/** @file cmdline.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 CMDLINE_H #define CMDLINE_H /* If we use autoconf. */ #ifdef HAVE_CONFIG_H #include "config.h" #endif #include /* for FILE */ #ifdef __cplusplus extern "C" { #endif /* __cplusplus */ #ifndef CMDLINE_PARSER_PACKAGE /** @brief the program name (used for printing errors) */ #define CMDLINE_PARSER_PACKAGE "Kinfold" #endif #ifndef CMDLINE_PARSER_PACKAGE_NAME /** @brief the complete program name (used for help and version) */ #define CMDLINE_PARSER_PACKAGE_NAME "Kinfold" #endif #ifndef CMDLINE_PARSER_VERSION /** @brief the program version */ #define CMDLINE_PARSER_VERSION VERSION #endif /** @brief Where the command line options are stored */ struct gengetopt_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. */ int dangle_arg; /**< @brief <0|1|2> set dangling end model to (none|normal|double) (default='2'). */ char * dangle_orig; /**< @brief <0|1|2> set dangling end model to (none|normal|double) original value given at command line. */ const char *dangle_help; /**< @brief <0|1|2> set dangling end model to (none|normal|double) help description. */ float Temp_arg; /**< @brief simulation temperature (default='37'). */ char * Temp_orig; /**< @brief simulation temperature original value given at command line. */ const char *Temp_help; /**< @brief simulation temperature help description. */ char * Par_arg; /**< @brief read energy-parameter-file. */ char * Par_orig; /**< @brief read energy-parameter-file original value given at command line. */ const char *Par_help; /**< @brief read energy-parameter-file help description. */ int logML_flag; /**< @brief use logarithmic multiloop energies instead of linear (default=on). */ const char *logML_help; /**< @brief use logarithmic multiloop energies instead of linear help description. */ int noShift_flag; /**< @brief turn off shift-moves (default=off). */ const char *noShift_help; /**< @brief turn off shift-moves help description. */ int noLP_flag; /**< @brief forbid structures with isolated base-pairs (default=off). */ const char *noLP_help; /**< @brief forbid structures with isolated base-pairs help description. */ char * seed_arg; /**< @brief set random number seed specify 3 integers as int=int=int (default='clock'). */ char * seed_orig; /**< @brief set random number seed specify 3 integers as int=int=int original value given at command line. */ const char *seed_help; /**< @brief set random number seed specify 3 integers as int=int=int help description. */ float time_arg; /**< @brief set maxtime of simulation (default='500'). */ char * time_orig; /**< @brief set maxtime of simulation original value given at command line. */ const char *time_help; /**< @brief set maxtime of simulation help description. */ int num_arg; /**< @brief set number of trajectories (default='1'). */ char * num_orig; /**< @brief set number of trajectories original value given at command line. */ const char *num_help; /**< @brief set number of trajectories help description. */ int start_flag; /**< @brief read start structure from stdin (otherwise use open chain) (default=off). */ const char *start_help; /**< @brief read start structure from stdin (otherwise use open chain) help description. */ int stop_flag; /**< @brief read stop structure(s) from stdin (optherwise use MFE) (default=off). */ const char *stop_help; /**< @brief read stop structure(s) from stdin (optherwise use MFE) help description. */ int met_flag; /**< @brief use Metropolis rule for rates (not Kawasaki rule) (default=off). */ const char *met_help; /**< @brief use Metropolis rule for rates (not Kawasaki rule) help description. */ int fpt_flag; /**< @brief compute first passage time (stop when a stop-structure is reached) (default=on). */ const char *fpt_help; /**< @brief compute first passage time (stop when a stop-structure is reached) help description. */ float grow_arg; /**< @brief grow chain every time units (default='0'). */ char * grow_orig; /**< @brief grow chain every time units original value given at command line. */ const char *grow_help; /**< @brief grow chain every time units help description. */ int glen_arg; /**< @brief initial size of growing chain (default='15'). */ char * glen_orig; /**< @brief initial size of growing chain original value given at command line. */ const char *glen_help; /**< @brief initial size of growing chain help description. */ double phi_arg; /**< @brief set phi value. */ char * phi_orig; /**< @brief set phi value original value given at command line. */ const char *phi_help; /**< @brief set phi value help description. */ char * pbounds_arg; /**< @brief specify 3 floats for phi_min, phi_inc, phi_max in the form . */ char * pbounds_orig; /**< @brief specify 3 floats for phi_min, phi_inc, phi_max in the form original value given at command line. */ const char *pbounds_help; /**< @brief specify 3 floats for phi_min, phi_inc, phi_max in the form help description. */ char * log_arg; /**< @brief set basename of log-file (default='kinout'). */ char * log_orig; /**< @brief set basename of log-file original value given at command line. */ const char *log_help; /**< @brief set basename of log-file help description. */ int silent_flag; /**< @brief no output to stdout (default=off). */ const char *silent_help; /**< @brief no output to stdout help description. */ int verbose_flag; /**< @brief more information to stdout (default=off). */ const char *verbose_help; /**< @brief more information to stdout help description. */ int lmin_flag; /**< @brief output only local minima to stdout (default=off). */ const char *lmin_help; /**< @brief output only local minima to stdout help description. */ float cut_arg; /**< @brief output structures with E <= to stdout (default='20'). */ char * cut_orig; /**< @brief output structures with E <= to stdout original value given at command line. */ const char *cut_help; /**< @brief output structures with E <= to stdout 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 dangle_given ; /**< @brief Whether dangle was given. */ unsigned int Temp_given ; /**< @brief Whether Temp was given. */ unsigned int Par_given ; /**< @brief Whether Par was given. */ unsigned int logML_given ; /**< @brief Whether logML was given. */ unsigned int noShift_given ; /**< @brief Whether noShift was given. */ unsigned int noLP_given ; /**< @brief Whether noLP was given. */ unsigned int seed_given ; /**< @brief Whether seed was given. */ unsigned int time_given ; /**< @brief Whether time was given. */ unsigned int num_given ; /**< @brief Whether num was given. */ unsigned int start_given ; /**< @brief Whether start was given. */ unsigned int stop_given ; /**< @brief Whether stop was given. */ unsigned int met_given ; /**< @brief Whether met was given. */ unsigned int fpt_given ; /**< @brief Whether fpt was given. */ unsigned int grow_given ; /**< @brief Whether grow was given. */ unsigned int glen_given ; /**< @brief Whether glen was given. */ unsigned int phi_given ; /**< @brief Whether phi was given. */ unsigned int pbounds_given ; /**< @brief Whether pbounds was given. */ unsigned int log_given ; /**< @brief Whether log was given. */ unsigned int silent_given ; /**< @brief Whether silent was given. */ unsigned int verbose_given ; /**< @brief Whether verbose was given. */ unsigned int lmin_given ; /**< @brief Whether lmin was given. */ unsigned int cut_given ; /**< @brief Whether cut was given. */ } ; /** @brief The additional parameters to pass to parser functions */ struct cmdline_parser_params { int override; /**< @brief whether to override possibly already present options (default 0) */ int initialize; /**< @brief whether to initialize the option structure gengetopt_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 gengetopt_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 *gengetopt_args_info_purpose; /** @brief the usage string of the program */ extern const char *gengetopt_args_info_usage; /** @brief all the lines making the help output */ extern const char *gengetopt_args_info_help[]; /** @brief all the lines making the full help output (including hidden options) */ extern const char *gengetopt_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 cmdline_parser (int argc, char **argv, struct gengetopt_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 cmdline_parser_ext() instead */ int cmdline_parser2 (int argc, char **argv, struct gengetopt_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 cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info, struct 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 cmdline_parser_dump(FILE *outfile, struct gengetopt_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 cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info); /** * Print the help */ void cmdline_parser_print_help(void); /** * Print the full help (including hidden options) */ void cmdline_parser_print_full_help(void); /** * Print the version */ void cmdline_parser_print_version(void); /** * Initializes all the fields a cmdline_parser_params structure * to their default values * @param params the structure to initialize */ void cmdline_parser_params_init(struct cmdline_parser_params *params); /** * Allocates dynamically a cmdline_parser_params structure and initializes * all its fields to their default values * @return the created and initialized cmdline_parser_params structure */ struct cmdline_parser_params *cmdline_parser_params_create(void); /** * Initializes the passed gengetopt_args_info structure's fields * (also set default values for options that have a default) * @param args_info the structure to initialize */ void cmdline_parser_init (struct gengetopt_args_info *args_info); /** * Deallocates the string fields of the gengetopt_args_info structure * (but does not deallocate the structure itself) * @param args_info the structure to deallocate */ void cmdline_parser_free (struct gengetopt_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 cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name); extern const char *cmdline_parser_dangle_values[]; /**< @brief Possible values for dangle. */ #ifdef __cplusplus } #endif /* __cplusplus */ #endif /* CMDLINE_H */