--- /dev/null
+/*
+ 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 <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#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=<k>:<l> backtrack structures from certain \n k,l-neighborhood only, can be specified \n multiple times (<k>:<l>,<m>:<n>,...)\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 (<k>:<l>,<m>:<n>,...)
+
+. */
+ 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);
+}
git://source.jalview.org / jabaws.git / blobdiff