--- /dev/null
+/** @file cmdline.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22.6
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CMDLINE_H
+#define CMDLINE_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_PACKAGE
+/** @brief the program name (used for printing errors) */
+#define CMDLINE_PARSER_PACKAGE "Jnet"
+#endif
+
+#ifndef CMDLINE_PARSER_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define CMDLINE_PARSER_PACKAGE_NAME "Jnet"
+#endif
+
+#ifndef CMDLINE_PARSER_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_VERSION "2.2"
+#endif
+
+/** @brief Where the command line options are stored */
+struct gengetopt_args_info
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * hmmer_arg; /**< @brief HMMER profile. */
+ char * hmmer_orig; /**< @brief HMMER profile original value given at command line. */
+ const char *hmmer_help; /**< @brief HMMER profile help description. */
+ char * pssm_arg; /**< @brief PSIBLAST PSSM. */
+ char * pssm_orig; /**< @brief PSIBLAST PSSM original value given at command line. */
+ const char *pssm_help; /**< @brief PSIBLAST PSSM help description. */
+ int test_flag; /**< @brief Flag for test style output (default=off). */
+ const char *test_help; /**< @brief Flag for test style output help description. */
+ const char *concise_help; /**< @brief concise output (default) help description. */
+ int human_arg; /**< @brief human readable output. Optionally, can take a width argument [default: 60]. */
+ char * human_orig; /**< @brief human readable output. Optionally, can take a width argument [default: 60] original value given at command line. */
+ const char *human_help; /**< @brief human readable output. Optionally, can take a width argument [default: 60] help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int hmmer_given ; /**< @brief Whether hmmer was given. */
+ unsigned int pssm_given ; /**< @brief Whether pssm was given. */
+ unsigned int test_given ; /**< @brief Whether test was given. */
+ unsigned int concise_given ; /**< @brief Whether concise was given. */
+ unsigned int human_given ; /**< @brief Whether human was given. */
+
+ int output_group_counter; /**< @brief Counter for group output */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure gengetopt_args_info (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure gengetopt_args_info (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *gengetopt_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *gengetopt_args_info_usage;
+/** @brief the description string of the program */
+extern const char *gengetopt_args_info_description;
+/** @brief all the lines making the help output */
+extern const char *gengetopt_args_info_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser (int argc, char **argv,
+ struct gengetopt_args_info *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_ext() instead
+ */
+int cmdline_parser2 (int argc, char **argv,
+ struct gengetopt_args_info *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_ext (int argc, char **argv,
+ struct gengetopt_args_info *args_info,
+ struct cmdline_parser_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_dump(FILE *outfile,
+ struct gengetopt_args_info *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_file_save(const char *filename,
+ struct gengetopt_args_info *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_params_init(struct cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_params structure
+ */
+struct cmdline_parser_params *cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed gengetopt_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_init (struct gengetopt_args_info *args_info);
+/**
+ * Deallocates the string fields of the gengetopt_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_free (struct gengetopt_args_info *args_info);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_required (struct gengetopt_args_info *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CMDLINE_H */
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