--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22.5
+ generated with the following command:
+ gengetopt -i RNAplex.ggo --file-name=RNAplex_cmdl --include-getopt --default-optional --func-name=RNAplex_cmdline_parser --arg-struct-name=RNAplex_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 "RNAplex_cmdl.h"
+
+const char *RNAplex_args_info_purpose = "Find targets of a query RNA";
+
+const char *RNAplex_args_info_usage = "Usage: RNAplex [options]\n";
+
+const char *RNAplex_args_info_description = "reads two RNA sequences from stdin or <filename> and computes optimal and \nsuboptimal secondary structures for their hybridization. The calculation is \nsimplified by allowing only inter-molecular base pairs. Accessibility effects \ncan be estimated by RNAplex if a RNAplfold accessibility profile is provided. \nThe computed optimal and suboptimal structure are written to stdout, one \nstructure per line. Each line consist of: The structure in dot bracket format \nwith a \"&\" separating the two strands. The range of the structure in the two \nsequences in the format \"from,to : from,to\"; the energy of duplex structure \nin kcal/mol.\nThe format is especially useful for computing the hybrid structure between a \nsmall probe sequence and a long target sequence.\n";
+
+const char *RNAplex_args_info_detailed_help[] = {
+ " -h, --help Print help and exit",
+ " --detailed-help Print help, including all details and hidden \n options, and exit",
+ " --version Print version and exit",
+ "\nInput Options:",
+ " Below are command line options which alter the general input behavior of this \n program\n",
+ " -q, --query=STRING File containing the query sequence.\n",
+ " Input sequences can be given piped to RNAplex or given in a query file with \n the -q option. Note that the -q option implies that the -t option is also \n used\n\n",
+ " -t, --target=STRING File containing the target sequence.\n",
+ " Input sequences can be given piped to RNAplex or given in a target file with \n the -t option. Note that the -t option implies that the -q option is also \n used\n\n",
+ " -a, --accessibility-dir=STRING\n Location of the accessibility profiles.\n",
+ " This option switches the accessibility modes on and indicates in which \n directory accessibility profiles as generated by RNAplfold can be found\n\n",
+ " -b, --binary Allow the reading and parsing of memory dumped \n opening energy file\n (default=off)",
+ " The -b option allows to read and process opening energy files which are saved \n in binary format\n This can reduce by a factor of 500x-1000x the time needed to process those \n files. RNAplex recognizes the corresponding opening energy files by looking \n for files named after the sequence and containing the suffix _openen_bin. \n Please look at the man page of RNAplfold if you need more information on how \n to produce binary opening energy files.\n\n",
+ " -P, --paramFile=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",
+ "\nAlgorithms:",
+ " Options which alter the computing behaviour of RNAplex.\n",
+ " -T, --temp=DOUBLE Rescale energy parameters to a temperature T. \n Default is 37C.\n\n",
+ " -l, --interaction-length=INT Maximal length of an interaction\n (default=`40')",
+ " Maximal allowed length of an interaction\n\n",
+ " -c, --extension-cost=INT Cost to add to each nucleotide in a duplex\n (default=`0')",
+ " Cost of extending a duplex by one nucleotide. Allows to find compact \n duplexes, having few/small bulges or interior loops Only useful when no \n accessibility profiles are available. This option is disabled if \n accessibility profiles are used (-a option)\n\n",
+ " -p, --probe-mode Compute Tm for probes (default=off)",
+ " Use this option if you want to compute the melting temperature of your probes\n\n",
+ " -Q, --probe-concentration=DOUBLE\n Set the probe concentration for the Tm \n computation\n\n (default=`0.1')",
+ " -N, --na-concentration=DOUBLE Set the Na+ concentration for the Tm \n computation\n\n (default=`1.0')",
+ " -M, --mg-concentration=DOUBLE Set the Mg2+ concentration for the Tm \n computation\n\n (default=`1.0')",
+ " -K, --k-concentration=DOUBLE Set the K+ concentration for the Tm computation\n\n (default=`1.0')",
+ " -U, --tris-concentration=DOUBLE\n Set the tris+ concentration for the Tm \n computation\n\n (default=`1.0')",
+ " -f, --fast-folding=INT Speedup of the target search\n (default=`0')",
+ " This option allows to decide if the backtracking has to be done (-f 0, -f 2) \n or not (-f 1). For -f 0 the structure is computed based on the standard \n energy model. This is the slowest and most precise mode of RNAplex. With -f \n 2, the structure is computed based on the approximated plex model. If a lot \n of targets are returned this is can greatly improve the runtime of RNAplex. \n -f 1 is the fastest mode, as no structure are recomputed \n\n",
+ " -V, --scale-accessibility=DOUBLE\n Rescale all opening energy by a factor V\n (default=`1.0')",
+ " Scale-factor for the accessibility. If V is set to 1 then the scaling has no \n effect on the accessibility.\n\n",
+ " -C, --constraint Calculate structures subject to constraints.\n (default=off)",
+ " The program reads first the sequence, then a string containing constraints on \n the structure for the query sequence encoded with the symbols:\n . (no constraint for this base)\n | (the corresponding base has to be paired)\n\n",
+ " -A, --alignment-mode Tells RNAplex to compute interactions based on \n alignments\n (default=off)",
+ " If the A option is set RNAplex expects clustalw files as input for the -q and \n -t option.\n\n",
+ " -k, --convert-to-bin If set, RNAplex will convert all opening energy \n file in a directory set by the -a option into \n binary opening energy files\n (default=off)",
+ " RNAplex can be used to convert existing text formatted opening energy files \n into binary formatted files. In this mode RNAplex does not compute \n interactions.\n\n",
+ "\nOutput:",
+ " Options that modify the output\n",
+ " -z, --duplex-distance=INT Distance between target 3' ends of two \n consecutive duplexes\n (default=`0')",
+ " Distance between the target 3'ends of two consecutive duplexes. Should be set \n to the maximal length of interaction to get good results\n Smaller z leads to larger overlaps between consecutive duplexes.\n\n",
+ " -e, --energy-threshold=DOUBLE Minimal energy for a duplex to be returned\n (default=`-100000')",
+ " Energy threshold for a duplex to be returned. The threshold is set on the \n total energy of interaction, i.e. the hybridization energy corrected for \n opening energy if -a is set or the energy corrected by -c. If unset, only the \n mfe will be returned\n\n",
+ " -I, --produce-ps=STRING Draw an alignment annotated interaction from \n RNAplex\n",
+ " This option allows to produce interaction figures in PS-format a la \n RNAalifold, where base-pair conservation is represented in color-coded \n format. In this mode no interaction are computed, but the -I option indicates \n the location of the file containing interactions between two RNA \n (alignments/sequence) from a previous run. If the -A option is not set a \n structure figure a la RNAfold with color-coded annotation of the \n accessibilities is returned\n\n",
+ " -L, --WindowLength=INT Tells how large the region around the target \n site should be for redrawing the alignment \n interaction\n (default=`1')",
+ " This option allow to specify how large the region surrounding the target site \n should be set when generating the alignment figure of the interaction\n\n",
+ "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to rna@tbi.univie.ac.at.\n",
+ 0
+};
+
+static void
+init_help_array(void)
+{
+ RNAplex_args_info_help[0] = RNAplex_args_info_detailed_help[0];
+ RNAplex_args_info_help[1] = RNAplex_args_info_detailed_help[1];
+ RNAplex_args_info_help[2] = RNAplex_args_info_detailed_help[2];
+ RNAplex_args_info_help[3] = RNAplex_args_info_detailed_help[3];
+ RNAplex_args_info_help[4] = RNAplex_args_info_detailed_help[4];
+ RNAplex_args_info_help[5] = RNAplex_args_info_detailed_help[5];
+ RNAplex_args_info_help[6] = RNAplex_args_info_detailed_help[7];
+ RNAplex_args_info_help[7] = RNAplex_args_info_detailed_help[9];
+ RNAplex_args_info_help[8] = RNAplex_args_info_detailed_help[11];
+ RNAplex_args_info_help[9] = RNAplex_args_info_detailed_help[13];
+ RNAplex_args_info_help[10] = RNAplex_args_info_detailed_help[15];
+ RNAplex_args_info_help[11] = RNAplex_args_info_detailed_help[16];
+ RNAplex_args_info_help[12] = RNAplex_args_info_detailed_help[17];
+ RNAplex_args_info_help[13] = RNAplex_args_info_detailed_help[18];
+ RNAplex_args_info_help[14] = RNAplex_args_info_detailed_help[20];
+ RNAplex_args_info_help[15] = RNAplex_args_info_detailed_help[22];
+ RNAplex_args_info_help[16] = RNAplex_args_info_detailed_help[24];
+ RNAplex_args_info_help[17] = RNAplex_args_info_detailed_help[25];
+ RNAplex_args_info_help[18] = RNAplex_args_info_detailed_help[26];
+ RNAplex_args_info_help[19] = RNAplex_args_info_detailed_help[27];
+ RNAplex_args_info_help[20] = RNAplex_args_info_detailed_help[28];
+ RNAplex_args_info_help[21] = RNAplex_args_info_detailed_help[29];
+ RNAplex_args_info_help[22] = RNAplex_args_info_detailed_help[31];
+ RNAplex_args_info_help[23] = RNAplex_args_info_detailed_help[33];
+ RNAplex_args_info_help[24] = RNAplex_args_info_detailed_help[35];
+ RNAplex_args_info_help[25] = RNAplex_args_info_detailed_help[37];
+ RNAplex_args_info_help[26] = RNAplex_args_info_detailed_help[39];
+ RNAplex_args_info_help[27] = RNAplex_args_info_detailed_help[40];
+ RNAplex_args_info_help[28] = RNAplex_args_info_detailed_help[41];
+ RNAplex_args_info_help[29] = RNAplex_args_info_detailed_help[43];
+ RNAplex_args_info_help[30] = RNAplex_args_info_detailed_help[45];
+ RNAplex_args_info_help[31] = RNAplex_args_info_detailed_help[47];
+ RNAplex_args_info_help[32] = RNAplex_args_info_detailed_help[49];
+ RNAplex_args_info_help[33] = 0;
+
+}
+
+const char *RNAplex_args_info_help[34];
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+ , ARG_DOUBLE
+} RNAplex_cmdline_parser_arg_type;
+
+static
+void clear_given (struct RNAplex_args_info *args_info);
+static
+void clear_args (struct RNAplex_args_info *args_info);
+
+static int
+RNAplex_cmdline_parser_internal (int argc, char **argv, struct RNAplex_args_info *args_info,
+ struct RNAplex_cmdline_parser_params *params, const char *additional_error);
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct RNAplex_args_info *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->detailed_help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->query_given = 0 ;
+ args_info->target_given = 0 ;
+ args_info->accessibility_dir_given = 0 ;
+ args_info->binary_given = 0 ;
+ args_info->paramFile_given = 0 ;
+ args_info->temp_given = 0 ;
+ args_info->interaction_length_given = 0 ;
+ args_info->extension_cost_given = 0 ;
+ args_info->probe_mode_given = 0 ;
+ args_info->probe_concentration_given = 0 ;
+ args_info->na_concentration_given = 0 ;
+ args_info->mg_concentration_given = 0 ;
+ args_info->k_concentration_given = 0 ;
+ args_info->tris_concentration_given = 0 ;
+ args_info->fast_folding_given = 0 ;
+ args_info->scale_accessibility_given = 0 ;
+ args_info->constraint_given = 0 ;
+ args_info->alignment_mode_given = 0 ;
+ args_info->convert_to_bin_given = 0 ;
+ args_info->duplex_distance_given = 0 ;
+ args_info->energy_threshold_given = 0 ;
+ args_info->produce_ps_given = 0 ;
+ args_info->WindowLength_given = 0 ;
+}
+
+static
+void clear_args (struct RNAplex_args_info *args_info)
+{
+ FIX_UNUSED (args_info);
+ args_info->query_arg = NULL;
+ args_info->query_orig = NULL;
+ args_info->target_arg = NULL;
+ args_info->target_orig = NULL;
+ args_info->accessibility_dir_arg = NULL;
+ args_info->accessibility_dir_orig = NULL;
+ args_info->binary_flag = 0;
+ args_info->paramFile_arg = NULL;
+ args_info->paramFile_orig = NULL;
+ args_info->temp_orig = NULL;
+ args_info->interaction_length_arg = 40;
+ args_info->interaction_length_orig = NULL;
+ args_info->extension_cost_arg = 0;
+ args_info->extension_cost_orig = NULL;
+ args_info->probe_mode_flag = 0;
+ args_info->probe_concentration_arg = 0.1;
+ args_info->probe_concentration_orig = NULL;
+ args_info->na_concentration_arg = 1.0;
+ args_info->na_concentration_orig = NULL;
+ args_info->mg_concentration_arg = 1.0;
+ args_info->mg_concentration_orig = NULL;
+ args_info->k_concentration_arg = 1.0;
+ args_info->k_concentration_orig = NULL;
+ args_info->tris_concentration_arg = 1.0;
+ args_info->tris_concentration_orig = NULL;
+ args_info->fast_folding_arg = 0;
+ args_info->fast_folding_orig = NULL;
+ args_info->scale_accessibility_arg = 1.0;
+ args_info->scale_accessibility_orig = NULL;
+ args_info->constraint_flag = 0;
+ args_info->alignment_mode_flag = 0;
+ args_info->convert_to_bin_flag = 0;
+ args_info->duplex_distance_arg = 0;
+ args_info->duplex_distance_orig = NULL;
+ args_info->energy_threshold_arg = -100000;
+ args_info->energy_threshold_orig = NULL;
+ args_info->produce_ps_arg = NULL;
+ args_info->produce_ps_orig = NULL;
+ args_info->WindowLength_arg = 1;
+ args_info->WindowLength_orig = NULL;
+
+}
+
+static
+void init_args_info(struct RNAplex_args_info *args_info)
+{
+
+ init_help_array();
+ args_info->help_help = RNAplex_args_info_detailed_help[0] ;
+ args_info->detailed_help_help = RNAplex_args_info_detailed_help[1] ;
+ args_info->version_help = RNAplex_args_info_detailed_help[2] ;
+ args_info->query_help = RNAplex_args_info_detailed_help[5] ;
+ args_info->target_help = RNAplex_args_info_detailed_help[7] ;
+ args_info->accessibility_dir_help = RNAplex_args_info_detailed_help[9] ;
+ args_info->binary_help = RNAplex_args_info_detailed_help[11] ;
+ args_info->paramFile_help = RNAplex_args_info_detailed_help[13] ;
+ args_info->temp_help = RNAplex_args_info_detailed_help[17] ;
+ args_info->interaction_length_help = RNAplex_args_info_detailed_help[18] ;
+ args_info->extension_cost_help = RNAplex_args_info_detailed_help[20] ;
+ args_info->probe_mode_help = RNAplex_args_info_detailed_help[22] ;
+ args_info->probe_concentration_help = RNAplex_args_info_detailed_help[24] ;
+ args_info->na_concentration_help = RNAplex_args_info_detailed_help[25] ;
+ args_info->mg_concentration_help = RNAplex_args_info_detailed_help[26] ;
+ args_info->k_concentration_help = RNAplex_args_info_detailed_help[27] ;
+ args_info->tris_concentration_help = RNAplex_args_info_detailed_help[28] ;
+ args_info->fast_folding_help = RNAplex_args_info_detailed_help[29] ;
+ args_info->scale_accessibility_help = RNAplex_args_info_detailed_help[31] ;
+ args_info->constraint_help = RNAplex_args_info_detailed_help[33] ;
+ args_info->alignment_mode_help = RNAplex_args_info_detailed_help[35] ;
+ args_info->convert_to_bin_help = RNAplex_args_info_detailed_help[37] ;
+ args_info->duplex_distance_help = RNAplex_args_info_detailed_help[41] ;
+ args_info->energy_threshold_help = RNAplex_args_info_detailed_help[43] ;
+ args_info->produce_ps_help = RNAplex_args_info_detailed_help[45] ;
+ args_info->WindowLength_help = RNAplex_args_info_detailed_help[47] ;
+
+}
+
+void
+RNAplex_cmdline_parser_print_version (void)
+{
+ printf ("%s %s\n",
+ (strlen(RNAPLEX_CMDLINE_PARSER_PACKAGE_NAME) ? RNAPLEX_CMDLINE_PARSER_PACKAGE_NAME : RNAPLEX_CMDLINE_PARSER_PACKAGE),
+ RNAPLEX_CMDLINE_PARSER_VERSION);
+}
+
+static void print_help_common(void) {
+ RNAplex_cmdline_parser_print_version ();
+
+ if (strlen(RNAplex_args_info_purpose) > 0)
+ printf("\n%s\n", RNAplex_args_info_purpose);
+
+ if (strlen(RNAplex_args_info_usage) > 0)
+ printf("\n%s\n", RNAplex_args_info_usage);
+
+ printf("\n");
+
+ if (strlen(RNAplex_args_info_description) > 0)
+ printf("%s\n\n", RNAplex_args_info_description);
+}
+
+void
+RNAplex_cmdline_parser_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (RNAplex_args_info_help[i])
+ printf("%s\n", RNAplex_args_info_help[i++]);
+}
+
+void
+RNAplex_cmdline_parser_print_detailed_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (RNAplex_args_info_detailed_help[i])
+ printf("%s\n", RNAplex_args_info_detailed_help[i++]);
+}
+
+void
+RNAplex_cmdline_parser_init (struct RNAplex_args_info *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+}
+
+void
+RNAplex_cmdline_parser_params_init(struct RNAplex_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 RNAplex_cmdline_parser_params *
+RNAplex_cmdline_parser_params_create(void)
+{
+ struct RNAplex_cmdline_parser_params *params =
+ (struct RNAplex_cmdline_parser_params *)malloc(sizeof(struct RNAplex_cmdline_parser_params));
+ RNAplex_cmdline_parser_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+
+static void
+RNAplex_cmdline_parser_release (struct RNAplex_args_info *args_info)
+{
+
+ free_string_field (&(args_info->query_arg));
+ free_string_field (&(args_info->query_orig));
+ free_string_field (&(args_info->target_arg));
+ free_string_field (&(args_info->target_orig));
+ free_string_field (&(args_info->accessibility_dir_arg));
+ free_string_field (&(args_info->accessibility_dir_orig));
+ free_string_field (&(args_info->paramFile_arg));
+ free_string_field (&(args_info->paramFile_orig));
+ free_string_field (&(args_info->temp_orig));
+ free_string_field (&(args_info->interaction_length_orig));
+ free_string_field (&(args_info->extension_cost_orig));
+ free_string_field (&(args_info->probe_concentration_orig));
+ free_string_field (&(args_info->na_concentration_orig));
+ free_string_field (&(args_info->mg_concentration_orig));
+ free_string_field (&(args_info->k_concentration_orig));
+ free_string_field (&(args_info->tris_concentration_orig));
+ free_string_field (&(args_info->fast_folding_orig));
+ free_string_field (&(args_info->scale_accessibility_orig));
+ free_string_field (&(args_info->duplex_distance_orig));
+ free_string_field (&(args_info->energy_threshold_orig));
+ free_string_field (&(args_info->produce_ps_arg));
+ free_string_field (&(args_info->produce_ps_orig));
+ free_string_field (&(args_info->WindowLength_orig));
+
+
+
+ clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
+{
+ FIX_UNUSED (values);
+ if (arg) {
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+
+int
+RNAplex_cmdline_parser_dump(FILE *outfile, struct RNAplex_args_info *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", RNAPLEX_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->query_given)
+ write_into_file(outfile, "query", args_info->query_orig, 0);
+ if (args_info->target_given)
+ write_into_file(outfile, "target", args_info->target_orig, 0);
+ if (args_info->accessibility_dir_given)
+ write_into_file(outfile, "accessibility-dir", args_info->accessibility_dir_orig, 0);
+ if (args_info->binary_given)
+ write_into_file(outfile, "binary", 0, 0 );
+ if (args_info->paramFile_given)
+ write_into_file(outfile, "paramFile", args_info->paramFile_orig, 0);
+ if (args_info->temp_given)
+ write_into_file(outfile, "temp", args_info->temp_orig, 0);
+ if (args_info->interaction_length_given)
+ write_into_file(outfile, "interaction-length", args_info->interaction_length_orig, 0);
+ if (args_info->extension_cost_given)
+ write_into_file(outfile, "extension-cost", args_info->extension_cost_orig, 0);
+ if (args_info->probe_mode_given)
+ write_into_file(outfile, "probe-mode", 0, 0 );
+ if (args_info->probe_concentration_given)
+ write_into_file(outfile, "probe-concentration", args_info->probe_concentration_orig, 0);
+ if (args_info->na_concentration_given)
+ write_into_file(outfile, "na-concentration", args_info->na_concentration_orig, 0);
+ if (args_info->mg_concentration_given)
+ write_into_file(outfile, "mg-concentration", args_info->mg_concentration_orig, 0);
+ if (args_info->k_concentration_given)
+ write_into_file(outfile, "k-concentration", args_info->k_concentration_orig, 0);
+ if (args_info->tris_concentration_given)
+ write_into_file(outfile, "tris-concentration", args_info->tris_concentration_orig, 0);
+ if (args_info->fast_folding_given)
+ write_into_file(outfile, "fast-folding", args_info->fast_folding_orig, 0);
+ if (args_info->scale_accessibility_given)
+ write_into_file(outfile, "scale-accessibility", args_info->scale_accessibility_orig, 0);
+ if (args_info->constraint_given)
+ write_into_file(outfile, "constraint", 0, 0 );
+ if (args_info->alignment_mode_given)
+ write_into_file(outfile, "alignment-mode", 0, 0 );
+ if (args_info->convert_to_bin_given)
+ write_into_file(outfile, "convert-to-bin", 0, 0 );
+ if (args_info->duplex_distance_given)
+ write_into_file(outfile, "duplex-distance", args_info->duplex_distance_orig, 0);
+ if (args_info->energy_threshold_given)
+ write_into_file(outfile, "energy-threshold", args_info->energy_threshold_orig, 0);
+ if (args_info->produce_ps_given)
+ write_into_file(outfile, "produce-ps", args_info->produce_ps_orig, 0);
+ if (args_info->WindowLength_given)
+ write_into_file(outfile, "WindowLength", args_info->WindowLength_orig, 0);
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+RNAplex_cmdline_parser_file_save(const char *filename, struct RNAplex_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", RNAPLEX_CMDLINE_PARSER_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = RNAplex_cmdline_parser_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+RNAplex_cmdline_parser_free (struct RNAplex_args_info *args_info)
+{
+ RNAplex_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;
+}
+
+int
+RNAplex_cmdline_parser (int argc, char **argv, struct RNAplex_args_info *args_info)
+{
+ return RNAplex_cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+RNAplex_cmdline_parser_ext (int argc, char **argv, struct RNAplex_args_info *args_info,
+ struct RNAplex_cmdline_parser_params *params)
+{
+ int result;
+ result = RNAplex_cmdline_parser_internal (argc, argv, args_info, params, 0);
+
+ if (result == EXIT_FAILURE)
+ {
+ RNAplex_cmdline_parser_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+RNAplex_cmdline_parser2 (int argc, char **argv, struct RNAplex_args_info *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct RNAplex_cmdline_parser_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = RNAplex_cmdline_parser_internal (argc, argv, args_info, ¶ms, 0);
+
+ if (result == EXIT_FAILURE)
+ {
+ RNAplex_cmdline_parser_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+RNAplex_cmdline_parser_required (struct RNAplex_args_info *args_info, const char *prog_name)
+{
+ FIX_UNUSED (args_info);
+ FIX_UNUSED (prog_name);
+ return EXIT_SUCCESS;
+}
+
+/*
+ * 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 RNAplex_cmdline_parser_params.check_ambiguity
+ * @param override @see RNAplex_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,
+ RNAplex_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 */
+ }
+
+ FIX_UNUSED (default_value);
+
+ 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 */
+}
+
+
+int
+RNAplex_cmdline_parser_internal (
+ int argc, char **argv, struct RNAplex_args_info *args_info,
+ struct RNAplex_cmdline_parser_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+
+ int error = 0;
+ struct RNAplex_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)
+ RNAplex_cmdline_parser_init (args_info);
+
+ RNAplex_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, 0 },
+ { "query", 1, NULL, 'q' },
+ { "target", 1, NULL, 't' },
+ { "accessibility-dir", 1, NULL, 'a' },
+ { "binary", 0, NULL, 'b' },
+ { "paramFile", 1, NULL, 'P' },
+ { "temp", 1, NULL, 'T' },
+ { "interaction-length", 1, NULL, 'l' },
+ { "extension-cost", 1, NULL, 'c' },
+ { "probe-mode", 0, NULL, 'p' },
+ { "probe-concentration", 1, NULL, 'Q' },
+ { "na-concentration", 1, NULL, 'N' },
+ { "mg-concentration", 1, NULL, 'M' },
+ { "k-concentration", 1, NULL, 'K' },
+ { "tris-concentration", 1, NULL, 'U' },
+ { "fast-folding", 1, NULL, 'f' },
+ { "scale-accessibility", 1, NULL, 'V' },
+ { "constraint", 0, NULL, 'C' },
+ { "alignment-mode", 0, NULL, 'A' },
+ { "convert-to-bin", 0, NULL, 'k' },
+ { "duplex-distance", 1, NULL, 'z' },
+ { "energy-threshold", 1, NULL, 'e' },
+ { "produce-ps", 1, NULL, 'I' },
+ { "WindowLength", 1, NULL, 'L' },
+ { 0, 0, 0, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hq:t:a:bP:T:l:c:pQ:N:M:K:U:f:V:CAkz:e:I:L:", 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. */
+ RNAplex_cmdline_parser_print_help ();
+ RNAplex_cmdline_parser_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'q': /* File containing the query sequence.
+. */
+
+
+ if (update_arg( (void *)&(args_info->query_arg),
+ &(args_info->query_orig), &(args_info->query_given),
+ &(local_args_info.query_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "query", 'q',
+ additional_error))
+ goto failure;
+
+ break;
+ case 't': /* File containing the target sequence.
+. */
+
+
+ if (update_arg( (void *)&(args_info->target_arg),
+ &(args_info->target_orig), &(args_info->target_given),
+ &(local_args_info.target_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "target", 't',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'a': /* Location of the accessibility profiles.
+. */
+
+
+ if (update_arg( (void *)&(args_info->accessibility_dir_arg),
+ &(args_info->accessibility_dir_orig), &(args_info->accessibility_dir_given),
+ &(local_args_info.accessibility_dir_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "accessibility-dir", 'a',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'b': /* Allow the reading and parsing of memory dumped opening energy file
+. */
+
+
+ if (update_arg((void *)&(args_info->binary_flag), 0, &(args_info->binary_given),
+ &(local_args_info.binary_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "binary", 'b',
+ 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->paramFile_arg),
+ &(args_info->paramFile_orig), &(args_info->paramFile_given),
+ &(local_args_info.paramFile_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "paramFile", 'P',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'T': /* Rescale energy parameters to a temperature T. 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 'l': /* Maximal length of an interaction
+. */
+
+
+ if (update_arg( (void *)&(args_info->interaction_length_arg),
+ &(args_info->interaction_length_orig), &(args_info->interaction_length_given),
+ &(local_args_info.interaction_length_given), optarg, 0, "40", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "interaction-length", 'l',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'c': /* Cost to add to each nucleotide in a duplex
+. */
+
+
+ if (update_arg( (void *)&(args_info->extension_cost_arg),
+ &(args_info->extension_cost_orig), &(args_info->extension_cost_given),
+ &(local_args_info.extension_cost_given), optarg, 0, "0", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "extension-cost", 'c',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'p': /* Compute Tm for probes. */
+
+
+ if (update_arg((void *)&(args_info->probe_mode_flag), 0, &(args_info->probe_mode_given),
+ &(local_args_info.probe_mode_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "probe-mode", 'p',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'Q': /* Set the probe concentration for the Tm computation
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->probe_concentration_arg),
+ &(args_info->probe_concentration_orig), &(args_info->probe_concentration_given),
+ &(local_args_info.probe_concentration_given), optarg, 0, "0.1", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "probe-concentration", 'Q',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'N': /* Set the Na+ concentration for the Tm computation
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->na_concentration_arg),
+ &(args_info->na_concentration_orig), &(args_info->na_concentration_given),
+ &(local_args_info.na_concentration_given), optarg, 0, "1.0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "na-concentration", 'N',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'M': /* Set the Mg2+ concentration for the Tm computation
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->mg_concentration_arg),
+ &(args_info->mg_concentration_orig), &(args_info->mg_concentration_given),
+ &(local_args_info.mg_concentration_given), optarg, 0, "1.0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "mg-concentration", 'M',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'K': /* Set the K+ concentration for the Tm computation
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->k_concentration_arg),
+ &(args_info->k_concentration_orig), &(args_info->k_concentration_given),
+ &(local_args_info.k_concentration_given), optarg, 0, "1.0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "k-concentration", 'K',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'U': /* Set the tris+ concentration for the Tm computation
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->tris_concentration_arg),
+ &(args_info->tris_concentration_orig), &(args_info->tris_concentration_given),
+ &(local_args_info.tris_concentration_given), optarg, 0, "1.0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "tris-concentration", 'U',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'f': /* Speedup of the target search
+. */
+
+
+ if (update_arg( (void *)&(args_info->fast_folding_arg),
+ &(args_info->fast_folding_orig), &(args_info->fast_folding_given),
+ &(local_args_info.fast_folding_given), optarg, 0, "0", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "fast-folding", 'f',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'V': /* Rescale all opening energy by a factor V
+. */
+
+
+ if (update_arg( (void *)&(args_info->scale_accessibility_arg),
+ &(args_info->scale_accessibility_orig), &(args_info->scale_accessibility_given),
+ &(local_args_info.scale_accessibility_given), optarg, 0, "1.0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "scale-accessibility", 'V',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'C': /* Calculate structures subject to constraints.
+. */
+
+
+ if (update_arg((void *)&(args_info->constraint_flag), 0, &(args_info->constraint_given),
+ &(local_args_info.constraint_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "constraint", 'C',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'A': /* Tells RNAplex to compute interactions based on alignments
+. */
+
+
+ if (update_arg((void *)&(args_info->alignment_mode_flag), 0, &(args_info->alignment_mode_given),
+ &(local_args_info.alignment_mode_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "alignment-mode", 'A',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'k': /* If set, RNAplex will convert all opening energy file in a directory set by the -a option into binary opening energy files
+. */
+
+
+ if (update_arg((void *)&(args_info->convert_to_bin_flag), 0, &(args_info->convert_to_bin_given),
+ &(local_args_info.convert_to_bin_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "convert-to-bin", 'k',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'z': /* Distance between target 3' ends of two consecutive duplexes
+. */
+
+
+ if (update_arg( (void *)&(args_info->duplex_distance_arg),
+ &(args_info->duplex_distance_orig), &(args_info->duplex_distance_given),
+ &(local_args_info.duplex_distance_given), optarg, 0, "0", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "duplex-distance", 'z',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'e': /* Minimal energy for a duplex to be returned
+. */
+
+
+ if (update_arg( (void *)&(args_info->energy_threshold_arg),
+ &(args_info->energy_threshold_orig), &(args_info->energy_threshold_given),
+ &(local_args_info.energy_threshold_given), optarg, 0, "-100000", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "energy-threshold", 'e',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'I': /* Draw an alignment annotated interaction from RNAplex
+. */
+
+
+ if (update_arg( (void *)&(args_info->produce_ps_arg),
+ &(args_info->produce_ps_orig), &(args_info->produce_ps_given),
+ &(local_args_info.produce_ps_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "produce-ps", 'I',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'L': /* Tells how large the region around the target site should be for redrawing the alignment interaction
+. */
+
+
+ if (update_arg( (void *)&(args_info->WindowLength_arg),
+ &(args_info->WindowLength_orig), &(args_info->WindowLength_given),
+ &(local_args_info.WindowLength_given), optarg, 0, "1", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "WindowLength", 'L',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ if (strcmp (long_options[option_index].name, "detailed-help") == 0) {
+ RNAplex_cmdline_parser_print_detailed_help ();
+ RNAplex_cmdline_parser_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+ }
+
+ if (strcmp (long_options[option_index].name, "version") == 0) {
+ RNAplex_cmdline_parser_print_version ();
+ RNAplex_cmdline_parser_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+ }
+
+ 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", RNAPLEX_CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+
+
+ RNAplex_cmdline_parser_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ return 0;
+
+failure:
+
+ RNAplex_cmdline_parser_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
git://source.jalview.org / jabaws.git / blobdiff