/* File autogenerated by gengetopt version 2.22.5 generated with the following command: gengetopt -i RNA2Dfold.ggo --file-name=RNA2Dfold_cmdl --include-getopt --default-optional --func-name=RNA2Dfold_cmdline_parser --arg-struct-name=RNA2Dfold_args_info The developers of gengetopt consider the fixed text that goes in all gengetopt output files to be in the public domain: we make no copyright claims on it. */ /* If we use autoconf. */ #ifdef HAVE_CONFIG_H #include "config.h" #endif #include #include #include #ifndef FIX_UNUSED #define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */ #endif #include "RNA2Dfold_cmdl.h" const char *RNA2Dfold_args_info_purpose = "Compute MFE structure, partition function and representative sample structures \nof k,l neighborhoods"; const char *RNA2Dfold_args_info_usage = "Usage: RNA2Dfold [OPTIONS]..."; const char *RNA2Dfold_args_info_description = "The program partitions the secondary structure space into (basepair)distance \nclasses according to two fixed reference structures. It expects a sequence and \ntwo secondary structures in dot-bracket notation as its inputs. For each \ndistance class, the MFE representative, Boltzmann probabilities and Gibbs free \nenergy is computed. Additionally, a stochastic backtracking routine allows to \nproduce samples of representative suboptimal secondary structures from each \npartition\n\n"; const char *RNA2Dfold_args_info_detailed_help[] = { " -h, --help Print help and exit", " --detailed-help Print help, including all details and hidden \n options, and exit", " -V, --version Print version and exit", "\nGeneral Options:", " Below are command line options which alter the general behavior of this \n program\n\n", " --noconv Do not automatically substitude nucleotide \n \"T\" with \"U\"\n\n (default=off)", " -j, --numThreads=INT Set the number of threads used for calculations \n (only available when compiled with OpenMP \n support)\n\n", "\nAlgorithms:", " -p, --partfunc calculate partition function and thus, \n Boltzmann probabilities and Gibbs free energy\n\n (default=off)", " --stochBT=INT backtrack a certain number of Boltzmann samples \n from the appropriate k,l neighborhood(s)\n\n", " --neighborhood=: backtrack structures from certain \n k,l-neighborhood only, can be specified \n multiple times (:,:,...)\n\n", " -S, --pfScale=DOUBLE scaling factor for pf to avoid overflows\n\n", " --noBT do not backtrack structures, calculate energy \n contributions only\n\n (default=off)", " -c, --circ Assume a circular (instead of linear) RNA \n molecule.\n\n (default=off)", "\nModel Details:", " -T, --temp=DOUBLE Rescale energy parameters to a temperature of \n temp C. Default is 37C.\n\n", " -K, --maxDist1=INT maximum distance to first reference structure", " If this value is set all structures that exhibit a basepair distance greater \n than maxDist1 will be thrown into a distance class denoted by K=L=-1\n\n", " -L, --maxDist2=INT maximum distance to second reference structure", " If this value is set all structures that exhibit a basepair distance greater \n than maxDist1 will be thrown into a distance class denoted by K=L=-1\n\n", " -4, --noTetra Do not include special tabulated stabilizing \n energies for tri-, tetra- and hexaloop \n hairpins. Mostly for testing.\n\n (default=off)", " -P, --parameterFile=paramfile Read energy parameters from paramfile, instead \n of using the default parameter set.\n", " A sample parameter file should accompany your distribution.\n See the RNAlib documentation for details on the file format.\n\n", " -d, --dangles=INT How to treat \"dangling end\" energies for \n bases adjacent to helices in free ends and \n multi-loops\n (possible values=\"0\", \"2\" default=`2')", " \n With -d2 dangling energies will be added for the bases adjacent to a helix on \n both sides\n in any case.\n The option -d0 ignores dangling ends altogether (mostly for debugging).\n\n", " --noGU Do not allow GU pairs\n\n (default=off)", " --noClosingGU Do not allow GU pairs at the end of helices\n\n (default=off)", "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to rna@tbi.univie.ac.at.\n\n", 0 }; static void init_help_array(void) { RNA2Dfold_args_info_help[0] = RNA2Dfold_args_info_detailed_help[0]; RNA2Dfold_args_info_help[1] = RNA2Dfold_args_info_detailed_help[1]; RNA2Dfold_args_info_help[2] = RNA2Dfold_args_info_detailed_help[2]; RNA2Dfold_args_info_help[3] = RNA2Dfold_args_info_detailed_help[3]; RNA2Dfold_args_info_help[4] = RNA2Dfold_args_info_detailed_help[4]; RNA2Dfold_args_info_help[5] = RNA2Dfold_args_info_detailed_help[5]; RNA2Dfold_args_info_help[6] = RNA2Dfold_args_info_detailed_help[6]; RNA2Dfold_args_info_help[7] = RNA2Dfold_args_info_detailed_help[7]; RNA2Dfold_args_info_help[8] = RNA2Dfold_args_info_detailed_help[8]; RNA2Dfold_args_info_help[9] = RNA2Dfold_args_info_detailed_help[9]; RNA2Dfold_args_info_help[10] = RNA2Dfold_args_info_detailed_help[10]; RNA2Dfold_args_info_help[11] = RNA2Dfold_args_info_detailed_help[11]; RNA2Dfold_args_info_help[12] = RNA2Dfold_args_info_detailed_help[12]; RNA2Dfold_args_info_help[13] = RNA2Dfold_args_info_detailed_help[13]; RNA2Dfold_args_info_help[14] = RNA2Dfold_args_info_detailed_help[14]; RNA2Dfold_args_info_help[15] = RNA2Dfold_args_info_detailed_help[15]; RNA2Dfold_args_info_help[16] = RNA2Dfold_args_info_detailed_help[16]; RNA2Dfold_args_info_help[17] = RNA2Dfold_args_info_detailed_help[18]; RNA2Dfold_args_info_help[18] = RNA2Dfold_args_info_detailed_help[20]; RNA2Dfold_args_info_help[19] = RNA2Dfold_args_info_detailed_help[21]; RNA2Dfold_args_info_help[20] = RNA2Dfold_args_info_detailed_help[23]; RNA2Dfold_args_info_help[21] = RNA2Dfold_args_info_detailed_help[25]; RNA2Dfold_args_info_help[22] = RNA2Dfold_args_info_detailed_help[26]; RNA2Dfold_args_info_help[23] = RNA2Dfold_args_info_detailed_help[27]; RNA2Dfold_args_info_help[24] = 0; } const char *RNA2Dfold_args_info_help[25]; typedef enum {ARG_NO , ARG_FLAG , ARG_STRING , ARG_INT , ARG_DOUBLE } RNA2Dfold_cmdline_parser_arg_type; static void clear_given (struct RNA2Dfold_args_info *args_info); static void clear_args (struct RNA2Dfold_args_info *args_info); static int RNA2Dfold_cmdline_parser_internal (int argc, char **argv, struct RNA2Dfold_args_info *args_info, struct RNA2Dfold_cmdline_parser_params *params, const char *additional_error); static int RNA2Dfold_cmdline_parser_required2 (struct RNA2Dfold_args_info *args_info, const char *prog_name, const char *additional_error); const char *RNA2Dfold_cmdline_parser_dangles_values[] = {"0", "2", 0}; /*< Possible values for dangles. */ static char * gengetopt_strdup (const char *s); static void clear_given (struct RNA2Dfold_args_info *args_info) { args_info->help_given = 0 ; args_info->detailed_help_given = 0 ; args_info->version_given = 0 ; args_info->noconv_given = 0 ; args_info->numThreads_given = 0 ; args_info->partfunc_given = 0 ; args_info->stochBT_given = 0 ; args_info->neighborhood_given = 0 ; args_info->pfScale_given = 0 ; args_info->noBT_given = 0 ; args_info->circ_given = 0 ; args_info->temp_given = 0 ; args_info->maxDist1_given = 0 ; args_info->maxDist2_given = 0 ; args_info->noTetra_given = 0 ; args_info->parameterFile_given = 0 ; args_info->dangles_given = 0 ; args_info->noGU_given = 0 ; args_info->noClosingGU_given = 0 ; } static void clear_args (struct RNA2Dfold_args_info *args_info) { FIX_UNUSED (args_info); args_info->noconv_flag = 0; args_info->numThreads_orig = NULL; args_info->partfunc_flag = 0; args_info->stochBT_orig = NULL; args_info->neighborhood_arg = NULL; args_info->neighborhood_orig = NULL; args_info->pfScale_orig = NULL; args_info->noBT_flag = 0; args_info->circ_flag = 0; args_info->temp_orig = NULL; args_info->maxDist1_orig = NULL; args_info->maxDist2_orig = NULL; args_info->noTetra_flag = 0; args_info->parameterFile_arg = NULL; args_info->parameterFile_orig = NULL; args_info->dangles_arg = 2; args_info->dangles_orig = NULL; args_info->noGU_flag = 0; args_info->noClosingGU_flag = 0; } static void init_args_info(struct RNA2Dfold_args_info *args_info) { init_help_array(); args_info->help_help = RNA2Dfold_args_info_detailed_help[0] ; args_info->detailed_help_help = RNA2Dfold_args_info_detailed_help[1] ; args_info->version_help = RNA2Dfold_args_info_detailed_help[2] ; args_info->noconv_help = RNA2Dfold_args_info_detailed_help[5] ; args_info->numThreads_help = RNA2Dfold_args_info_detailed_help[6] ; args_info->partfunc_help = RNA2Dfold_args_info_detailed_help[8] ; args_info->stochBT_help = RNA2Dfold_args_info_detailed_help[9] ; args_info->neighborhood_help = RNA2Dfold_args_info_detailed_help[10] ; args_info->neighborhood_min = 0; args_info->neighborhood_max = 0; args_info->pfScale_help = RNA2Dfold_args_info_detailed_help[11] ; args_info->noBT_help = RNA2Dfold_args_info_detailed_help[12] ; args_info->circ_help = RNA2Dfold_args_info_detailed_help[13] ; args_info->temp_help = RNA2Dfold_args_info_detailed_help[15] ; args_info->maxDist1_help = RNA2Dfold_args_info_detailed_help[16] ; args_info->maxDist2_help = RNA2Dfold_args_info_detailed_help[18] ; args_info->noTetra_help = RNA2Dfold_args_info_detailed_help[20] ; args_info->parameterFile_help = RNA2Dfold_args_info_detailed_help[21] ; args_info->dangles_help = RNA2Dfold_args_info_detailed_help[23] ; args_info->noGU_help = RNA2Dfold_args_info_detailed_help[25] ; args_info->noClosingGU_help = RNA2Dfold_args_info_detailed_help[26] ; } void RNA2Dfold_cmdline_parser_print_version (void) { printf ("%s %s\n", (strlen(RNA2DFOLD_CMDLINE_PARSER_PACKAGE_NAME) ? RNA2DFOLD_CMDLINE_PARSER_PACKAGE_NAME : RNA2DFOLD_CMDLINE_PARSER_PACKAGE), RNA2DFOLD_CMDLINE_PARSER_VERSION); } static void print_help_common(void) { RNA2Dfold_cmdline_parser_print_version (); if (strlen(RNA2Dfold_args_info_purpose) > 0) printf("\n%s\n", RNA2Dfold_args_info_purpose); if (strlen(RNA2Dfold_args_info_usage) > 0) printf("\n%s\n", RNA2Dfold_args_info_usage); printf("\n"); if (strlen(RNA2Dfold_args_info_description) > 0) printf("%s\n\n", RNA2Dfold_args_info_description); } void RNA2Dfold_cmdline_parser_print_help (void) { int i = 0; print_help_common(); while (RNA2Dfold_args_info_help[i]) printf("%s\n", RNA2Dfold_args_info_help[i++]); } void RNA2Dfold_cmdline_parser_print_detailed_help (void) { int i = 0; print_help_common(); while (RNA2Dfold_args_info_detailed_help[i]) printf("%s\n", RNA2Dfold_args_info_detailed_help[i++]); } void RNA2Dfold_cmdline_parser_init (struct RNA2Dfold_args_info *args_info) { clear_given (args_info); clear_args (args_info); init_args_info (args_info); } void RNA2Dfold_cmdline_parser_params_init(struct RNA2Dfold_cmdline_parser_params *params) { if (params) { params->override = 0; params->initialize = 1; params->check_required = 1; params->check_ambiguity = 0; params->print_errors = 1; } } struct RNA2Dfold_cmdline_parser_params * RNA2Dfold_cmdline_parser_params_create(void) { struct RNA2Dfold_cmdline_parser_params *params = (struct RNA2Dfold_cmdline_parser_params *)malloc(sizeof(struct RNA2Dfold_cmdline_parser_params)); RNA2Dfold_cmdline_parser_params_init(params); return params; } static void free_string_field (char **s) { if (*s) { free (*s); *s = 0; } } /** @brief generic value variable */ union generic_value { int int_arg; double double_arg; char *string_arg; const char *default_string_arg; }; /** @brief holds temporary values for multiple options */ struct generic_list { union generic_value arg; char *orig; struct generic_list *next; }; /** * @brief add a node at the head of the list */ static void add_node(struct generic_list **list) { struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list)); new_node->next = *list; *list = new_node; new_node->arg.string_arg = 0; new_node->orig = 0; } static void free_multiple_string_field(unsigned int len, char ***arg, char ***orig) { unsigned int i; if (*arg) { for (i = 0; i < len; ++i) { free_string_field(&((*arg)[i])); free_string_field(&((*orig)[i])); } free_string_field(&((*arg)[0])); /* free default string */ free (*arg); *arg = 0; free (*orig); *orig = 0; } } static void RNA2Dfold_cmdline_parser_release (struct RNA2Dfold_args_info *args_info) { free_string_field (&(args_info->numThreads_orig)); free_string_field (&(args_info->stochBT_orig)); free_multiple_string_field (args_info->neighborhood_given, &(args_info->neighborhood_arg), &(args_info->neighborhood_orig)); free_string_field (&(args_info->pfScale_orig)); free_string_field (&(args_info->temp_orig)); free_string_field (&(args_info->maxDist1_orig)); free_string_field (&(args_info->maxDist2_orig)); free_string_field (&(args_info->parameterFile_arg)); free_string_field (&(args_info->parameterFile_orig)); free_string_field (&(args_info->dangles_orig)); clear_given (args_info); } /** * @param val the value to check * @param values the possible values * @return the index of the matched value: * -1 if no value matched, * -2 if more than one value has matched */ static int check_possible_values(const char *val, const char *values[]) { int i, found, last; size_t len; if (!val) /* otherwise strlen() crashes below */ return -1; /* -1 means no argument for the option */ found = last = 0; for (i = 0, len = strlen(val); values[i]; ++i) { if (strncmp(val, values[i], len) == 0) { ++found; last = i; if (strlen(values[i]) == len) return i; /* exact macth no need to check more */ } } if (found == 1) /* one match: OK */ return last; return (found ? -2 : -1); /* return many values or none matched */ } static void write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[]) { int found = -1; if (arg) { if (values) { found = check_possible_values(arg, values); } if (found >= 0) fprintf(outfile, "%s=\"%s\" # %s\n", opt, arg, values[found]); else fprintf(outfile, "%s=\"%s\"\n", opt, arg); } else { fprintf(outfile, "%s\n", opt); } } static void write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, const char *values[]) { int i; for (i = 0; i < len; ++i) write_into_file(outfile, opt, (arg ? arg[i] : 0), values); } int RNA2Dfold_cmdline_parser_dump(FILE *outfile, struct RNA2Dfold_args_info *args_info) { int i = 0; if (!outfile) { fprintf (stderr, "%s: cannot dump options to stream\n", RNA2DFOLD_CMDLINE_PARSER_PACKAGE); return EXIT_FAILURE; } if (args_info->help_given) write_into_file(outfile, "help", 0, 0 ); if (args_info->detailed_help_given) write_into_file(outfile, "detailed-help", 0, 0 ); if (args_info->version_given) write_into_file(outfile, "version", 0, 0 ); if (args_info->noconv_given) write_into_file(outfile, "noconv", 0, 0 ); if (args_info->numThreads_given) write_into_file(outfile, "numThreads", args_info->numThreads_orig, 0); if (args_info->partfunc_given) write_into_file(outfile, "partfunc", 0, 0 ); if (args_info->stochBT_given) write_into_file(outfile, "stochBT", args_info->stochBT_orig, 0); write_multiple_into_file(outfile, args_info->neighborhood_given, "neighborhood", args_info->neighborhood_orig, 0); if (args_info->pfScale_given) write_into_file(outfile, "pfScale", args_info->pfScale_orig, 0); if (args_info->noBT_given) write_into_file(outfile, "noBT", 0, 0 ); if (args_info->circ_given) write_into_file(outfile, "circ", 0, 0 ); if (args_info->temp_given) write_into_file(outfile, "temp", args_info->temp_orig, 0); if (args_info->maxDist1_given) write_into_file(outfile, "maxDist1", args_info->maxDist1_orig, 0); if (args_info->maxDist2_given) write_into_file(outfile, "maxDist2", args_info->maxDist2_orig, 0); if (args_info->noTetra_given) write_into_file(outfile, "noTetra", 0, 0 ); if (args_info->parameterFile_given) write_into_file(outfile, "parameterFile", args_info->parameterFile_orig, 0); if (args_info->dangles_given) write_into_file(outfile, "dangles", args_info->dangles_orig, RNA2Dfold_cmdline_parser_dangles_values); if (args_info->noGU_given) write_into_file(outfile, "noGU", 0, 0 ); if (args_info->noClosingGU_given) write_into_file(outfile, "noClosingGU", 0, 0 ); i = EXIT_SUCCESS; return i; } int RNA2Dfold_cmdline_parser_file_save(const char *filename, struct RNA2Dfold_args_info *args_info) { FILE *outfile; int i = 0; outfile = fopen(filename, "w"); if (!outfile) { fprintf (stderr, "%s: cannot open file for writing: %s\n", RNA2DFOLD_CMDLINE_PARSER_PACKAGE, filename); return EXIT_FAILURE; } i = RNA2Dfold_cmdline_parser_dump(outfile, args_info); fclose (outfile); return i; } void RNA2Dfold_cmdline_parser_free (struct RNA2Dfold_args_info *args_info) { RNA2Dfold_cmdline_parser_release (args_info); } /** @brief replacement of strdup, which is not standard */ char * gengetopt_strdup (const char *s) { char *result = 0; if (!s) return result; result = (char*)malloc(strlen(s) + 1); if (result == (char*)0) return (char*)0; strcpy(result, s); return result; } static char * get_multiple_arg_token(const char *arg) { const char *tok; char *ret; size_t len, num_of_escape, i, j; if (!arg) return 0; tok = strchr (arg, ','); num_of_escape = 0; /* make sure it is not escaped */ while (tok) { if (*(tok-1) == '\\') { /* find the next one */ tok = strchr (tok+1, ','); ++num_of_escape; } else break; } if (tok) len = (size_t)(tok - arg + 1); else len = strlen (arg) + 1; len -= num_of_escape; ret = (char *) malloc (len); i = 0; j = 0; while (arg[i] && (j < len-1)) { if (arg[i] == '\\' && arg[ i + 1 ] && arg[ i + 1 ] == ',') ++i; ret[j++] = arg[i++]; } ret[len-1] = '\0'; return ret; } static const char * get_multiple_arg_token_next(const char *arg) { const char *tok; if (!arg) return 0; tok = strchr (arg, ','); /* make sure it is not escaped */ while (tok) { if (*(tok-1) == '\\') { /* find the next one */ tok = strchr (tok+1, ','); } else break; } if (! tok || strlen(tok) == 1) return 0; return tok+1; } static int check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc); int check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc) { int error = 0; if (option_given && (min > 0 || max > 0)) { if (min > 0 && max > 0) { if (min == max) { /* specific occurrences */ if (option_given != (unsigned int) min) { fprintf (stderr, "%s: %s option occurrences must be %d\n", prog_name, option_desc, min); error = 1; } } else if (option_given < (unsigned int) min || option_given > (unsigned int) max) { /* range occurrences */ fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n", prog_name, option_desc, min, max); error = 1; } } else if (min > 0) { /* at least check */ if (option_given < min) { fprintf (stderr, "%s: %s option occurrences must be at least %d\n", prog_name, option_desc, min); error = 1; } } else if (max > 0) { /* at most check */ if (option_given > max) { fprintf (stderr, "%s: %s option occurrences must be at most %d\n", prog_name, option_desc, max); error = 1; } } } return error; } int RNA2Dfold_cmdline_parser (int argc, char **argv, struct RNA2Dfold_args_info *args_info) { return RNA2Dfold_cmdline_parser2 (argc, argv, args_info, 0, 1, 1); } int RNA2Dfold_cmdline_parser_ext (int argc, char **argv, struct RNA2Dfold_args_info *args_info, struct RNA2Dfold_cmdline_parser_params *params) { int result; result = RNA2Dfold_cmdline_parser_internal (argc, argv, args_info, params, 0); if (result == EXIT_FAILURE) { RNA2Dfold_cmdline_parser_free (args_info); exit (EXIT_FAILURE); } return result; } int RNA2Dfold_cmdline_parser2 (int argc, char **argv, struct RNA2Dfold_args_info *args_info, int override, int initialize, int check_required) { int result; struct RNA2Dfold_cmdline_parser_params params; params.override = override; params.initialize = initialize; params.check_required = check_required; params.check_ambiguity = 0; params.print_errors = 1; result = RNA2Dfold_cmdline_parser_internal (argc, argv, args_info, ¶ms, 0); if (result == EXIT_FAILURE) { RNA2Dfold_cmdline_parser_free (args_info); exit (EXIT_FAILURE); } return result; } int RNA2Dfold_cmdline_parser_required (struct RNA2Dfold_args_info *args_info, const char *prog_name) { int result = EXIT_SUCCESS; if (RNA2Dfold_cmdline_parser_required2(args_info, prog_name, 0) > 0) result = EXIT_FAILURE; if (result == EXIT_FAILURE) { RNA2Dfold_cmdline_parser_free (args_info); exit (EXIT_FAILURE); } return result; } int RNA2Dfold_cmdline_parser_required2 (struct RNA2Dfold_args_info *args_info, const char *prog_name, const char *additional_error) { int error = 0; FIX_UNUSED (additional_error); /* checks for required options */ if (check_multiple_option_occurrences(prog_name, args_info->neighborhood_given, args_info->neighborhood_min, args_info->neighborhood_max, "'--neighborhood'")) error = 1; /* checks for dependences among options */ if (args_info->neighborhood_given && ! args_info->stochBT_given) { fprintf (stderr, "%s: '--neighborhood' option depends on option 'stochBT'%s\n", prog_name, (additional_error ? additional_error : "")); error = 1; } return error; } /* * Extracted from the glibc source tree, version 2.3.6 * * Licensed under the GPL as per the whole glibc source tree. * * This file was modified so that getopt_long can be called * many times without risking previous memory to be spoiled. * * Modified by Andre Noll and Lorenzo Bettini for use in * GNU gengetopt generated files. * */ /* * we must include anything we need since this file is not thought to be * inserted in a file already using getopt.h * * Lorenzo */ struct option { const char *name; /* has_arg can't be an enum because some compilers complain about type mismatches in all the code that assumes it is an int. */ int has_arg; int *flag; int val; }; /* This version of `getopt' appears to the caller like standard Unix `getopt' but it behaves differently for the user, since it allows the user to intersperse the options with the other arguments. As `getopt' works, it permutes the elements of ARGV so that, when it is done, all the options precede everything else. Thus all application programs are extended to handle flexible argument order. */ /* If the field `flag' is not NULL, it points to a variable that is set to the value given in the field `val' when the option is found, but left unchanged if the option is not found. To have a long-named option do something other than set an `int' to a compiled-in constant, such as set a value from `custom_optarg', set the option's `flag' field to zero and its `val' field to a nonzero value (the equivalent single-letter option character, if there is one). For long options that have a zero `flag' field, `getopt' returns the contents of the `val' field. */ /* Names for the values of the `has_arg' field of `struct option'. */ #ifndef no_argument #define no_argument 0 #endif #ifndef required_argument #define required_argument 1 #endif #ifndef optional_argument #define optional_argument 2 #endif struct custom_getopt_data { /* * These have exactly the same meaning as the corresponding global variables, * except that they are used for the reentrant versions of getopt. */ int custom_optind; int custom_opterr; int custom_optopt; char *custom_optarg; /* True if the internal members have been initialized. */ int initialized; /* * The next char to be scanned in the option-element in which the last option * character we returned was found. This allows us to pick up the scan where * we left off. If this is zero, or a null string, it means resume the scan by * advancing to the next ARGV-element. */ char *nextchar; /* * Describe the part of ARGV that contains non-options that have been skipped. * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is * the index after the last of them. */ int first_nonopt; int last_nonopt; }; /* * the variables optarg, optind, opterr and optopt are renamed with * the custom_ prefix so that they don't interfere with getopt ones. * * Moreover they're static so they are visible only from within the * file where this very file will be included. */ /* * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an * option that takes an argument, the argument value is returned here. */ static char *custom_optarg; /* * Index in ARGV of the next element to be scanned. This is used for * communication to and from the caller and for communication between * successive calls to `custom_getopt'. * * On entry to `custom_getopt', 1 means this is the first call; initialize. * * When `custom_getopt' returns -1, this is the index of the first of the non-option * elements that the caller should itself scan. * * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV * has been scanned so far. * * 1003.2 says this must be 1 before any call. */ static int custom_optind = 1; /* * Callers store zero here to inhibit the error message for unrecognized * options. */ static int custom_opterr = 1; /* * Set to an option character which was unrecognized. This must be initialized * on some systems to avoid linking in the system's own getopt implementation. */ static int custom_optopt = '?'; /* * Exchange two adjacent subsequences of ARGV. One subsequence is elements * [first_nonopt,last_nonopt) which contains all the non-options that have been * skipped so far. The other is elements [last_nonopt,custom_optind), which contains * all the options processed since those non-options were skipped. * `first_nonopt' and `last_nonopt' are relocated so that they describe the new * indices of the non-options in ARGV after they are moved. */ static void exchange(char **argv, struct custom_getopt_data *d) { int bottom = d->first_nonopt; int middle = d->last_nonopt; int top = d->custom_optind; char *tem; /* * Exchange the shorter segment with the far end of the longer segment. * That puts the shorter segment into the right place. It leaves the * longer segment in the right place overall, but it consists of two * parts that need to be swapped next. */ while (top > middle && middle > bottom) { if (top - middle > middle - bottom) { /* Bottom segment is the short one. */ int len = middle - bottom; int i; /* Swap it with the top part of the top segment. */ for (i = 0; i < len; i++) { tem = argv[bottom + i]; argv[bottom + i] = argv[top - (middle - bottom) + i]; argv[top - (middle - bottom) + i] = tem; } /* Exclude the moved bottom segment from further swapping. */ top -= len; } else { /* Top segment is the short one. */ int len = top - middle; int i; /* Swap it with the bottom part of the bottom segment. */ for (i = 0; i < len; i++) { tem = argv[bottom + i]; argv[bottom + i] = argv[middle + i]; argv[middle + i] = tem; } /* Exclude the moved top segment from further swapping. */ bottom += len; } } /* Update records for the slots the non-options now occupy. */ d->first_nonopt += (d->custom_optind - d->last_nonopt); d->last_nonopt = d->custom_optind; } /* Initialize the internal data when the first call is made. */ static void custom_getopt_initialize(struct custom_getopt_data *d) { /* * Start processing options with ARGV-element 1 (since ARGV-element 0 * is the program name); the sequence of previously skipped non-option * ARGV-elements is empty. */ d->first_nonopt = d->last_nonopt = d->custom_optind; d->nextchar = NULL; d->initialized = 1; } #define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0') /* return: zero: continue, nonzero: return given value to user */ static int shuffle_argv(int argc, char *const *argv,const struct option *longopts, struct custom_getopt_data *d) { /* * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been * moved back by the user (who may also have changed the arguments). */ if (d->last_nonopt > d->custom_optind) d->last_nonopt = d->custom_optind; if (d->first_nonopt > d->custom_optind) d->first_nonopt = d->custom_optind; /* * If we have just processed some options following some * non-options, exchange them so that the options come first. */ if (d->first_nonopt != d->last_nonopt && d->last_nonopt != d->custom_optind) exchange((char **) argv, d); else if (d->last_nonopt != d->custom_optind) d->first_nonopt = d->custom_optind; /* * Skip any additional non-options and extend the range of * non-options previously skipped. */ while (d->custom_optind < argc && NONOPTION_P) d->custom_optind++; d->last_nonopt = d->custom_optind; /* * The special ARGV-element `--' means premature end of options. Skip * it like a null option, then exchange with previous non-options as if * it were an option, then skip everything else like a non-option. */ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) { d->custom_optind++; if (d->first_nonopt != d->last_nonopt && d->last_nonopt != d->custom_optind) exchange((char **) argv, d); else if (d->first_nonopt == d->last_nonopt) d->first_nonopt = d->custom_optind; d->last_nonopt = argc; d->custom_optind = argc; } /* * If we have done all the ARGV-elements, stop the scan and back over * any non-options that we skipped and permuted. */ if (d->custom_optind == argc) { /* * Set the next-arg-index to point at the non-options that we * previously skipped, so the caller will digest them. */ if (d->first_nonopt != d->last_nonopt) d->custom_optind = d->first_nonopt; return -1; } /* * If we have come to a non-option and did not permute it, either stop * the scan or describe it to the caller and pass it by. */ if (NONOPTION_P) { d->custom_optarg = argv[d->custom_optind++]; return 1; } /* * We have found another option-ARGV-element. Skip the initial * punctuation. */ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-')); return 0; } /* * Check whether the ARGV-element is a long option. * * If there's a long option "fubar" and the ARGV-element is "-fu", consider * that an abbreviation of the long option, just like "--fu", and not "-f" with * arg "u". * * This distinction seems to be the most useful approach. * */ static int check_long_opt(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *longind, int print_errors, struct custom_getopt_data *d) { char *nameend; const struct option *p; const struct option *pfound = NULL; int exact = 0; int ambig = 0; int indfound = -1; int option_index; for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++) /* Do nothing. */ ; /* Test all long options for either exact match or abbreviated matches */ for (p = longopts, option_index = 0; p->name; p++, option_index++) if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) { if ((unsigned int) (nameend - d->nextchar) == (unsigned int) strlen(p->name)) { /* Exact match found. */ pfound = p; indfound = option_index; exact = 1; break; } else if (pfound == NULL) { /* First nonexact match found. */ pfound = p; indfound = option_index; } else if (pfound->has_arg != p->has_arg || pfound->flag != p->flag || pfound->val != p->val) /* Second or later nonexact match found. */ ambig = 1; } if (ambig && !exact) { if (print_errors) { fprintf(stderr, "%s: option `%s' is ambiguous\n", argv[0], argv[d->custom_optind]); } d->nextchar += strlen(d->nextchar); d->custom_optind++; d->custom_optopt = 0; return '?'; } if (pfound) { option_index = indfound; d->custom_optind++; if (*nameend) { if (pfound->has_arg != no_argument) d->custom_optarg = nameend + 1; else { if (print_errors) { if (argv[d->custom_optind - 1][1] == '-') { /* --option */ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n", argv[0], pfound->name); } else { /* +option or -option */ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n", argv[0], argv[d->custom_optind - 1][0], pfound->name); } } d->nextchar += strlen(d->nextchar); d->custom_optopt = pfound->val; return '?'; } } else if (pfound->has_arg == required_argument) { if (d->custom_optind < argc) d->custom_optarg = argv[d->custom_optind++]; else { if (print_errors) { fprintf(stderr, "%s: option `%s' requires an argument\n", argv[0], argv[d->custom_optind - 1]); } d->nextchar += strlen(d->nextchar); d->custom_optopt = pfound->val; return optstring[0] == ':' ? ':' : '?'; } } d->nextchar += strlen(d->nextchar); if (longind != NULL) *longind = option_index; if (pfound->flag) { *(pfound->flag) = pfound->val; return 0; } return pfound->val; } /* * Can't find it as a long option. If this is not getopt_long_only, or * the option starts with '--' or is not a valid short option, then * it's an error. Otherwise interpret it as a short option. */ if (print_errors) { if (argv[d->custom_optind][1] == '-') { /* --option */ fprintf(stderr, "%s: unrecognized option `--%s'\n", argv[0], d->nextchar); } else { /* +option or -option */ fprintf(stderr, "%s: unrecognized option `%c%s'\n", argv[0], argv[d->custom_optind][0], d->nextchar); } } d->nextchar = (char *) ""; d->custom_optind++; d->custom_optopt = 0; return '?'; } static int check_short_opt(int argc, char *const *argv, const char *optstring, int print_errors, struct custom_getopt_data *d) { char c = *d->nextchar++; const char *temp = strchr(optstring, c); /* Increment `custom_optind' when we start to process its last character. */ if (*d->nextchar == '\0') ++d->custom_optind; if (!temp || c == ':') { if (print_errors) fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c); d->custom_optopt = c; return '?'; } if (temp[1] == ':') { if (temp[2] == ':') { /* This is an option that accepts an argument optionally. */ if (*d->nextchar != '\0') { d->custom_optarg = d->nextchar; d->custom_optind++; } else d->custom_optarg = NULL; d->nextchar = NULL; } else { /* This is an option that requires an argument. */ if (*d->nextchar != '\0') { d->custom_optarg = d->nextchar; /* * If we end this ARGV-element by taking the * rest as an arg, we must advance to the next * element now. */ d->custom_optind++; } else if (d->custom_optind == argc) { if (print_errors) { fprintf(stderr, "%s: option requires an argument -- %c\n", argv[0], c); } d->custom_optopt = c; if (optstring[0] == ':') c = ':'; else c = '?'; } else /* * We already incremented `custom_optind' once; * increment it again when taking next ARGV-elt * as argument. */ d->custom_optarg = argv[d->custom_optind++]; d->nextchar = NULL; } } return c; } /* * Scan elements of ARGV for option characters given in OPTSTRING. * * If an element of ARGV starts with '-', and is not exactly "-" or "--", * then it is an option element. The characters of this element * (aside from the initial '-') are option characters. If `getopt' * is called repeatedly, it returns successively each of the option characters * from each of the option elements. * * If `getopt' finds another option character, it returns that character, * updating `custom_optind' and `nextchar' so that the next call to `getopt' can * resume the scan with the following option character or ARGV-element. * * If there are no more option characters, `getopt' returns -1. * Then `custom_optind' is the index in ARGV of the first ARGV-element * that is not an option. (The ARGV-elements have been permuted * so that those that are not options now come last.) * * OPTSTRING is a string containing the legitimate option characters. * If an option character is seen that is not listed in OPTSTRING, * return '?' after printing an error message. If you set `custom_opterr' to * zero, the error message is suppressed but we still return '?'. * * If a char in OPTSTRING is followed by a colon, that means it wants an arg, * so the following text in the same ARGV-element, or the text of the following * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that * wants an optional arg; if there is text in the current ARGV-element, * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero. * * If OPTSTRING starts with `-' or `+', it requests different methods of * handling the non-option ARGV-elements. * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above. * * Long-named options begin with `--' instead of `-'. * Their names may be abbreviated as long as the abbreviation is unique * or is an exact match for some defined option. If they have an * argument, it follows the option name in the same ARGV-element, separated * from the option name by a `=', or else the in next ARGV-element. * When `getopt' finds a long-named option, it returns 0 if that option's * `flag' field is nonzero, the value of the option's `val' field * if the `flag' field is zero. * * The elements of ARGV aren't really const, because we permute them. * But we pretend they're const in the prototype to be compatible * with other systems. * * LONGOPTS is a vector of `struct option' terminated by an * element containing a name which is zero. * * LONGIND returns the index in LONGOPT of the long-named option found. * It is only valid when a long-named option has been found by the most * recent call. * * Return the option character from OPTS just read. Return -1 when there are * no more options. For unrecognized options, or options missing arguments, * `custom_optopt' is set to the option letter, and '?' is returned. * * The OPTS string is a list of characters which are recognized option letters, * optionally followed by colons, specifying that that letter takes an * argument, to be placed in `custom_optarg'. * * If a letter in OPTS is followed by two colons, its argument is optional. * This behavior is specific to the GNU `getopt'. * * The argument `--' causes premature termination of argument scanning, * explicitly telling `getopt' that there are no more options. If OPTS begins * with `--', then non-option arguments are treated as arguments to the option * '\0'. This behavior is specific to the GNU `getopt'. */ static int getopt_internal_r(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *longind, struct custom_getopt_data *d) { int ret, print_errors = d->custom_opterr; if (optstring[0] == ':') print_errors = 0; if (argc < 1) return -1; d->custom_optarg = NULL; /* * This is a big difference with GNU getopt, since optind == 0 * means initialization while here 1 means first call. */ if (d->custom_optind == 0 || !d->initialized) { if (d->custom_optind == 0) d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */ custom_getopt_initialize(d); } if (d->nextchar == NULL || *d->nextchar == '\0') { ret = shuffle_argv(argc, argv, longopts, d); if (ret) return ret; } if (longopts && (argv[d->custom_optind][1] == '-' )) return check_long_opt(argc, argv, optstring, longopts, longind, print_errors, d); return check_short_opt(argc, argv, optstring, print_errors, d); } static int custom_getopt_internal(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *longind) { int result; /* Keep a global copy of all internal members of d */ static struct custom_getopt_data d; d.custom_optind = custom_optind; d.custom_opterr = custom_opterr; result = getopt_internal_r(argc, argv, optstring, longopts, longind, &d); custom_optind = d.custom_optind; custom_optarg = d.custom_optarg; custom_optopt = d.custom_optopt; return result; } static int custom_getopt_long (int argc, char *const *argv, const char *options, const struct option *long_options, int *opt_index) { return custom_getopt_internal(argc, argv, options, long_options, opt_index); } static char *package_name = 0; /** * @brief updates an option * @param field the generic pointer to the field to update * @param orig_field the pointer to the orig field * @param field_given the pointer to the number of occurrence of this option * @param prev_given the pointer to the number of occurrence already seen * @param value the argument for this option (if null no arg was specified) * @param possible_values the possible values for this option (if specified) * @param default_value the default value (in case the option only accepts fixed values) * @param arg_type the type of this option * @param check_ambiguity @see RNA2Dfold_cmdline_parser_params.check_ambiguity * @param override @see RNA2Dfold_cmdline_parser_params.override * @param no_free whether to free a possible previous value * @param multiple_option whether this is a multiple option * @param long_opt the corresponding long option * @param short_opt the corresponding short option (or '-' if none) * @param additional_error possible further error specification */ static int update_arg(void *field, char **orig_field, unsigned int *field_given, unsigned int *prev_given, char *value, const char *possible_values[], const char *default_value, RNA2Dfold_cmdline_parser_arg_type arg_type, int check_ambiguity, int override, int no_free, int multiple_option, const char *long_opt, char short_opt, const char *additional_error) { char *stop_char = 0; const char *val = value; int found; char **string_field; FIX_UNUSED (field); stop_char = 0; found = 0; if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given))) { if (short_opt != '-') fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", package_name, long_opt, short_opt, (additional_error ? additional_error : "")); else fprintf (stderr, "%s: `--%s' option given more than once%s\n", package_name, long_opt, (additional_error ? additional_error : "")); return 1; /* failure */ } if (possible_values && (found = check_possible_values((value ? value : default_value), possible_values)) < 0) { if (short_opt != '-') fprintf (stderr, "%s: %s argument, \"%s\", for option `--%s' (`-%c')%s\n", package_name, (found == -2) ? "ambiguous" : "invalid", value, long_opt, short_opt, (additional_error ? additional_error : "")); else fprintf (stderr, "%s: %s argument, \"%s\", for option `--%s'%s\n", package_name, (found == -2) ? "ambiguous" : "invalid", value, long_opt, (additional_error ? additional_error : "")); return 1; /* failure */ } if (field_given && *field_given && ! override) return 0; if (prev_given) (*prev_given)++; if (field_given) (*field_given)++; if (possible_values) val = possible_values[found]; switch(arg_type) { case ARG_FLAG: *((int *)field) = !*((int *)field); break; case ARG_INT: if (val) *((int *)field) = strtol (val, &stop_char, 0); break; case ARG_DOUBLE: if (val) *((double *)field) = strtod (val, &stop_char); break; case ARG_STRING: if (val) { string_field = (char **)field; if (!no_free && *string_field) free (*string_field); /* free previous string */ *string_field = gengetopt_strdup (val); } break; default: break; }; /* check numeric conversion */ switch(arg_type) { case ARG_INT: case ARG_DOUBLE: if (val && !(stop_char && *stop_char == '\0')) { fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val); return 1; /* failure */ } break; default: ; }; /* store the original value */ switch(arg_type) { case ARG_NO: case ARG_FLAG: break; default: if (value && orig_field) { if (no_free) { *orig_field = value; } else { if (*orig_field) free (*orig_field); /* free previous string */ *orig_field = gengetopt_strdup (value); } } }; return 0; /* OK */ } /** * @brief store information about a multiple option in a temporary list * @param list where to (temporarily) store multiple options */ static int update_multiple_arg_temp(struct generic_list **list, unsigned int *prev_given, const char *val, const char *possible_values[], const char *default_value, RNA2Dfold_cmdline_parser_arg_type arg_type, const char *long_opt, char short_opt, const char *additional_error) { /* store single arguments */ char *multi_token; const char *multi_next; if (arg_type == ARG_NO) { (*prev_given)++; return 0; /* OK */ } multi_token = get_multiple_arg_token(val); multi_next = get_multiple_arg_token_next (val); while (1) { add_node (list); if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0, prev_given, multi_token, possible_values, default_value, arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) { if (multi_token) free(multi_token); return 1; /* failure */ } if (multi_next) { multi_token = get_multiple_arg_token(multi_next); multi_next = get_multiple_arg_token_next (multi_next); } else break; } return 0; /* OK */ } /** * @brief free the passed list (including possible string argument) */ static void free_list(struct generic_list *list, short string_arg) { if (list) { struct generic_list *tmp; while (list) { tmp = list; if (string_arg && list->arg.string_arg) free (list->arg.string_arg); if (list->orig) free (list->orig); list = list->next; free (tmp); } } } /** * @brief updates a multiple option starting from the passed list */ static void update_multiple_arg(void *field, char ***orig_field, unsigned int field_given, unsigned int prev_given, union generic_value *default_value, RNA2Dfold_cmdline_parser_arg_type arg_type, struct generic_list *list) { int i; struct generic_list *tmp; if (prev_given && list) { *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *)); switch(arg_type) { case ARG_INT: *((int **)field) = (int *)realloc (*((int **)field), (field_given + prev_given) * sizeof (int)); break; case ARG_DOUBLE: *((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break; case ARG_STRING: *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break; default: break; }; for (i = (prev_given - 1); i >= 0; --i) { tmp = list; switch(arg_type) { case ARG_INT: (*((int **)field))[i + field_given] = tmp->arg.int_arg; break; case ARG_DOUBLE: (*((double **)field))[i + field_given] = tmp->arg.double_arg; break; case ARG_STRING: (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break; default: break; } (*orig_field) [i + field_given] = list->orig; list = list->next; free (tmp); } } else { /* set the default value */ if (default_value && ! field_given) { switch(arg_type) { case ARG_INT: if (! *((int **)field)) { *((int **)field) = (int *)malloc (sizeof (int)); (*((int **)field))[0] = default_value->int_arg; } break; case ARG_DOUBLE: if (! *((double **)field)) { *((double **)field) = (double *)malloc (sizeof (double)); (*((double **)field))[0] = default_value->double_arg; } break; case ARG_STRING: if (! *((char ***)field)) { *((char ***)field) = (char **)malloc (sizeof (char *)); (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg); } break; default: break; } if (!(*orig_field)) { *orig_field = (char **) malloc (sizeof (char *)); (*orig_field)[0] = 0; } } } } int RNA2Dfold_cmdline_parser_internal ( int argc, char **argv, struct RNA2Dfold_args_info *args_info, struct RNA2Dfold_cmdline_parser_params *params, const char *additional_error) { int c; /* Character of the parsed option. */ struct generic_list * neighborhood_list = NULL; int error = 0; struct RNA2Dfold_args_info local_args_info; int override; int initialize; int check_required; int check_ambiguity; char *optarg; int optind; int opterr; int optopt; package_name = argv[0]; override = params->override; initialize = params->initialize; check_required = params->check_required; check_ambiguity = params->check_ambiguity; if (initialize) RNA2Dfold_cmdline_parser_init (args_info); RNA2Dfold_cmdline_parser_init (&local_args_info); optarg = 0; optind = 0; opterr = params->print_errors; optopt = '?'; while (1) { int option_index = 0; static struct option long_options[] = { { "help", 0, NULL, 'h' }, { "detailed-help", 0, NULL, 0 }, { "version", 0, NULL, 'V' }, { "noconv", 0, NULL, 0 }, { "numThreads", 1, NULL, 'j' }, { "partfunc", 0, NULL, 'p' }, { "stochBT", 1, NULL, 0 }, { "neighborhood", 1, NULL, 0 }, { "pfScale", 1, NULL, 'S' }, { "noBT", 0, NULL, 0 }, { "circ", 0, NULL, 'c' }, { "temp", 1, NULL, 'T' }, { "maxDist1", 1, NULL, 'K' }, { "maxDist2", 1, NULL, 'L' }, { "noTetra", 0, NULL, '4' }, { "parameterFile", 1, NULL, 'P' }, { "dangles", 1, NULL, 'd' }, { "noGU", 0, NULL, 0 }, { "noClosingGU", 0, NULL, 0 }, { 0, 0, 0, 0 } }; custom_optarg = optarg; custom_optind = optind; custom_opterr = opterr; custom_optopt = optopt; c = custom_getopt_long (argc, argv, "hVj:pS:cT:K:L:4P:d:", long_options, &option_index); optarg = custom_optarg; optind = custom_optind; opterr = custom_opterr; optopt = custom_optopt; if (c == -1) break; /* Exit from `while (1)' loop. */ switch (c) { case 'h': /* Print help and exit. */ RNA2Dfold_cmdline_parser_print_help (); RNA2Dfold_cmdline_parser_free (&local_args_info); exit (EXIT_SUCCESS); case 'V': /* Print version and exit. */ RNA2Dfold_cmdline_parser_print_version (); RNA2Dfold_cmdline_parser_free (&local_args_info); exit (EXIT_SUCCESS); case 'j': /* Set the number of threads used for calculations (only available when compiled with OpenMP support) . */ if (update_arg( (void *)&(args_info->numThreads_arg), &(args_info->numThreads_orig), &(args_info->numThreads_given), &(local_args_info.numThreads_given), optarg, 0, 0, ARG_INT, check_ambiguity, override, 0, 0, "numThreads", 'j', additional_error)) goto failure; break; case 'p': /* calculate partition function and thus, Boltzmann probabilities and Gibbs free energy . */ if (update_arg((void *)&(args_info->partfunc_flag), 0, &(args_info->partfunc_given), &(local_args_info.partfunc_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "partfunc", 'p', additional_error)) goto failure; break; case 'S': /* scaling factor for pf to avoid overflows . */ if (update_arg( (void *)&(args_info->pfScale_arg), &(args_info->pfScale_orig), &(args_info->pfScale_given), &(local_args_info.pfScale_given), optarg, 0, 0, ARG_DOUBLE, check_ambiguity, override, 0, 0, "pfScale", 'S', additional_error)) goto failure; break; case 'c': /* Assume a circular (instead of linear) RNA molecule. . */ if (update_arg((void *)&(args_info->circ_flag), 0, &(args_info->circ_given), &(local_args_info.circ_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "circ", 'c', additional_error)) goto failure; break; case 'T': /* Rescale energy parameters to a temperature of temp C. Default is 37C. . */ if (update_arg( (void *)&(args_info->temp_arg), &(args_info->temp_orig), &(args_info->temp_given), &(local_args_info.temp_given), optarg, 0, 0, ARG_DOUBLE, check_ambiguity, override, 0, 0, "temp", 'T', additional_error)) goto failure; break; case 'K': /* maximum distance to first reference structure. */ if (update_arg( (void *)&(args_info->maxDist1_arg), &(args_info->maxDist1_orig), &(args_info->maxDist1_given), &(local_args_info.maxDist1_given), optarg, 0, 0, ARG_INT, check_ambiguity, override, 0, 0, "maxDist1", 'K', additional_error)) goto failure; break; case 'L': /* maximum distance to second reference structure. */ if (update_arg( (void *)&(args_info->maxDist2_arg), &(args_info->maxDist2_orig), &(args_info->maxDist2_given), &(local_args_info.maxDist2_given), optarg, 0, 0, ARG_INT, check_ambiguity, override, 0, 0, "maxDist2", 'L', additional_error)) goto failure; break; case '4': /* Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. . */ if (update_arg((void *)&(args_info->noTetra_flag), 0, &(args_info->noTetra_given), &(local_args_info.noTetra_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "noTetra", '4', additional_error)) goto failure; break; case 'P': /* Read energy parameters from paramfile, instead of using the default parameter set. . */ if (update_arg( (void *)&(args_info->parameterFile_arg), &(args_info->parameterFile_orig), &(args_info->parameterFile_given), &(local_args_info.parameterFile_given), optarg, 0, 0, ARG_STRING, check_ambiguity, override, 0, 0, "parameterFile", 'P', additional_error)) goto failure; break; case 'd': /* How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops . */ if (update_arg( (void *)&(args_info->dangles_arg), &(args_info->dangles_orig), &(args_info->dangles_given), &(local_args_info.dangles_given), optarg, RNA2Dfold_cmdline_parser_dangles_values, "2", ARG_INT, check_ambiguity, override, 0, 0, "dangles", 'd', additional_error)) goto failure; break; case 0: /* Long option with no short option */ if (strcmp (long_options[option_index].name, "detailed-help") == 0) { RNA2Dfold_cmdline_parser_print_detailed_help (); RNA2Dfold_cmdline_parser_free (&local_args_info); exit (EXIT_SUCCESS); } /* Do not automatically substitude nucleotide \"T\" with \"U\" . */ if (strcmp (long_options[option_index].name, "noconv") == 0) { if (update_arg((void *)&(args_info->noconv_flag), 0, &(args_info->noconv_given), &(local_args_info.noconv_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "noconv", '-', additional_error)) goto failure; } /* backtrack a certain number of Boltzmann samples from the appropriate k,l neighborhood(s) . */ else if (strcmp (long_options[option_index].name, "stochBT") == 0) { if (update_arg( (void *)&(args_info->stochBT_arg), &(args_info->stochBT_orig), &(args_info->stochBT_given), &(local_args_info.stochBT_given), optarg, 0, 0, ARG_INT, check_ambiguity, override, 0, 0, "stochBT", '-', additional_error)) goto failure; } /* backtrack structures from certain k,l-neighborhood only, can be specified multiple times (:,:,...) . */ else if (strcmp (long_options[option_index].name, "neighborhood") == 0) { if (update_multiple_arg_temp(&neighborhood_list, &(local_args_info.neighborhood_given), optarg, 0, 0, ARG_STRING, "neighborhood", '-', additional_error)) goto failure; } /* do not backtrack structures, calculate energy contributions only . */ else if (strcmp (long_options[option_index].name, "noBT") == 0) { if (update_arg((void *)&(args_info->noBT_flag), 0, &(args_info->noBT_given), &(local_args_info.noBT_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "noBT", '-', additional_error)) goto failure; } /* Do not allow GU pairs . */ else if (strcmp (long_options[option_index].name, "noGU") == 0) { if (update_arg((void *)&(args_info->noGU_flag), 0, &(args_info->noGU_given), &(local_args_info.noGU_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "noGU", '-', additional_error)) goto failure; } /* Do not allow GU pairs at the end of helices . */ else if (strcmp (long_options[option_index].name, "noClosingGU") == 0) { if (update_arg((void *)&(args_info->noClosingGU_flag), 0, &(args_info->noClosingGU_given), &(local_args_info.noClosingGU_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "noClosingGU", '-', additional_error)) goto failure; } break; case '?': /* Invalid option. */ /* `getopt_long' already printed an error message. */ goto failure; default: /* bug: option not considered. */ fprintf (stderr, "%s: option unknown: %c%s\n", RNA2DFOLD_CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : "")); abort (); } /* switch */ } /* while */ update_multiple_arg((void *)&(args_info->neighborhood_arg), &(args_info->neighborhood_orig), args_info->neighborhood_given, local_args_info.neighborhood_given, 0, ARG_STRING, neighborhood_list); args_info->neighborhood_given += local_args_info.neighborhood_given; local_args_info.neighborhood_given = 0; if (check_required) { error += RNA2Dfold_cmdline_parser_required2 (args_info, argv[0], additional_error); } RNA2Dfold_cmdline_parser_release (&local_args_info); if ( error ) return (EXIT_FAILURE); return 0; failure: free_list (neighborhood_list, 1 ); RNA2Dfold_cmdline_parser_release (&local_args_info); return (EXIT_FAILURE); }