--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22.5
+ generated with the following command:
+ gengetopt -i RNAsnoop.ggo --file-name=RNAsnoop_cmdl --include-getopt --default-optional --func-name=RNAsnoop_cmdline_parser --arg-struct-name=RNAsnoop_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 "RNAsnoop_cmdl.h"
+
+const char *RNAsnoop_args_info_purpose = "Find targets of a query H/ACA snoRNA";
+
+const char *RNAsnoop_args_info_usage = "Usage: RNAsnoop [options]\n";
+
+const char *RNAsnoop_args_info_description = "reads a target RNA sequence and a H/ACA snoRNA sequence\nfrom a target and query file, respectively and computes optimal\nand suboptimal secondary structures for their hybridization. The\ncalculation can be done roughly done in O(nm), where is n the length\nof the target sequence and m is the length of the snoRNA stem, as it\nis specially tailored to the special case of H/ACA snoRNA. For general\npurpose target predictions, please have a look at RNAduplex, RNAup,\nRNAcofold and RNAplex. Accessibility effects can be estimated by\nRNAsnoop if a RNAplfold accessibility profile is provided. \n\nThe computed optimal and suboptimal structure are written to\nstdout, one structure per line. Each line consist\nof: The structure in dot bracket format with a \"&\" separating the\ntwo strands. The '<>' brackets represent snoRNA intramolecular\ninteractions, while the '()' brackets represent intermolecular\ninteractions between the snoRNA and its target.\n\nThe range of the structure in the two sequences in the format\n\"from,to : from,to\"; the energy of duplex structure in\nkcal/mol. If available the opening energy are also returned.\n";
+
+const char *RNAsnoop_args_info_detailed_help[] = {
+ " --help Print help and exit",
+ " --detailed-help Print help, including all details and hidden \n options, and exit",
+ " -V, --version Print version and exit",
+ "\nInput Options:",
+ " Below are command line options which alter the general input behavior of \n RNAsnoop\n",
+ " -L, --alignmentLength=INT Limit the extent of the interactions to L \n nucleotides (default=`25')",
+ " -C, --constraint Calculate the stem structure subject to \n constraints.\n (default=off)",
+ " The program reads first the stem sequence, then a string containing \n constraints on the structure encoded with the symbols:\n\n . (no constraint for this base)\n\n | (the corresponding base has to be paired\n\n x (the base is unpaired)\n\n < (base i is paired with a base j>i)\n\n > (base i is paired with a base j<i)\n\n and matching brackets ( ) (base i pairs base j)\n\n With the exception of \"|\", constraints will disallow all pairs conflicting \n with the constraint. This is usually sufficient to enforce the constraint, \n but occasionally a base may stay unpaired in spite of constraints. PF folding \n ignores constraints of type \"|\".\n\n",
+ " -s, --query=STRING File containing the query sequence.\n",
+ " Input sequences can be given piped to RNAsnoop or given in a query file with \n the -s option. Note that the -s 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 RNAsnoop or given in a target file with \n the -t optionNote that the -t option implies that the -s option is also used\n\n",
+ " -S, --suffix=STRING Specificy the suffix that was added by RNAup to \n the accessibility files\n\n (default=`_u1_to_30.out')",
+ " -P, --from-RNAplfold=STRING Specify the directory where accessibility \n profile generated by RNAplfold are found\n\n",
+ "\nAlgorithms:",
+ " Options which alter the computing behaviour of RNAplex.\n Please note that the options allowing to filter out snoRNA-RNA\n duplexes expect the energy to be given in decacal/mol instead of\n kcal/mol. A threshold of -2.8(kcal/mol) should be given as -280(decacal/mol)\n",
+ " -A, --alignment-mode Specify if RNAsnoop gets alignments or single \n sequences as input\n\n (default=off)",
+ " -f, --fast-folding=INT Speedup of the target search (default=`1')",
+ " This option allows to decide if the backtracking has to be\n done (-f 1) or not (-f 0). For -f 1 the structure is computed based\n on the standard energy model. This is the slowest mode of RNAsnoop. -f\n 0 is the fastest mode, as no structure are recomputed and only the\n interaction energy is returned\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\n compact duplexes, having few/small bulges or interior loops. Only\n useful when no accessibility profiles are available. This option is\n disabled if accessibility profiles are used (-P option)\n\n",
+ " -o, --minimal-right-duplex=INT\n Minimal Right Duplex Energy\n\n (default=`-270')",
+ " -l, --minimal-loop-energy=INT Minimal Right Duplex Energy\n (default=`-280')",
+ " Minimal Stem Loop Energy of the snoRNA. The energy should be\n given in decacalories, i.e. a minimal stem-loop energy of -2.8\n kcal/mol corresponds to -280 decacal/mol\n\n",
+ " -p, --minimal-left-duplex=INT Minimal Left Duplex Energy\n\n (default=`-170')",
+ " -q, --minimal-duplex=INT Minimal Duplex Energy\n\n (default=`-1090')",
+ " -d, --duplex-distance=INT Distance between target 3' ends of two \n consecutive duplexes\n (default=`2')",
+ " Distance between the target 3'ends of two consecutive\n duplexes. Should be set to the maximal length of interaction to get\n good results. Smaller d leads to larger overlaps between consecutive\n duplexes\n\n",
+ " -h, --minimal-stem-length=INT Minimal snoRNA stem length\n\n (default=`5')",
+ " -i, --maximal-stem-length=INT Maximal snoRNA stem length\n\n (default=`120')",
+ " -j, --minimal-duplex-box-length=INT\n Minimal distance between the duplex end and the \n H/ACA box\n\n (default=`11')",
+ " -k, --maximal-duplex-box-length=INT\n Maximal distance between the duplex end and the \n H/ACA box\n\n (default=`16')",
+ " -m, --minimal-snoRNA-stem-loop-length=INT\n Minimal number of nucleotides between the \n beginning of stem loop and\n beginning of the snoRNA sequence\n\n (default=`1')",
+ " -n, --maximal-snoRNA-stem-loop-length=INT\n Maximal number of nucleotides between the \n beginning of stem loop and\n beginning of the snoRNA sequence\n\n (default=`100000')",
+ " -v, --minimal-snoRNA-duplex-length=INT\n Minimal distance between duplex start and \n snoRNA\n\n (default=`0')",
+ " -w, --maximal-snoRNA-duplex-length=INT\n Maximal distance between duplex start and \n snoRNA\n\n (default=`0')",
+ " -x, --minimal-duplex-stem-energy=INT\n Minimal duplex stem energy\n\n (default=`-1370')",
+ " -y, --minimal-total-energy=INT\n Minimal total energy\n\n (default=`100000')",
+ " -a, --maximal-stem-asymmetry=INT\n Maximal snoRNA stem asymmetry\n\n (default=`30')",
+ " -b, --minimal-lower-stem-energy=INT\n Minimal lower stem energy\n\n (default=`100000')",
+ "\nOutput options:",
+ " Options that modifies the output\n\n",
+ " -e, --energy-threshold=DOUBLE Maximal energy difference between the mfe and \n the desired suboptimal\n (default=`-1')",
+ " Energy range for a duplex to be returned. The threshold is set on the total \n energy of interaction, i.e. the hybridizationenergy corrected for opening \n energy if -a is set or the energy corrected by -c. If unset, only the mfe \n will be returned\n\n",
+ " -I, --produce-ps Draw annotated 2D structures for a list of \n dot-bracket structures\n (default=off)",
+ " This option allows to produce interaction figures in PS-format with \n conservation/accessibility annotation, if available\n\n",
+ " -O, --output_directory=STRING Set where the generated figures should be \n stored\n\n (default=`./')",
+ " -N, --direct-redraw Outputs 2D interactions concurrently with the \n interaction calculation for each suboptimal \n interaction. The -I option should be \n preferred.\n\n (default=off)",
+ " -U, --from-RNAup=STRING Specify the directory where accessibility \n profiles generated by RNAup are found\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)
+{
+ RNAsnoop_args_info_help[0] = RNAsnoop_args_info_detailed_help[0];
+ RNAsnoop_args_info_help[1] = RNAsnoop_args_info_detailed_help[1];
+ RNAsnoop_args_info_help[2] = RNAsnoop_args_info_detailed_help[2];
+ RNAsnoop_args_info_help[3] = RNAsnoop_args_info_detailed_help[3];
+ RNAsnoop_args_info_help[4] = RNAsnoop_args_info_detailed_help[4];
+ RNAsnoop_args_info_help[5] = RNAsnoop_args_info_detailed_help[5];
+ RNAsnoop_args_info_help[6] = RNAsnoop_args_info_detailed_help[6];
+ RNAsnoop_args_info_help[7] = RNAsnoop_args_info_detailed_help[8];
+ RNAsnoop_args_info_help[8] = RNAsnoop_args_info_detailed_help[10];
+ RNAsnoop_args_info_help[9] = RNAsnoop_args_info_detailed_help[12];
+ RNAsnoop_args_info_help[10] = RNAsnoop_args_info_detailed_help[13];
+ RNAsnoop_args_info_help[11] = RNAsnoop_args_info_detailed_help[14];
+ RNAsnoop_args_info_help[12] = RNAsnoop_args_info_detailed_help[15];
+ RNAsnoop_args_info_help[13] = RNAsnoop_args_info_detailed_help[16];
+ RNAsnoop_args_info_help[14] = RNAsnoop_args_info_detailed_help[17];
+ RNAsnoop_args_info_help[15] = RNAsnoop_args_info_detailed_help[19];
+ RNAsnoop_args_info_help[16] = RNAsnoop_args_info_detailed_help[21];
+ RNAsnoop_args_info_help[17] = RNAsnoop_args_info_detailed_help[22];
+ RNAsnoop_args_info_help[18] = RNAsnoop_args_info_detailed_help[24];
+ RNAsnoop_args_info_help[19] = RNAsnoop_args_info_detailed_help[25];
+ RNAsnoop_args_info_help[20] = RNAsnoop_args_info_detailed_help[26];
+ RNAsnoop_args_info_help[21] = RNAsnoop_args_info_detailed_help[28];
+ RNAsnoop_args_info_help[22] = RNAsnoop_args_info_detailed_help[29];
+ RNAsnoop_args_info_help[23] = RNAsnoop_args_info_detailed_help[30];
+ RNAsnoop_args_info_help[24] = RNAsnoop_args_info_detailed_help[31];
+ RNAsnoop_args_info_help[25] = RNAsnoop_args_info_detailed_help[32];
+ RNAsnoop_args_info_help[26] = RNAsnoop_args_info_detailed_help[33];
+ RNAsnoop_args_info_help[27] = RNAsnoop_args_info_detailed_help[34];
+ RNAsnoop_args_info_help[28] = RNAsnoop_args_info_detailed_help[35];
+ RNAsnoop_args_info_help[29] = RNAsnoop_args_info_detailed_help[36];
+ RNAsnoop_args_info_help[30] = RNAsnoop_args_info_detailed_help[37];
+ RNAsnoop_args_info_help[31] = RNAsnoop_args_info_detailed_help[38];
+ RNAsnoop_args_info_help[32] = RNAsnoop_args_info_detailed_help[39];
+ RNAsnoop_args_info_help[33] = RNAsnoop_args_info_detailed_help[40];
+ RNAsnoop_args_info_help[34] = RNAsnoop_args_info_detailed_help[41];
+ RNAsnoop_args_info_help[35] = RNAsnoop_args_info_detailed_help[42];
+ RNAsnoop_args_info_help[36] = RNAsnoop_args_info_detailed_help[44];
+ RNAsnoop_args_info_help[37] = RNAsnoop_args_info_detailed_help[46];
+ RNAsnoop_args_info_help[38] = RNAsnoop_args_info_detailed_help[47];
+ RNAsnoop_args_info_help[39] = RNAsnoop_args_info_detailed_help[48];
+ RNAsnoop_args_info_help[40] = RNAsnoop_args_info_detailed_help[49];
+ RNAsnoop_args_info_help[41] = 0;
+
+}
+
+const char *RNAsnoop_args_info_help[42];
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+ , ARG_DOUBLE
+} RNAsnoop_cmdline_parser_arg_type;
+
+static
+void clear_given (struct RNAsnoop_args_info *args_info);
+static
+void clear_args (struct RNAsnoop_args_info *args_info);
+
+static int
+RNAsnoop_cmdline_parser_internal (int argc, char **argv, struct RNAsnoop_args_info *args_info,
+ struct RNAsnoop_cmdline_parser_params *params, const char *additional_error);
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct RNAsnoop_args_info *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->detailed_help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->alignmentLength_given = 0 ;
+ args_info->constraint_given = 0 ;
+ args_info->query_given = 0 ;
+ args_info->target_given = 0 ;
+ args_info->suffix_given = 0 ;
+ args_info->from_RNAplfold_given = 0 ;
+ args_info->alignment_mode_given = 0 ;
+ args_info->fast_folding_given = 0 ;
+ args_info->extension_cost_given = 0 ;
+ args_info->minimal_right_duplex_given = 0 ;
+ args_info->minimal_loop_energy_given = 0 ;
+ args_info->minimal_left_duplex_given = 0 ;
+ args_info->minimal_duplex_given = 0 ;
+ args_info->duplex_distance_given = 0 ;
+ args_info->minimal_stem_length_given = 0 ;
+ args_info->maximal_stem_length_given = 0 ;
+ args_info->minimal_duplex_box_length_given = 0 ;
+ args_info->maximal_duplex_box_length_given = 0 ;
+ args_info->minimal_snoRNA_stem_loop_length_given = 0 ;
+ args_info->maximal_snoRNA_stem_loop_length_given = 0 ;
+ args_info->minimal_snoRNA_duplex_length_given = 0 ;
+ args_info->maximal_snoRNA_duplex_length_given = 0 ;
+ args_info->minimal_duplex_stem_energy_given = 0 ;
+ args_info->minimal_total_energy_given = 0 ;
+ args_info->maximal_stem_asymmetry_given = 0 ;
+ args_info->minimal_lower_stem_energy_given = 0 ;
+ args_info->energy_threshold_given = 0 ;
+ args_info->produce_ps_given = 0 ;
+ args_info->output_directory_given = 0 ;
+ args_info->direct_redraw_given = 0 ;
+ args_info->from_RNAup_given = 0 ;
+}
+
+static
+void clear_args (struct RNAsnoop_args_info *args_info)
+{
+ FIX_UNUSED (args_info);
+ args_info->alignmentLength_arg = 25;
+ args_info->alignmentLength_orig = NULL;
+ args_info->constraint_flag = 0;
+ args_info->query_arg = NULL;
+ args_info->query_orig = NULL;
+ args_info->target_arg = NULL;
+ args_info->target_orig = NULL;
+ args_info->suffix_arg = gengetopt_strdup ("_u1_to_30.out");
+ args_info->suffix_orig = NULL;
+ args_info->from_RNAplfold_arg = NULL;
+ args_info->from_RNAplfold_orig = NULL;
+ args_info->alignment_mode_flag = 0;
+ args_info->fast_folding_arg = 1;
+ args_info->fast_folding_orig = NULL;
+ args_info->extension_cost_arg = 0;
+ args_info->extension_cost_orig = NULL;
+ args_info->minimal_right_duplex_arg = -270;
+ args_info->minimal_right_duplex_orig = NULL;
+ args_info->minimal_loop_energy_arg = -280;
+ args_info->minimal_loop_energy_orig = NULL;
+ args_info->minimal_left_duplex_arg = -170;
+ args_info->minimal_left_duplex_orig = NULL;
+ args_info->minimal_duplex_arg = -1090;
+ args_info->minimal_duplex_orig = NULL;
+ args_info->duplex_distance_arg = 2;
+ args_info->duplex_distance_orig = NULL;
+ args_info->minimal_stem_length_arg = 5;
+ args_info->minimal_stem_length_orig = NULL;
+ args_info->maximal_stem_length_arg = 120;
+ args_info->maximal_stem_length_orig = NULL;
+ args_info->minimal_duplex_box_length_arg = 11;
+ args_info->minimal_duplex_box_length_orig = NULL;
+ args_info->maximal_duplex_box_length_arg = 16;
+ args_info->maximal_duplex_box_length_orig = NULL;
+ args_info->minimal_snoRNA_stem_loop_length_arg = 1;
+ args_info->minimal_snoRNA_stem_loop_length_orig = NULL;
+ args_info->maximal_snoRNA_stem_loop_length_arg = 100000;
+ args_info->maximal_snoRNA_stem_loop_length_orig = NULL;
+ args_info->minimal_snoRNA_duplex_length_arg = 0;
+ args_info->minimal_snoRNA_duplex_length_orig = NULL;
+ args_info->maximal_snoRNA_duplex_length_arg = 0;
+ args_info->maximal_snoRNA_duplex_length_orig = NULL;
+ args_info->minimal_duplex_stem_energy_arg = -1370;
+ args_info->minimal_duplex_stem_energy_orig = NULL;
+ args_info->minimal_total_energy_arg = 100000;
+ args_info->minimal_total_energy_orig = NULL;
+ args_info->maximal_stem_asymmetry_arg = 30;
+ args_info->maximal_stem_asymmetry_orig = NULL;
+ args_info->minimal_lower_stem_energy_arg = 100000;
+ args_info->minimal_lower_stem_energy_orig = NULL;
+ args_info->energy_threshold_arg = -1;
+ args_info->energy_threshold_orig = NULL;
+ args_info->produce_ps_flag = 0;
+ args_info->output_directory_arg = gengetopt_strdup ("./");
+ args_info->output_directory_orig = NULL;
+ args_info->direct_redraw_flag = 0;
+ args_info->from_RNAup_arg = NULL;
+ args_info->from_RNAup_orig = NULL;
+
+}
+
+static
+void init_args_info(struct RNAsnoop_args_info *args_info)
+{
+
+ init_help_array();
+ args_info->help_help = RNAsnoop_args_info_detailed_help[0] ;
+ args_info->detailed_help_help = RNAsnoop_args_info_detailed_help[1] ;
+ args_info->version_help = RNAsnoop_args_info_detailed_help[2] ;
+ args_info->alignmentLength_help = RNAsnoop_args_info_detailed_help[5] ;
+ args_info->constraint_help = RNAsnoop_args_info_detailed_help[6] ;
+ args_info->query_help = RNAsnoop_args_info_detailed_help[8] ;
+ args_info->target_help = RNAsnoop_args_info_detailed_help[10] ;
+ args_info->suffix_help = RNAsnoop_args_info_detailed_help[12] ;
+ args_info->from_RNAplfold_help = RNAsnoop_args_info_detailed_help[13] ;
+ args_info->alignment_mode_help = RNAsnoop_args_info_detailed_help[16] ;
+ args_info->fast_folding_help = RNAsnoop_args_info_detailed_help[17] ;
+ args_info->extension_cost_help = RNAsnoop_args_info_detailed_help[19] ;
+ args_info->minimal_right_duplex_help = RNAsnoop_args_info_detailed_help[21] ;
+ args_info->minimal_loop_energy_help = RNAsnoop_args_info_detailed_help[22] ;
+ args_info->minimal_left_duplex_help = RNAsnoop_args_info_detailed_help[24] ;
+ args_info->minimal_duplex_help = RNAsnoop_args_info_detailed_help[25] ;
+ args_info->duplex_distance_help = RNAsnoop_args_info_detailed_help[26] ;
+ args_info->minimal_stem_length_help = RNAsnoop_args_info_detailed_help[28] ;
+ args_info->maximal_stem_length_help = RNAsnoop_args_info_detailed_help[29] ;
+ args_info->minimal_duplex_box_length_help = RNAsnoop_args_info_detailed_help[30] ;
+ args_info->maximal_duplex_box_length_help = RNAsnoop_args_info_detailed_help[31] ;
+ args_info->minimal_snoRNA_stem_loop_length_help = RNAsnoop_args_info_detailed_help[32] ;
+ args_info->maximal_snoRNA_stem_loop_length_help = RNAsnoop_args_info_detailed_help[33] ;
+ args_info->minimal_snoRNA_duplex_length_help = RNAsnoop_args_info_detailed_help[34] ;
+ args_info->maximal_snoRNA_duplex_length_help = RNAsnoop_args_info_detailed_help[35] ;
+ args_info->minimal_duplex_stem_energy_help = RNAsnoop_args_info_detailed_help[36] ;
+ args_info->minimal_total_energy_help = RNAsnoop_args_info_detailed_help[37] ;
+ args_info->maximal_stem_asymmetry_help = RNAsnoop_args_info_detailed_help[38] ;
+ args_info->minimal_lower_stem_energy_help = RNAsnoop_args_info_detailed_help[39] ;
+ args_info->energy_threshold_help = RNAsnoop_args_info_detailed_help[42] ;
+ args_info->produce_ps_help = RNAsnoop_args_info_detailed_help[44] ;
+ args_info->output_directory_help = RNAsnoop_args_info_detailed_help[46] ;
+ args_info->direct_redraw_help = RNAsnoop_args_info_detailed_help[47] ;
+ args_info->from_RNAup_help = RNAsnoop_args_info_detailed_help[48] ;
+
+}
+
+void
+RNAsnoop_cmdline_parser_print_version (void)
+{
+ printf ("%s %s\n",
+ (strlen(RNASNOOP_CMDLINE_PARSER_PACKAGE_NAME) ? RNASNOOP_CMDLINE_PARSER_PACKAGE_NAME : RNASNOOP_CMDLINE_PARSER_PACKAGE),
+ RNASNOOP_CMDLINE_PARSER_VERSION);
+}
+
+static void print_help_common(void) {
+ RNAsnoop_cmdline_parser_print_version ();
+
+ if (strlen(RNAsnoop_args_info_purpose) > 0)
+ printf("\n%s\n", RNAsnoop_args_info_purpose);
+
+ if (strlen(RNAsnoop_args_info_usage) > 0)
+ printf("\n%s\n", RNAsnoop_args_info_usage);
+
+ printf("\n");
+
+ if (strlen(RNAsnoop_args_info_description) > 0)
+ printf("%s\n\n", RNAsnoop_args_info_description);
+}
+
+void
+RNAsnoop_cmdline_parser_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (RNAsnoop_args_info_help[i])
+ printf("%s\n", RNAsnoop_args_info_help[i++]);
+}
+
+void
+RNAsnoop_cmdline_parser_print_detailed_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (RNAsnoop_args_info_detailed_help[i])
+ printf("%s\n", RNAsnoop_args_info_detailed_help[i++]);
+}
+
+void
+RNAsnoop_cmdline_parser_init (struct RNAsnoop_args_info *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+}
+
+void
+RNAsnoop_cmdline_parser_params_init(struct RNAsnoop_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 RNAsnoop_cmdline_parser_params *
+RNAsnoop_cmdline_parser_params_create(void)
+{
+ struct RNAsnoop_cmdline_parser_params *params =
+ (struct RNAsnoop_cmdline_parser_params *)malloc(sizeof(struct RNAsnoop_cmdline_parser_params));
+ RNAsnoop_cmdline_parser_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+
+static void
+RNAsnoop_cmdline_parser_release (struct RNAsnoop_args_info *args_info)
+{
+
+ free_string_field (&(args_info->alignmentLength_orig));
+ 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->suffix_arg));
+ free_string_field (&(args_info->suffix_orig));
+ free_string_field (&(args_info->from_RNAplfold_arg));
+ free_string_field (&(args_info->from_RNAplfold_orig));
+ free_string_field (&(args_info->fast_folding_orig));
+ free_string_field (&(args_info->extension_cost_orig));
+ free_string_field (&(args_info->minimal_right_duplex_orig));
+ free_string_field (&(args_info->minimal_loop_energy_orig));
+ free_string_field (&(args_info->minimal_left_duplex_orig));
+ free_string_field (&(args_info->minimal_duplex_orig));
+ free_string_field (&(args_info->duplex_distance_orig));
+ free_string_field (&(args_info->minimal_stem_length_orig));
+ free_string_field (&(args_info->maximal_stem_length_orig));
+ free_string_field (&(args_info->minimal_duplex_box_length_orig));
+ free_string_field (&(args_info->maximal_duplex_box_length_orig));
+ free_string_field (&(args_info->minimal_snoRNA_stem_loop_length_orig));
+ free_string_field (&(args_info->maximal_snoRNA_stem_loop_length_orig));
+ free_string_field (&(args_info->minimal_snoRNA_duplex_length_orig));
+ free_string_field (&(args_info->maximal_snoRNA_duplex_length_orig));
+ free_string_field (&(args_info->minimal_duplex_stem_energy_orig));
+ free_string_field (&(args_info->minimal_total_energy_orig));
+ free_string_field (&(args_info->maximal_stem_asymmetry_orig));
+ free_string_field (&(args_info->minimal_lower_stem_energy_orig));
+ free_string_field (&(args_info->energy_threshold_orig));
+ free_string_field (&(args_info->output_directory_arg));
+ free_string_field (&(args_info->output_directory_orig));
+ free_string_field (&(args_info->from_RNAup_arg));
+ free_string_field (&(args_info->from_RNAup_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
+RNAsnoop_cmdline_parser_dump(FILE *outfile, struct RNAsnoop_args_info *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", RNASNOOP_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->alignmentLength_given)
+ write_into_file(outfile, "alignmentLength", args_info->alignmentLength_orig, 0);
+ if (args_info->constraint_given)
+ write_into_file(outfile, "constraint", 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->suffix_given)
+ write_into_file(outfile, "suffix", args_info->suffix_orig, 0);
+ if (args_info->from_RNAplfold_given)
+ write_into_file(outfile, "from-RNAplfold", args_info->from_RNAplfold_orig, 0);
+ if (args_info->alignment_mode_given)
+ write_into_file(outfile, "alignment-mode", 0, 0 );
+ if (args_info->fast_folding_given)
+ write_into_file(outfile, "fast-folding", args_info->fast_folding_orig, 0);
+ if (args_info->extension_cost_given)
+ write_into_file(outfile, "extension-cost", args_info->extension_cost_orig, 0);
+ if (args_info->minimal_right_duplex_given)
+ write_into_file(outfile, "minimal-right-duplex", args_info->minimal_right_duplex_orig, 0);
+ if (args_info->minimal_loop_energy_given)
+ write_into_file(outfile, "minimal-loop-energy", args_info->minimal_loop_energy_orig, 0);
+ if (args_info->minimal_left_duplex_given)
+ write_into_file(outfile, "minimal-left-duplex", args_info->minimal_left_duplex_orig, 0);
+ if (args_info->minimal_duplex_given)
+ write_into_file(outfile, "minimal-duplex", args_info->minimal_duplex_orig, 0);
+ if (args_info->duplex_distance_given)
+ write_into_file(outfile, "duplex-distance", args_info->duplex_distance_orig, 0);
+ if (args_info->minimal_stem_length_given)
+ write_into_file(outfile, "minimal-stem-length", args_info->minimal_stem_length_orig, 0);
+ if (args_info->maximal_stem_length_given)
+ write_into_file(outfile, "maximal-stem-length", args_info->maximal_stem_length_orig, 0);
+ if (args_info->minimal_duplex_box_length_given)
+ write_into_file(outfile, "minimal-duplex-box-length", args_info->minimal_duplex_box_length_orig, 0);
+ if (args_info->maximal_duplex_box_length_given)
+ write_into_file(outfile, "maximal-duplex-box-length", args_info->maximal_duplex_box_length_orig, 0);
+ if (args_info->minimal_snoRNA_stem_loop_length_given)
+ write_into_file(outfile, "minimal-snoRNA-stem-loop-length", args_info->minimal_snoRNA_stem_loop_length_orig, 0);
+ if (args_info->maximal_snoRNA_stem_loop_length_given)
+ write_into_file(outfile, "maximal-snoRNA-stem-loop-length", args_info->maximal_snoRNA_stem_loop_length_orig, 0);
+ if (args_info->minimal_snoRNA_duplex_length_given)
+ write_into_file(outfile, "minimal-snoRNA-duplex-length", args_info->minimal_snoRNA_duplex_length_orig, 0);
+ if (args_info->maximal_snoRNA_duplex_length_given)
+ write_into_file(outfile, "maximal-snoRNA-duplex-length", args_info->maximal_snoRNA_duplex_length_orig, 0);
+ if (args_info->minimal_duplex_stem_energy_given)
+ write_into_file(outfile, "minimal-duplex-stem-energy", args_info->minimal_duplex_stem_energy_orig, 0);
+ if (args_info->minimal_total_energy_given)
+ write_into_file(outfile, "minimal-total-energy", args_info->minimal_total_energy_orig, 0);
+ if (args_info->maximal_stem_asymmetry_given)
+ write_into_file(outfile, "maximal-stem-asymmetry", args_info->maximal_stem_asymmetry_orig, 0);
+ if (args_info->minimal_lower_stem_energy_given)
+ write_into_file(outfile, "minimal-lower-stem-energy", args_info->minimal_lower_stem_energy_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", 0, 0 );
+ if (args_info->output_directory_given)
+ write_into_file(outfile, "output_directory", args_info->output_directory_orig, 0);
+ if (args_info->direct_redraw_given)
+ write_into_file(outfile, "direct-redraw", 0, 0 );
+ if (args_info->from_RNAup_given)
+ write_into_file(outfile, "from-RNAup", args_info->from_RNAup_orig, 0);
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+RNAsnoop_cmdline_parser_file_save(const char *filename, struct RNAsnoop_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", RNASNOOP_CMDLINE_PARSER_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = RNAsnoop_cmdline_parser_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+RNAsnoop_cmdline_parser_free (struct RNAsnoop_args_info *args_info)
+{
+ RNAsnoop_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
+RNAsnoop_cmdline_parser (int argc, char **argv, struct RNAsnoop_args_info *args_info)
+{
+ return RNAsnoop_cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+RNAsnoop_cmdline_parser_ext (int argc, char **argv, struct RNAsnoop_args_info *args_info,
+ struct RNAsnoop_cmdline_parser_params *params)
+{
+ int result;
+ result = RNAsnoop_cmdline_parser_internal (argc, argv, args_info, params, 0);
+
+ if (result == EXIT_FAILURE)
+ {
+ RNAsnoop_cmdline_parser_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+RNAsnoop_cmdline_parser2 (int argc, char **argv, struct RNAsnoop_args_info *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct RNAsnoop_cmdline_parser_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = RNAsnoop_cmdline_parser_internal (argc, argv, args_info, ¶ms, 0);
+
+ if (result == EXIT_FAILURE)
+ {
+ RNAsnoop_cmdline_parser_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+RNAsnoop_cmdline_parser_required (struct RNAsnoop_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 RNAsnoop_cmdline_parser_params.check_ambiguity
+ * @param override @see RNAsnoop_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,
+ RNAsnoop_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
+RNAsnoop_cmdline_parser_internal (
+ int argc, char **argv, struct RNAsnoop_args_info *args_info,
+ struct RNAsnoop_cmdline_parser_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+
+ int error = 0;
+ struct RNAsnoop_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)
+ RNAsnoop_cmdline_parser_init (args_info);
+
+ RNAsnoop_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, 0 },
+ { "detailed-help", 0, NULL, 0 },
+ { "version", 0, NULL, 'V' },
+ { "alignmentLength", 1, NULL, 'L' },
+ { "constraint", 0, NULL, 'C' },
+ { "query", 1, NULL, 's' },
+ { "target", 1, NULL, 't' },
+ { "suffix", 1, NULL, 'S' },
+ { "from-RNAplfold", 1, NULL, 'P' },
+ { "alignment-mode", 0, NULL, 'A' },
+ { "fast-folding", 1, NULL, 'f' },
+ { "extension-cost", 1, NULL, 'c' },
+ { "minimal-right-duplex", 1, NULL, 'o' },
+ { "minimal-loop-energy", 1, NULL, 'l' },
+ { "minimal-left-duplex", 1, NULL, 'p' },
+ { "minimal-duplex", 1, NULL, 'q' },
+ { "duplex-distance", 1, NULL, 'd' },
+ { "minimal-stem-length", 1, NULL, 'h' },
+ { "maximal-stem-length", 1, NULL, 'i' },
+ { "minimal-duplex-box-length", 1, NULL, 'j' },
+ { "maximal-duplex-box-length", 1, NULL, 'k' },
+ { "minimal-snoRNA-stem-loop-length", 1, NULL, 'm' },
+ { "maximal-snoRNA-stem-loop-length", 1, NULL, 'n' },
+ { "minimal-snoRNA-duplex-length", 1, NULL, 'v' },
+ { "maximal-snoRNA-duplex-length", 1, NULL, 'w' },
+ { "minimal-duplex-stem-energy", 1, NULL, 'x' },
+ { "minimal-total-energy", 1, NULL, 'y' },
+ { "maximal-stem-asymmetry", 1, NULL, 'a' },
+ { "minimal-lower-stem-energy", 1, NULL, 'b' },
+ { "energy-threshold", 1, NULL, 'e' },
+ { "produce-ps", 0, NULL, 'I' },
+ { "output_directory", 1, NULL, 'O' },
+ { "direct-redraw", 0, NULL, 'N' },
+ { "from-RNAup", 1, NULL, 'U' },
+ { 0, 0, 0, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "VL:Cs:t:S:P:Af:c:o:l:p:q:d:h:i:j:k:m:n:v:w:x:y:a:b:e:IO:NU:", 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 'V': /* Print version and exit. */
+ RNAsnoop_cmdline_parser_print_version ();
+ RNAsnoop_cmdline_parser_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'L': /* Limit the extent of the interactions to L nucleotides. */
+
+
+ if (update_arg( (void *)&(args_info->alignmentLength_arg),
+ &(args_info->alignmentLength_orig), &(args_info->alignmentLength_given),
+ &(local_args_info.alignmentLength_given), optarg, 0, "25", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "alignmentLength", 'L',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'C': /* Calculate the stem structure 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 's': /* 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", 's',
+ 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 'S': /* Specificy the suffix that was added by RNAup to the accessibility files
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->suffix_arg),
+ &(args_info->suffix_orig), &(args_info->suffix_given),
+ &(local_args_info.suffix_given), optarg, 0, "_u1_to_30.out", ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "suffix", 'S',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'P': /* Specify the directory where accessibility profile generated by RNAplfold are found
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->from_RNAplfold_arg),
+ &(args_info->from_RNAplfold_orig), &(args_info->from_RNAplfold_given),
+ &(local_args_info.from_RNAplfold_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "from-RNAplfold", 'P',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'A': /* Specify if RNAsnoop gets alignments or single sequences as input
+
+. */
+
+
+ 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 '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, "1", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "fast-folding", 'f',
+ 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 'o': /* Minimal Right Duplex Energy
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_right_duplex_arg),
+ &(args_info->minimal_right_duplex_orig), &(args_info->minimal_right_duplex_given),
+ &(local_args_info.minimal_right_duplex_given), optarg, 0, "-270", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-right-duplex", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'l': /* Minimal Right Duplex Energy
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_loop_energy_arg),
+ &(args_info->minimal_loop_energy_orig), &(args_info->minimal_loop_energy_given),
+ &(local_args_info.minimal_loop_energy_given), optarg, 0, "-280", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-loop-energy", 'l',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'p': /* Minimal Left Duplex Energy
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_left_duplex_arg),
+ &(args_info->minimal_left_duplex_orig), &(args_info->minimal_left_duplex_given),
+ &(local_args_info.minimal_left_duplex_given), optarg, 0, "-170", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-left-duplex", 'p',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'q': /* Minimal Duplex Energy
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_duplex_arg),
+ &(args_info->minimal_duplex_orig), &(args_info->minimal_duplex_given),
+ &(local_args_info.minimal_duplex_given), optarg, 0, "-1090", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-duplex", 'q',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'd': /* 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, "2", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "duplex-distance", 'd',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'h': /* Minimal snoRNA stem length
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_stem_length_arg),
+ &(args_info->minimal_stem_length_orig), &(args_info->minimal_stem_length_given),
+ &(local_args_info.minimal_stem_length_given), optarg, 0, "5", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-stem-length", 'h',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Maximal snoRNA stem length
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->maximal_stem_length_arg),
+ &(args_info->maximal_stem_length_orig), &(args_info->maximal_stem_length_given),
+ &(local_args_info.maximal_stem_length_given), optarg, 0, "120", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "maximal-stem-length", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'j': /* Minimal distance between the duplex end and the H/ACA box
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_duplex_box_length_arg),
+ &(args_info->minimal_duplex_box_length_orig), &(args_info->minimal_duplex_box_length_given),
+ &(local_args_info.minimal_duplex_box_length_given), optarg, 0, "11", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-duplex-box-length", 'j',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'k': /* Maximal distance between the duplex end and the H/ACA box
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->maximal_duplex_box_length_arg),
+ &(args_info->maximal_duplex_box_length_orig), &(args_info->maximal_duplex_box_length_given),
+ &(local_args_info.maximal_duplex_box_length_given), optarg, 0, "16", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "maximal-duplex-box-length", 'k',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'm': /* Minimal number of nucleotides between the beginning of stem loop and
+ beginning of the snoRNA sequence
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_snoRNA_stem_loop_length_arg),
+ &(args_info->minimal_snoRNA_stem_loop_length_orig), &(args_info->minimal_snoRNA_stem_loop_length_given),
+ &(local_args_info.minimal_snoRNA_stem_loop_length_given), optarg, 0, "1", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-snoRNA-stem-loop-length", 'm',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'n': /* Maximal number of nucleotides between the beginning of stem loop and
+ beginning of the snoRNA sequence
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->maximal_snoRNA_stem_loop_length_arg),
+ &(args_info->maximal_snoRNA_stem_loop_length_orig), &(args_info->maximal_snoRNA_stem_loop_length_given),
+ &(local_args_info.maximal_snoRNA_stem_loop_length_given), optarg, 0, "100000", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "maximal-snoRNA-stem-loop-length", 'n',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'v': /* Minimal distance between duplex start and snoRNA
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_snoRNA_duplex_length_arg),
+ &(args_info->minimal_snoRNA_duplex_length_orig), &(args_info->minimal_snoRNA_duplex_length_given),
+ &(local_args_info.minimal_snoRNA_duplex_length_given), optarg, 0, "0", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-snoRNA-duplex-length", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'w': /* Maximal distance between duplex start and snoRNA
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->maximal_snoRNA_duplex_length_arg),
+ &(args_info->maximal_snoRNA_duplex_length_orig), &(args_info->maximal_snoRNA_duplex_length_given),
+ &(local_args_info.maximal_snoRNA_duplex_length_given), optarg, 0, "0", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "maximal-snoRNA-duplex-length", 'w',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'x': /* Minimal duplex stem energy
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_duplex_stem_energy_arg),
+ &(args_info->minimal_duplex_stem_energy_orig), &(args_info->minimal_duplex_stem_energy_given),
+ &(local_args_info.minimal_duplex_stem_energy_given), optarg, 0, "-1370", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-duplex-stem-energy", 'x',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'y': /* Minimal total energy
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_total_energy_arg),
+ &(args_info->minimal_total_energy_orig), &(args_info->minimal_total_energy_given),
+ &(local_args_info.minimal_total_energy_given), optarg, 0, "100000", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-total-energy", 'y',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'a': /* Maximal snoRNA stem asymmetry
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->maximal_stem_asymmetry_arg),
+ &(args_info->maximal_stem_asymmetry_orig), &(args_info->maximal_stem_asymmetry_given),
+ &(local_args_info.maximal_stem_asymmetry_given), optarg, 0, "30", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "maximal-stem-asymmetry", 'a',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'b': /* Minimal lower stem energy
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->minimal_lower_stem_energy_arg),
+ &(args_info->minimal_lower_stem_energy_orig), &(args_info->minimal_lower_stem_energy_given),
+ &(local_args_info.minimal_lower_stem_energy_given), optarg, 0, "100000", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minimal-lower-stem-energy", 'b',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'e': /* Maximal energy difference between the mfe and the desired suboptimal
+. */
+
+
+ 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, "-1", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "energy-threshold", 'e',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'I': /* Draw annotated 2D structures for a list of dot-bracket structures
+. */
+
+
+ if (update_arg((void *)&(args_info->produce_ps_flag), 0, &(args_info->produce_ps_given),
+ &(local_args_info.produce_ps_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "produce-ps", 'I',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'O': /* Set where the generated figures should be stored
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->output_directory_arg),
+ &(args_info->output_directory_orig), &(args_info->output_directory_given),
+ &(local_args_info.output_directory_given), optarg, 0, "./", ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output_directory", 'O',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'N': /* Outputs 2D interactions concurrently with the interaction calculation for each suboptimal interaction. The -I option should be preferred.
+
+. */
+
+
+ if (update_arg((void *)&(args_info->direct_redraw_flag), 0, &(args_info->direct_redraw_given),
+ &(local_args_info.direct_redraw_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "direct-redraw", 'N',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'U': /* Specify the directory where accessibility profiles generated by RNAup are found
+
+. */
+
+
+ if (update_arg( (void *)&(args_info->from_RNAup_arg),
+ &(args_info->from_RNAup_orig), &(args_info->from_RNAup_given),
+ &(local_args_info.from_RNAup_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "from-RNAup", 'U',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ if (strcmp (long_options[option_index].name, "help") == 0) {
+ RNAsnoop_cmdline_parser_print_help ();
+ RNAsnoop_cmdline_parser_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+ }
+
+ if (strcmp (long_options[option_index].name, "detailed-help") == 0) {
+ RNAsnoop_cmdline_parser_print_detailed_help ();
+ RNAsnoop_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", RNASNOOP_CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+
+
+ RNAsnoop_cmdline_parser_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ return 0;
+
+failure:
+
+ RNAsnoop_cmdline_parser_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
git://source.jalview.org / jabaws.git / blobdiff