X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2FViennaRNA%2FProgs%2FRNAplfold_cmdl.h;fp=binaries%2Fsrc%2FViennaRNA%2FProgs%2FRNAplfold_cmdl.h;h=e6b50863fee900a5434886155d269a00fdaa70c2;hb=7522ace91fc0804a9719dbac9f68bc8154da3132;hp=0000000000000000000000000000000000000000;hpb=8116c0444fe98e8eb21bcdd8ded06e1429085823;p=jabaws.git diff --git a/binaries/src/ViennaRNA/Progs/RNAplfold_cmdl.h b/binaries/src/ViennaRNA/Progs/RNAplfold_cmdl.h new file mode 100644 index 0000000..e6b5086 --- /dev/null +++ b/binaries/src/ViennaRNA/Progs/RNAplfold_cmdl.h @@ -0,0 +1,338 @@ +/** @file RNAplfold_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 RNAPLFOLD_CMDL_H +#define RNAPLFOLD_CMDL_H + +/* If we use autoconf. */ +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include /* for FILE */ + +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +#ifndef RNAPLFOLD_CMDLINE_PARSER_PACKAGE +/** @brief the program name (used for printing errors) */ +#define RNAPLFOLD_CMDLINE_PARSER_PACKAGE "RNAplfold" +#endif + +#ifndef RNAPLFOLD_CMDLINE_PARSER_PACKAGE_NAME +/** @brief the complete program name (used for help and version) */ +#define RNAPLFOLD_CMDLINE_PARSER_PACKAGE_NAME "RNAplfold" +#endif + +#ifndef RNAPLFOLD_CMDLINE_PARSER_VERSION +/** @brief the program version */ +#define RNAPLFOLD_CMDLINE_PARSER_VERSION VERSION +#endif + +/** @brief Where the command line options are stored */ +struct RNAplfold_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 *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 winsize_arg; /**< @brief Average the pair probabilities over windows of given size + + (default='70'). */ + char * winsize_orig; /**< @brief Average the pair probabilities over windows of given size + + original value given at command line. */ + const char *winsize_help; /**< @brief Average the pair probabilities over windows of given size + + help description. */ + int span_arg; /**< @brief Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with j-i > span will be allowed. Defaults to winsize if parameter is omitted + +. */ + char * span_orig; /**< @brief Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with j-i > span will be allowed. Defaults to winsize if parameter is omitted + + original value given at command line. */ + const char *span_help; /**< @brief Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with j-i > span will be allowed. Defaults to winsize if parameter is omitted + + 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. */ + int print_onthefly_flag; /**< @brief Save memory by printing out everything during computation. + NOTE: activated per default for sequences over 1M bp. + + (default=off). */ + const char *print_onthefly_help; /**< @brief Save memory by printing out everything during computation. + NOTE: activated per default for sequences over 1M bp. + + help description. */ + int ulength_arg; /**< @brief Compute the mean probability that regions of length 1 to a given length are unpaired. Output is saved in a _lunp file. + + (default='31'). */ + char * ulength_orig; /**< @brief Compute the mean probability that regions of length 1 to a given length are unpaired. Output is saved in a _lunp file. + + original value given at command line. */ + const char *ulength_help; /**< @brief Compute the mean probability that regions of length 1 to a given length are unpaired. Output is saved in a _lunp file. + + help description. */ + int opening_energies_flag; /**< @brief Switch output from probabilities to their logarithms, which are NOT exactly the mean energies needed to the respective stretch of bases! + NOTE: This actives -u option. + + (default=off). */ + const char *opening_energies_help; /**< @brief Switch output from probabilities to their logarithms, which are NOT exactly the mean energies needed to the respective stretch of bases! + NOTE: This actives -u option. + + help description. */ + int plex_output_flag; /**< @brief Create additional output files for RNAplex. + + (default=off). */ + const char *plex_output_help; /**< @brief Create additional output files for RNAplex. + + 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. */ + 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 tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. + + (default=off). */ + const char *noTetra_help; /**< @brief Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. + + help description. */ + int dangles_arg; /**< @brief How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops + (default='2'). */ + char * dangles_orig; /**< @brief How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops + original value given at command line. */ + const char *dangles_help; /**< @brief How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops + 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. */ + 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 binaries_flag; /**< @brief Output accessibility profiles in binary format + . (default=off). */ + const char *binaries_help; /**< @brief Output accessibility profiles in binary format + . help description. */ + char * nsp_arg; /**< @brief Allow other pairs in addition to the usual AU,GC,and GU pairs. +. */ + 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. */ + int energyModel_arg; /**< @brief Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs. + +. */ + char * energyModel_orig; /**< @brief Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs. + + original value given at command line. */ + const char *energyModel_help; /**< @brief Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs. + + help description. */ + double betaScale_arg; /**< @brief Set the scaling of the Boltzmann factors + (default='1.'). */ + char * betaScale_orig; /**< @brief Set the scaling of the Boltzmann factors + original value given at command line. */ + const char *betaScale_help; /**< @brief Set the scaling of the Boltzmann factors + help description. */ + + unsigned int help_given ; /**< @brief Whether help was given. */ + unsigned int detailed_help_given ; /**< @brief Whether detailed-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 winsize_given ; /**< @brief Whether winsize was given. */ + unsigned int span_given ; /**< @brief Whether span was given. */ + unsigned int cutoff_given ; /**< @brief Whether cutoff was given. */ + unsigned int print_onthefly_given ; /**< @brief Whether print_onthefly was given. */ + unsigned int ulength_given ; /**< @brief Whether ulength was given. */ + unsigned int opening_energies_given ; /**< @brief Whether opening_energies was given. */ + unsigned int plex_output_given ; /**< @brief Whether plex_output was given. */ + unsigned int noconv_given ; /**< @brief Whether noconv was given. */ + unsigned int temp_given ; /**< @brief Whether temp was given. */ + unsigned int noTetra_given ; /**< @brief Whether noTetra was given. */ + unsigned int dangles_given ; /**< @brief Whether dangles 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 paramFile_given ; /**< @brief Whether paramFile was given. */ + unsigned int binaries_given ; /**< @brief Whether binaries was given. */ + unsigned int nsp_given ; /**< @brief Whether nsp was given. */ + unsigned int energyModel_given ; /**< @brief Whether energyModel was given. */ + unsigned int betaScale_given ; /**< @brief Whether betaScale was given. */ + +} ; + +/** @brief The additional parameters to pass to parser functions */ +struct RNAplfold_cmdline_parser_params +{ + int override; /**< @brief whether to override possibly already present options (default 0) */ + int initialize; /**< @brief whether to initialize the option structure RNAplfold_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 RNAplfold_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 *RNAplfold_args_info_purpose; +/** @brief the usage string of the program */ +extern const char *RNAplfold_args_info_usage; +/** @brief all the lines making the help output */ +extern const char *RNAplfold_args_info_help[]; +/** @brief all the lines making the full help output (including hidden options) */ +extern const char *RNAplfold_args_info_full_help[]; +/** @brief all the lines making the detailed help output (including hidden options and details) */ +extern const char *RNAplfold_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 RNAplfold_cmdline_parser (int argc, char **argv, + struct RNAplfold_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 RNAplfold_cmdline_parser_ext() instead + */ +int RNAplfold_cmdline_parser2 (int argc, char **argv, + struct RNAplfold_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 RNAplfold_cmdline_parser_ext (int argc, char **argv, + struct RNAplfold_args_info *args_info, + struct RNAplfold_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 RNAplfold_cmdline_parser_dump(FILE *outfile, + struct RNAplfold_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 RNAplfold_cmdline_parser_file_save(const char *filename, + struct RNAplfold_args_info *args_info); + +/** + * Print the help + */ +void RNAplfold_cmdline_parser_print_help(void); +/** + * Print the full help (including hidden options) + */ +void RNAplfold_cmdline_parser_print_full_help(void); +/** + * Print the detailed help (including hidden options and details) + */ +void RNAplfold_cmdline_parser_print_detailed_help(void); +/** + * Print the version + */ +void RNAplfold_cmdline_parser_print_version(void); + +/** + * Initializes all the fields a RNAplfold_cmdline_parser_params structure + * to their default values + * @param params the structure to initialize + */ +void RNAplfold_cmdline_parser_params_init(struct RNAplfold_cmdline_parser_params *params); + +/** + * Allocates dynamically a RNAplfold_cmdline_parser_params structure and initializes + * all its fields to their default values + * @return the created and initialized RNAplfold_cmdline_parser_params structure + */ +struct RNAplfold_cmdline_parser_params *RNAplfold_cmdline_parser_params_create(void); + +/** + * Initializes the passed RNAplfold_args_info structure's fields + * (also set default values for options that have a default) + * @param args_info the structure to initialize + */ +void RNAplfold_cmdline_parser_init (struct RNAplfold_args_info *args_info); +/** + * Deallocates the string fields of the RNAplfold_args_info structure + * (but does not deallocate the structure itself) + * @param args_info the structure to deallocate + */ +void RNAplfold_cmdline_parser_free (struct RNAplfold_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 RNAplfold_cmdline_parser_required (struct RNAplfold_args_info *args_info, + const char *prog_name); + + +#ifdef __cplusplus +} +#endif /* __cplusplus */ +#endif /* RNAPLFOLD_CMDL_H */