; /**< @brief Whether minimal-stem-length was given. */ unsigned int maximal_stem_length_given ; /**< @brief Whether maximal-stem-length was given. */ unsigned int minimal_duplex_box_length_given ; /**< @brief Whether minimal-duplex-box-length was given. */ unsigned int maximal_duplex_box_length_given ; /**< @brief Whether maximal-duplex-box-length was given. */ unsigned int minimal_snoRNA_stem_loop_length_given ; /**< @brief Whether minimal-snoRNA-stem-loop-length was given. */ unsigned int maximal_snoRNA_stem_loop_length_given ; /**< @brief Whether maximal-snoRNA-stem-loop-length was given. */ unsigned int minimal_snoRNA_duplex_length_given ; /**< @brief Whether minimal-snoRNA-duplex-length was given. */ unsigned int maximal_snoRNA_duplex_length_given ; /**< @brief Whether maximal-snoRNA-duplex-length was given. */ unsigned int minimal_duplex_stem_energy_given ; /**< @brief Whether minimal-duplex-stem-energy was given. */ unsigned int minimal_total_energy_given ; /**< @brief Whether minimal-total-energy was given. */ unsigned int maximal_stem_asymmetry_given ; /**< @brief Whether maximal-stem-asymmetry was given. */ unsigned int minimal_lower_stem_energy_given ; /**< @brief Whether minimal-lower-stem-energy 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 output_directory_given ; /**< @brief Whether output_directory was given. */ unsigned int direct_redraw_given ; /**< @brief Whether direct-redraw was given. */ unsigned int from_RNAup_given ; /**< @brief Whether from-RNAup was given. */ } ; /** @brief The additional parameters to pass to parser functions */ struct RNAsnoop_cmdline_parser_params { int override; /**< @brief whether to override possibly already present options (default 0) */ int initialize; /**< @brief whether to initialize the option structure RNAsnoop_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 RNAsnoop_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 *RNAsnoop_args_info_purpose; /** @brief the usage string of the program */ extern const char *RNAsnoop_args_info_usage; /** @brief all the lines making the help output */ extern const char *RNAsnoop_args_info_help[]; /** @brief all the lines making the detailed help output (including hidden options and details) */ extern const char *RNAsnoop_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 RNAsnoop_cmdline_parser (int argc, char **argv, struct RNAsnoop_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 RNAsnoop_cmdline_parser_ext() instead */ int RNAsnoop_cmdline_parser2 (int argc, char **argv, struct RNAsnoop_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 RNAsnoop_cmdline_parser_ext (int argc, char **argv, struct RNAsnoop_args_info *args_info, struct RNAsnoop_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 RNAsnoop_cmdline_parser_dump(FILE *outfile, struct RNAsnoop_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 RNAsnoop_cmdline_parser_file_save(const char *filename, struct RNAsnoop_args_info *args_info); /** * Print the help */ void RNAsnoop_cmdline_parser_print_help(void); /** * Print the detailed help (including hidden options and details) */ void RNAsnoop_cmdline_parser_print_detailed_help(void); /** * Print the version */ void RNAsnoop_cmdline_parser_print_version(void); /** * Initializes all the fields a RNAsnoop_cmdline_parser_params structure * to their default values * @param params the structure to initialize */ void RNAsnoop_cmdline_parser_params_init(struct RNAsnoop_cmdline_parser_params *params); /** * Allocates dynamically a RNAsnoop_cmdline_parser_params structure and initializes * all its fields to their default values * @return the created and initialized RNAsnoop_cmdline_parser_params structure */ struct RNAsnoop_cmdline_parser_params *RNAsnoop_cmdline_parser_params_create(void); /** * Initializes the passed RNAsnoop_args_info structure's fields * (also set default values for options that have a default) * @param args_info the structure to initialize */ void RNAsnoop_cmdline_parser_init (struct RNAsnoop_args_info *args_info); /** * Deallocates the string fields of the RNAsnoop_args_info structure * (but does not deallocate the structure itself) * @param args_info the structure to deallocate */ void RNAsnoop_cmdline_parser_free (struct RNAsnoop_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 RNAsnoop_cmdline_parser_required (struct RNAsnoop_args_info *args_info, const char *prog_name); #ifdef __cplusplus } #endif /* __cplusplus */ #endif /* RNASNOOP_CMDL_H */