--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22.6
+ generated with the following command:
+ gengetopt
+
+ 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 <getopt.h>
+
+#include "cmdline.h"
+
+const char *gengetopt_args_info_purpose = "A consensus neural network protein secondary structure prediction method\n- Trained with SCOP 1.75 data and UniRef90 release 15.4";
+
+const char *gengetopt_args_info_usage = "Usage: Jnet [OPTIONS]...";
+
+const char *gengetopt_args_info_versiontext = "";
+
+const char *gengetopt_args_info_description = "";
+
+const char *gengetopt_args_info_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ " -H, --hmmer=filename HMMER profile",
+ " -p, --pssm=filename PSIBLAST PSSM",
+ " -T, --test Flag for test style output (default=off)",
+ "\n Group: output\n Output options",
+ " --concise concise output (default)",
+ " --human[=INT] human readable output. Optionally, can take a width\n argument [default: 60]",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+} cmdline_parser_arg_type;
+
+static
+void clear_given (struct gengetopt_args_info *args_info);
+static
+void clear_args (struct gengetopt_args_info *args_info);
+
+static int
+cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
+ struct cmdline_parser_params *params, const char *additional_error);
+
+static int
+cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct gengetopt_args_info *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->hmmer_given = 0 ;
+ args_info->pssm_given = 0 ;
+ args_info->test_given = 0 ;
+ args_info->concise_given = 0 ;
+ args_info->human_given = 0 ;
+ args_info->output_group_counter = 0 ;
+}
+
+static
+void clear_args (struct gengetopt_args_info *args_info)
+{
+ FIX_UNUSED (args_info);
+ args_info->hmmer_arg = NULL;
+ args_info->hmmer_orig = NULL;
+ args_info->pssm_arg = NULL;
+ args_info->pssm_orig = NULL;
+ args_info->test_flag = 0;
+ args_info->human_orig = NULL;
+
+}
+
+static
+void init_args_info(struct gengetopt_args_info *args_info)
+{
+
+
+ args_info->help_help = gengetopt_args_info_help[0] ;
+ args_info->version_help = gengetopt_args_info_help[1] ;
+ args_info->hmmer_help = gengetopt_args_info_help[2] ;
+ args_info->pssm_help = gengetopt_args_info_help[3] ;
+ args_info->test_help = gengetopt_args_info_help[4] ;
+ args_info->concise_help = gengetopt_args_info_help[6] ;
+ args_info->human_help = gengetopt_args_info_help[7] ;
+
+}
+
+void
+cmdline_parser_print_version (void)
+{
+ printf ("%s %s\n",
+ (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
+ CMDLINE_PARSER_VERSION);
+
+ if (strlen(gengetopt_args_info_versiontext) > 0)
+ printf("\n%s\n", gengetopt_args_info_versiontext);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_print_version ();
+
+ if (strlen(gengetopt_args_info_purpose) > 0)
+ printf("\n%s\n", gengetopt_args_info_purpose);
+
+ if (strlen(gengetopt_args_info_usage) > 0)
+ printf("\n%s\n", gengetopt_args_info_usage);
+
+ printf("\n");
+
+ if (strlen(gengetopt_args_info_description) > 0)
+ printf("%s\n\n", gengetopt_args_info_description);
+}
+
+void
+cmdline_parser_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (gengetopt_args_info_help[i])
+ printf("%s\n", gengetopt_args_info_help[i++]);
+}
+
+void
+cmdline_parser_init (struct gengetopt_args_info *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+}
+
+void
+cmdline_parser_params_init(struct 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 cmdline_parser_params *
+cmdline_parser_params_create(void)
+{
+ struct cmdline_parser_params *params =
+ (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
+ cmdline_parser_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+
+static void
+cmdline_parser_release (struct gengetopt_args_info *args_info)
+{
+
+ free_string_field (&(args_info->hmmer_arg));
+ free_string_field (&(args_info->hmmer_orig));
+ free_string_field (&(args_info->pssm_arg));
+ free_string_field (&(args_info->pssm_orig));
+ free_string_field (&(args_info->human_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
+cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->hmmer_given)
+ write_into_file(outfile, "hmmer", args_info->hmmer_orig, 0);
+ if (args_info->pssm_given)
+ write_into_file(outfile, "pssm", args_info->pssm_orig, 0);
+ if (args_info->test_given)
+ write_into_file(outfile, "test", 0, 0 );
+ if (args_info->concise_given)
+ write_into_file(outfile, "concise", 0, 0 );
+ if (args_info->human_given)
+ write_into_file(outfile, "human", args_info->human_orig, 0);
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_file_save(const char *filename, struct gengetopt_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", CMDLINE_PARSER_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_free (struct gengetopt_args_info *args_info)
+{
+ cmdline_parser_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = 0;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+static void
+reset_group_output(struct gengetopt_args_info *args_info)
+{
+ if (! args_info->output_group_counter)
+ return;
+
+ args_info->concise_given = 0 ;
+ args_info->human_given = 0 ;
+ free_string_field (&(args_info->human_orig));
+
+ args_info->output_group_counter = 0;
+}
+
+int
+cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
+{
+ return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
+ struct cmdline_parser_params *params)
+{
+ int result;
+ result = cmdline_parser_internal (argc, argv, args_info, params, 0);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_internal (argc, argv, args_info, ¶ms, 0);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
+{
+ int error_occurred = 0;
+ FIX_UNUSED (additional_error);
+
+ /* checks for required options */
+ if (! args_info->hmmer_given)
+ {
+ fprintf (stderr, "%s: '--hmmer' ('-H') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error_occurred = 1;
+ }
+
+
+ /* checks for dependences among options */
+
+ return error_occurred;
+}
+
+
+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 cmdline_parser_params.check_ambiguity
+ * @param override @see 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,
+ 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_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:
+ 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
+cmdline_parser_internal (
+ int argc, char **argv, struct gengetopt_args_info *args_info,
+ struct cmdline_parser_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+
+ int error_occurred = 0;
+ struct gengetopt_args_info local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_init (args_info);
+
+ 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' },
+ { "version", 0, NULL, 'V' },
+ { "hmmer", 1, NULL, 'H' },
+ { "pssm", 1, NULL, 'p' },
+ { "test", 0, NULL, 'T' },
+ { "concise", 0, NULL, 0 },
+ { "human", 2, NULL, 0 },
+ { 0, 0, 0, 0 }
+ };
+
+ c = getopt_long (argc, argv, "hVH:p:T", long_options, &option_index);
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_print_help ();
+ cmdline_parser_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_print_version ();
+ cmdline_parser_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'H': /* HMMER profile. */
+
+
+ if (update_arg( (void *)&(args_info->hmmer_arg),
+ &(args_info->hmmer_orig), &(args_info->hmmer_given),
+ &(local_args_info.hmmer_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "hmmer", 'H',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'p': /* PSIBLAST PSSM. */
+
+
+ if (update_arg( (void *)&(args_info->pssm_arg),
+ &(args_info->pssm_orig), &(args_info->pssm_given),
+ &(local_args_info.pssm_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "pssm", 'p',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'T': /* Flag for test style output. */
+
+
+ if (update_arg((void *)&(args_info->test_flag), 0, &(args_info->test_given),
+ &(local_args_info.test_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "test", 'T',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* concise output (default). */
+ if (strcmp (long_options[option_index].name, "concise") == 0)
+ {
+
+ if (args_info->output_group_counter && override)
+ reset_group_output (args_info);
+ args_info->output_group_counter += 1;
+
+ if (update_arg( 0 ,
+ 0 , &(args_info->concise_given),
+ &(local_args_info.concise_given), optarg, 0, 0, ARG_NO,
+ check_ambiguity, override, 0, 0,
+ "concise", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* human readable output. Optionally, can take a width argument [default: 60]. */
+ else if (strcmp (long_options[option_index].name, "human") == 0)
+ {
+
+ if (args_info->output_group_counter && override)
+ reset_group_output (args_info);
+ args_info->output_group_counter += 1;
+
+ if (update_arg( (void *)&(args_info->human_arg),
+ &(args_info->human_orig), &(args_info->human_given),
+ &(local_args_info.human_given), optarg, 0, 0, ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "human", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+ if (args_info->output_group_counter > 1)
+ {
+ fprintf (stderr, "%s: %d options of group output were given. At most one is required%s.\n", argv[0], args_info->output_group_counter, (additional_error ? additional_error : ""));
+ error_occurred = 1;
+ }
+
+
+
+ if (check_required)
+ {
+ error_occurred += cmdline_parser_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_release (&local_args_info);
+
+ if ( error_occurred )
+ return (EXIT_FAILURE);
+
+ return 0;
+
+failure:
+
+ cmdline_parser_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
git://source.jalview.org / jpred.git / blobdiff