--- /dev/null
+/** @file RNAsnoop_cmdl.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22.5
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef RNASNOOP_CMDL_H
+#define RNASNOOP_CMDL_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 RNASNOOP_CMDLINE_PARSER_PACKAGE
+/** @brief the program name (used for printing errors) */
+#define RNASNOOP_CMDLINE_PARSER_PACKAGE "RNAsnoop"
+#endif
+
+#ifndef RNASNOOP_CMDLINE_PARSER_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define RNASNOOP_CMDLINE_PARSER_PACKAGE_NAME "RNAsnoop"
+#endif
+
+#ifndef RNASNOOP_CMDLINE_PARSER_VERSION
+/** @brief the program version */
+#define RNASNOOP_CMDLINE_PARSER_VERSION VERSION
+#endif
+
+/** @brief Where the command line options are stored */
+struct RNAsnoop_args_info
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *detailed_help_help; /**< @brief Print help, including all details and hidden options, and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ int alignmentLength_arg; /**< @brief Limit the extent of the interactions to L nucleotides (default='25'). */
+ char * alignmentLength_orig; /**< @brief Limit the extent of the interactions to L nucleotides original value given at command line. */
+ const char *alignmentLength_help; /**< @brief Limit the extent of the interactions to L nucleotides help description. */
+ int constraint_flag; /**< @brief Calculate the stem structure subject to constraints.
+ (default=off). */
+ const char *constraint_help; /**< @brief Calculate the stem structure subject to constraints.
+ help description. */
+ char * query_arg; /**< @brief File containing the query sequence.
+. */
+ char * query_orig; /**< @brief File containing the query sequence.
+ original value given at command line. */
+ const char *query_help; /**< @brief File containing the query sequence.
+ help description. */
+ char * target_arg; /**< @brief File containing the target sequence.
+. */
+ char * target_orig; /**< @brief File containing the target sequence.
+ original value given at command line. */
+ const char *target_help; /**< @brief File containing the target sequence.
+ help description. */
+ char * suffix_arg; /**< @brief Specificy the suffix that was added by RNAup to the accessibility files
+
+ (default='_u1_to_30.out'). */
+ char * suffix_orig; /**< @brief Specificy the suffix that was added by RNAup to the accessibility files
+
+ original value given at command line. */
+ const char *suffix_help; /**< @brief Specificy the suffix that was added by RNAup to the accessibility files
+
+ help description. */
+ char * from_RNAplfold_arg; /**< @brief Specify the directory where accessibility profile generated by RNAplfold are found
+
+. */
+ char * from_RNAplfold_orig; /**< @brief Specify the directory where accessibility profile generated by RNAplfold are found
+
+ original value given at command line. */
+ const char *from_RNAplfold_help; /**< @brief Specify the directory where accessibility profile generated by RNAplfold are found
+
+ help description. */
+ int alignment_mode_flag; /**< @brief Specify if RNAsnoop gets alignments or single sequences as input
+
+ (default=off). */
+ const char *alignment_mode_help; /**< @brief Specify if RNAsnoop gets alignments or single sequences as input
+
+ help description. */
+ int fast_folding_arg; /**< @brief Speedup of the target search (default='1'). */
+ char * fast_folding_orig; /**< @brief Speedup of the target search original value given at command line. */
+ const char *fast_folding_help; /**< @brief Speedup of the target search help description. */
+ int extension_cost_arg; /**< @brief Cost to add to each nucleotide in a duplex (default='0'). */
+ char * extension_cost_orig; /**< @brief Cost to add to each nucleotide in a duplex original value given at command line. */
+ const char *extension_cost_help; /**< @brief Cost to add to each nucleotide in a duplex help description. */
+ int minimal_right_duplex_arg; /**< @brief Minimal Right Duplex Energy
+
+ (default='-270'). */
+ char * minimal_right_duplex_orig; /**< @brief Minimal Right Duplex Energy
+
+ original value given at command line. */
+ const char *minimal_right_duplex_help; /**< @brief Minimal Right Duplex Energy
+
+ help description. */
+ int minimal_loop_energy_arg; /**< @brief Minimal Right Duplex Energy
+ (default='-280'). */
+ char * minimal_loop_energy_orig; /**< @brief Minimal Right Duplex Energy
+ original value given at command line. */
+ const char *minimal_loop_energy_help; /**< @brief Minimal Right Duplex Energy
+ help description. */
+ int minimal_left_duplex_arg; /**< @brief Minimal Left Duplex Energy
+
+ (default='-170'). */
+ char * minimal_left_duplex_orig; /**< @brief Minimal Left Duplex Energy
+
+ original value given at command line. */
+ const char *minimal_left_duplex_help; /**< @brief Minimal Left Duplex Energy
+
+ help description. */
+ int minimal_duplex_arg; /**< @brief Minimal Duplex Energy
+
+ (default='-1090'). */
+ char * minimal_duplex_orig; /**< @brief Minimal Duplex Energy
+
+ original value given at command line. */
+ const char *minimal_duplex_help; /**< @brief Minimal Duplex Energy
+
+ help description. */
+ int duplex_distance_arg; /**< @brief Distance between target 3' ends of two consecutive duplexes
+ (default='2'). */
+ char * duplex_distance_orig; /**< @brief Distance between target 3' ends of two consecutive duplexes
+ original value given at command line. */
+ const char *duplex_distance_help; /**< @brief Distance between target 3' ends of two consecutive duplexes
+ help description. */
+ int minimal_stem_length_arg; /**< @brief Minimal snoRNA stem length
+
+ (default='5'). */
+ char * minimal_stem_length_orig; /**< @brief Minimal snoRNA stem length
+
+ original value given at command line. */
+ const char *minimal_stem_length_help; /**< @brief Minimal snoRNA stem length
+
+ help description. */
+ int maximal_stem_length_arg; /**< @brief Maximal snoRNA stem length
+
+ (default='120'). */
+ char * maximal_stem_length_orig; /**< @brief Maximal snoRNA stem length
+
+ original value given at command line. */
+ const char *maximal_stem_length_help; /**< @brief Maximal snoRNA stem length
+
+ help description. */
+ int minimal_duplex_box_length_arg; /**< @brief Minimal distance between the duplex end and the H/ACA box
+
+ (default='11'). */
+ char * minimal_duplex_box_length_orig; /**< @brief Minimal distance between the duplex end and the H/ACA box
+
+ original value given at command line. */
+ const char *minimal_duplex_box_length_help; /**< @brief Minimal distance between the duplex end and the H/ACA box
+
+ help description. */
+ int maximal_duplex_box_length_arg; /**< @brief Maximal distance between the duplex end and the H/ACA box
+
+ (default='16'). */
+ char * maximal_duplex_box_length_orig; /**< @brief Maximal distance between the duplex end and the H/ACA box
+
+ original value given at command line. */
+ const char *maximal_duplex_box_length_help; /**< @brief Maximal distance between the duplex end and the H/ACA box
+
+ help description. */
+ int minimal_snoRNA_stem_loop_length_arg; /**< @brief Minimal number of nucleotides between the beginning of stem loop and
+ beginning of the snoRNA sequence
+
+ (default='1'). */
+ char * minimal_snoRNA_stem_loop_length_orig; /**< @brief Minimal number of nucleotides between the beginning of stem loop and
+ beginning of the snoRNA sequence
+
+ original value given at command line. */
+ const char *minimal_snoRNA_stem_loop_length_help; /**< @brief Minimal number of nucleotides between the beginning of stem loop and
+ beginning of the snoRNA sequence
+
+ help description. */
+ int maximal_snoRNA_stem_loop_length_arg; /**< @brief Maximal number of nucleotides between the beginning of stem loop and
+ beginning of the snoRNA sequence
+
+ (default='100000'). */
+ char * maximal_snoRNA_stem_loop_length_orig; /**< @brief Maximal number of nucleotides between the beginning of stem loop and
+ beginning of the snoRNA sequence
+
+ original value given at command line. */
+ const char *maximal_snoRNA_stem_loop_length_help; /**< @brief Maximal number of nucleotides between the beginning of stem loop and
+ beginning of the snoRNA sequence
+
+ help description. */
+ int minimal_snoRNA_duplex_length_arg; /**< @brief Minimal distance between duplex start and snoRNA
+
+ (default='0'). */
+ char * minimal_snoRNA_duplex_length_orig; /**< @brief Minimal distance between duplex start and snoRNA
+
+ original value given at command line. */
+ const char *minimal_snoRNA_duplex_length_help; /**< @brief Minimal distance between duplex start and snoRNA
+
+ help description. */
+ int maximal_snoRNA_duplex_length_arg; /**< @brief Maximal distance between duplex start and snoRNA
+
+ (default='0'). */
+ char * maximal_snoRNA_duplex_length_orig; /**< @brief Maximal distance between duplex start and snoRNA
+
+ original value given at command line. */
+ const char *maximal_snoRNA_duplex_length_help; /**< @brief Maximal distance between duplex start and snoRNA
+
+ help description. */
+ int minimal_duplex_stem_energy_arg; /**< @brief Minimal duplex stem energy
+
+ (default='-1370'). */
+ char * minimal_duplex_stem_energy_orig; /**< @brief Minimal duplex stem energy
+
+ original value given at command line. */
+ const char *minimal_duplex_stem_energy_help; /**< @brief Minimal duplex stem energy
+
+ help description. */
+ int minimal_total_energy_arg; /**< @brief Minimal total energy
+
+ (default='100000'). */
+ char * minimal_total_energy_orig; /**< @brief Minimal total energy
+
+ original value given at command line. */
+ const char *minimal_total_energy_help; /**< @brief Minimal total energy
+
+ help description. */
+ int maximal_stem_asymmetry_arg; /**< @brief Maximal snoRNA stem asymmetry
+
+ (default='30'). */
+ char * maximal_stem_asymmetry_orig; /**< @brief Maximal snoRNA stem asymmetry
+
+ original value given at command line. */
+ const char *maximal_stem_asymmetry_help; /**< @brief Maximal snoRNA stem asymmetry
+
+ help description. */
+ int minimal_lower_stem_energy_arg; /**< @brief Minimal lower stem energy
+
+ (default='100000'). */
+ char * minimal_lower_stem_energy_orig; /**< @brief Minimal lower stem energy
+
+ original value given at command line. */
+ const char *minimal_lower_stem_energy_help; /**< @brief Minimal lower stem energy
+
+ help description. */
+ double energy_threshold_arg; /**< @brief Maximal energy difference between the mfe and the desired suboptimal
+ (default='-1'). */
+ char * energy_threshold_orig; /**< @brief Maximal energy difference between the mfe and the desired suboptimal
+ original value given at command line. */
+ const char *energy_threshold_help; /**< @brief Maximal energy difference between the mfe and the desired suboptimal
+ help description. */
+ int produce_ps_flag; /**< @brief Draw annotated 2D structures for a list of dot-bracket structures
+ (default=off). */
+ const char *produce_ps_help; /**< @brief Draw annotated 2D structures for a list of dot-bracket structures
+ help description. */
+ char * output_directory_arg; /**< @brief Set where the generated figures should be stored
+
+ (default='./'). */
+ char * output_directory_orig; /**< @brief Set where the generated figures should be stored
+
+ original value given at command line. */
+ const char *output_directory_help; /**< @brief Set where the generated figures should be stored
+
+ help description. */
+ int direct_redraw_flag; /**< @brief Outputs 2D interactions concurrently with the interaction calculation for each suboptimal interaction. The -I option should be preferred.
+
+ (default=off). */
+ const char *direct_redraw_help; /**< @brief Outputs 2D interactions concurrently with the interaction calculation for each suboptimal interaction. The -I option should be preferred.
+
+ help description. */
+ char * from_RNAup_arg; /**< @brief Specify the directory where accessibility profiles generated by RNAup are found
+
+. */
+ char * from_RNAup_orig; /**< @brief Specify the directory where accessibility profiles generated by RNAup are found
+
+ original value given at command line. */
+ const char *from_RNAup_help; /**< @brief Specify the directory where accessibility profiles generated by RNAup are found
+
+ help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int detailed_help_given ; /**< @brief Whether detailed-help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int alignmentLength_given ; /**< @brief Whether alignmentLength was given. */
+ unsigned int constraint_given ; /**< @brief Whether constraint was given. */
+ unsigned int query_given ; /**< @brief Whether query was given. */
+ unsigned int target_given ; /**< @brief Whether target was given. */
+ unsigned int suffix_given ; /**< @brief Whether suffix was given. */
+ unsigned int from_RNAplfold_given ; /**< @brief Whether from-RNAplfold was given. */
+ unsigned int alignment_mode_given ; /**< @brief Whether alignment-mode was given. */
+ unsigned int fast_folding_given ; /**< @brief Whether fast-folding was given. */
+ unsigned int extension_cost_given ; /**< @brief Whether extension-cost was given. */
+ unsigned int minimal_right_duplex_given ; /**< @brief Whether minimal-right-duplex was given. */
+ unsigned int minimal_loop_energy_given ; /**< @brief Whether minimal-loop-energy was given. */
+ unsigned int minimal_left_duplex_given ; /**< @brief Whether minimal-left-duplex was given. */
+ unsigned int minimal_duplex_given ; /**< @brief Whether minimal-duplex was given. */
+ unsigned int duplex_distance_given ; /**< @brief Whether duplex-distance was given. */
+ unsigned int minimal_stem_length_given ; /**< @brief Whether minimal-stem-length was given. */
+ unsigned int maximal_stem_length_given ; /**< @brief Whether maximal-stem-length was given. */
+ unsigned int minimal_duplex_box_length_given ; /**< @brief Whether minimal-duplex-box-length was given. */
+ unsigned int maximal_duplex_box_length_given ; /**< @brief Whether maximal-duplex-box-length was given. */
+ unsigned int minimal_snoRNA_stem_loop_length_given ; /**< @brief Whether minimal-snoRNA-stem-loop-length was given. */
+ unsigned int maximal_snoRNA_stem_loop_length_given ; /**< @brief Whether maximal-snoRNA-stem-loop-length was given. */
+ unsigned int minimal_snoRNA_duplex_length_given ; /**< @brief Whether minimal-snoRNA-duplex-length was given. */
+ unsigned int maximal_snoRNA_duplex_length_given ; /**< @brief Whether maximal-snoRNA-duplex-length was given. */
+ unsigned int minimal_duplex_stem_energy_given ; /**< @brief Whether minimal-duplex-stem-energy was given. */
+ unsigned int minimal_total_energy_given ; /**< @brief Whether minimal-total-energy was given. */
+ unsigned int maximal_stem_asymmetry_given ; /**< @brief Whether maximal-stem-asymmetry was given. */
+ unsigned int minimal_lower_stem_energy_given ; /**< @brief Whether minimal-lower-stem-energy was given. */
+ unsigned int energy_threshold_given ; /**< @brief Whether energy-threshold was given. */
+ unsigned int produce_ps_given ; /**< @brief Whether produce-ps was given. */
+ unsigned int output_directory_given ; /**< @brief Whether output_directory was given. */
+ unsigned int direct_redraw_given ; /**< @brief Whether direct-redraw was given. */
+ unsigned int from_RNAup_given ; /**< @brief Whether from-RNAup was given. */
+
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct RNAsnoop_cmdline_parser_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure RNAsnoop_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 RNAsnoop_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 *RNAsnoop_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *RNAsnoop_args_info_usage;
+/** @brief all the lines making the help output */
+extern const char *RNAsnoop_args_info_help[];
+/** @brief all the lines making the detailed help output (including hidden options and details) */
+extern const char *RNAsnoop_args_info_detailed_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 RNAsnoop_cmdline_parser (int argc, char **argv,
+ struct RNAsnoop_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 RNAsnoop_cmdline_parser_ext() instead
+ */
+int RNAsnoop_cmdline_parser2 (int argc, char **argv,
+ struct RNAsnoop_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 RNAsnoop_cmdline_parser_ext (int argc, char **argv,
+ struct RNAsnoop_args_info *args_info,
+ struct RNAsnoop_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 RNAsnoop_cmdline_parser_dump(FILE *outfile,
+ struct RNAsnoop_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 RNAsnoop_cmdline_parser_file_save(const char *filename,
+ struct RNAsnoop_args_info *args_info);
+
+/**
+ * Print the help
+ */
+void RNAsnoop_cmdline_parser_print_help(void);
+/**
+ * Print the detailed help (including hidden options and details)
+ */
+void RNAsnoop_cmdline_parser_print_detailed_help(void);
+/**
+ * Print the version
+ */
+void RNAsnoop_cmdline_parser_print_version(void);
+
+/**
+ * Initializes all the fields a RNAsnoop_cmdline_parser_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void RNAsnoop_cmdline_parser_params_init(struct RNAsnoop_cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a RNAsnoop_cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized RNAsnoop_cmdline_parser_params structure
+ */
+struct RNAsnoop_cmdline_parser_params *RNAsnoop_cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed RNAsnoop_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void RNAsnoop_cmdline_parser_init (struct RNAsnoop_args_info *args_info);
+/**
+ * Deallocates the string fields of the RNAsnoop_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void RNAsnoop_cmdline_parser_free (struct RNAsnoop_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 RNAsnoop_cmdline_parser_required (struct RNAsnoop_args_info *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* RNASNOOP_CMDL_H */
git://source.jalview.org / jabaws.git / blobdiff