--- /dev/null
+/** @file RNAalifold_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 RNAALIFOLD_CMDL_H
+#define RNAALIFOLD_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 RNAALIFOLD_CMDLINE_PARSER_PACKAGE
+/** @brief the program name (used for printing errors) */
+#define RNAALIFOLD_CMDLINE_PARSER_PACKAGE "RNAalifold"
+#endif
+
+#ifndef RNAALIFOLD_CMDLINE_PARSER_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define RNAALIFOLD_CMDLINE_PARSER_PACKAGE_NAME "RNAalifold"
+#endif
+
+#ifndef RNAALIFOLD_CMDLINE_PARSER_VERSION
+/** @brief the program version */
+#define RNAALIFOLD_CMDLINE_PARSER_VERSION VERSION
+#endif
+
+/** @brief Where the command line options are stored */
+struct RNAalifold_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 *full_help_help; /**< @brief Print help, including hidden options, and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ int constraint_flag; /**< @brief Calculate structures subject to constraints.
+ The constraining structure will be read from 'stdin', the alignment has to be given as a file name on the command line.
+ (default=off). */
+ const char *constraint_help; /**< @brief Calculate structures subject to constraints.
+ The constraining structure will be read from 'stdin', the alignment has to be given as a file name on the command line.
+ help description. */
+ int color_flag; /**< @brief Produce a colored version of the consensus strcture plot \"alirna.ps\" (default b&w only)
+
+ (default=off). */
+ const char *color_help; /**< @brief Produce a colored version of the consensus strcture plot \"alirna.ps\" (default b&w only)
+
+ help description. */
+ int aln_flag; /**< @brief Produce a colored and structure annotated alignment in PostScript format in the file \"aln.ps\" in the current directory.
+
+ (default=off). */
+ const char *aln_help; /**< @brief Produce a colored and structure annotated alignment in PostScript format in the file \"aln.ps\" in the current directory.
+
+ help description. */
+ int noPS_flag; /**< @brief Do not produce postscript output
+
+ (default=off). */
+ const char *noPS_help; /**< @brief Do not produce postscript output
+
+ help description. */
+ int partfunc_arg; /**< @brief Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only.
+ (default='1'). */
+ char * partfunc_orig; /**< @brief Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only.
+ original value given at command line. */
+ const char *partfunc_help; /**< @brief Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only.
+ help description. */
+ float MEA_arg; /**< @brief Calculate an MEA (maximum expected accuracy) structure.
+ (default='1.'). */
+ char * MEA_orig; /**< @brief Calculate an MEA (maximum expected accuracy) structure.
+ original value given at command line. */
+ const char *MEA_help; /**< @brief Calculate an MEA (maximum expected accuracy) structure.
+ help description. */
+ int mis_flag; /**< @brief Output \"most informative sequence\" instead of simple consensus: For each column of the alignment output the set of nucleotides with frequence greater than average in IUPAC notation.
+
+ (default=off). */
+ const char *mis_help; /**< @brief Output \"most informative sequence\" instead of simple consensus: For each column of the alignment output the set of nucleotides with frequence greater than average in IUPAC notation.
+
+ help description. */
+ int stochBT_arg; /**< @brief Stochastic backtrack. Compute a certain number of random structures with a probability dependend on the partition function. See -p option in RNAsubopt.
+
+. */
+ char * stochBT_orig; /**< @brief Stochastic backtrack. Compute a certain number of random structures with a probability dependend on the partition function. See -p option in RNAsubopt.
+
+ original value given at command line. */
+ const char *stochBT_help; /**< @brief Stochastic backtrack. Compute a certain number of random structures with a probability dependend on the partition function. See -p option in RNAsubopt.
+
+ help description. */
+ int stochBT_en_arg; /**< @brief same as \"-s\" but also print out the energies and probabilities of the backtraced structures.
+
+. */
+ char * stochBT_en_orig; /**< @brief same as \"-s\" but also print out the energies and probabilities of the backtraced structures.
+
+ original value given at command line. */
+ const char *stochBT_en_help; /**< @brief same as \"-s\" but also print out the energies and probabilities of the backtraced structures.
+
+ help description. */
+ double pfScale_arg; /**< @brief In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows).
+. */
+ char * pfScale_orig; /**< @brief In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows).
+ original value given at command line. */
+ const char *pfScale_help; /**< @brief In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows).
+ help description. */
+ int circ_flag; /**< @brief Assume a circular (instead of linear) RNA molecule.
+
+ (default=off). */
+ const char *circ_help; /**< @brief Assume a circular (instead of linear) RNA molecule.
+
+ help description. */
+ double bppmThreshold_arg; /**< @brief Set the threshold for base pair probabilities included in the postscript output
+ (default='1e-6'). */
+ char * bppmThreshold_orig; /**< @brief Set the threshold for base pair probabilities included in the postscript output
+ original value given at command line. */
+ const char *bppmThreshold_help; /**< @brief Set the threshold for base pair probabilities included in the postscript output
+ help description. */
+ int gquad_flag; /**< @brief Incoorporate G-Quadruplex formation into the structure prediction algorithm
+ (default=off). */
+ const char *gquad_help; /**< @brief Incoorporate G-Quadruplex formation into the structure prediction algorithm
+ help description. */
+ double temp_arg; /**< @brief Rescale energy parameters to a temperature of temp C. Default is 37C.
+
+. */
+ char * temp_orig; /**< @brief Rescale energy parameters to a temperature of temp C. Default is 37C.
+
+ original value given at command line. */
+ const char *temp_help; /**< @brief Rescale energy parameters to a temperature of temp C. Default is 37C.
+
+ help description. */
+ int noTetra_flag; /**< @brief Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.
+
+ (default=off). */
+ const char *noTetra_help; /**< @brief Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.
+
+ help description. */
+ int dangles_arg; /**< @brief How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops
+ (default='2'). */
+ char * dangles_orig; /**< @brief How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops
+ original value given at command line. */
+ const char *dangles_help; /**< @brief How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops
+ help description. */
+ int noLP_flag; /**< @brief Produce structures without lonely pairs (helices of length 1).
+ (default=off). */
+ const char *noLP_help; /**< @brief Produce structures without lonely pairs (helices of length 1).
+ help description. */
+ int noGU_flag; /**< @brief Do not allow GU pairs
+
+ (default=off). */
+ const char *noGU_help; /**< @brief Do not allow GU pairs
+
+ help description. */
+ int noClosingGU_flag; /**< @brief Do not allow GU pairs at the end of helices
+
+ (default=off). */
+ const char *noClosingGU_help; /**< @brief Do not allow GU pairs at the end of helices
+
+ help description. */
+ double cfactor_arg; /**< @brief Set the weight of the covariance term in the energy function
+
+ (default='1.0'). */
+ char * cfactor_orig; /**< @brief Set the weight of the covariance term in the energy function
+
+ original value given at command line. */
+ const char *cfactor_help; /**< @brief Set the weight of the covariance term in the energy function
+
+ help description. */
+ double nfactor_arg; /**< @brief Set the penalty for non-compatible sequences in the covariance term of the energy function
+
+ (default='1.0'). */
+ char * nfactor_orig; /**< @brief Set the penalty for non-compatible sequences in the covariance term of the energy function
+
+ original value given at command line. */
+ const char *nfactor_help; /**< @brief Set the penalty for non-compatible sequences in the covariance term of the energy function
+
+ help description. */
+ int endgaps_flag; /**< @brief Score pairs with endgaps same as gap-gap pairs.
+
+ (default=off). */
+ const char *endgaps_help; /**< @brief Score pairs with endgaps same as gap-gap pairs.
+
+ help description. */
+ char * ribosum_file_arg; /**< @brief use specified Ribosum Matrix instead of normal energy model. Matrixes to use should be 6x6 matrices, the order of the terms is AU, CG, GC, GU, UA, UG.
+
+. */
+ char * ribosum_file_orig; /**< @brief use specified Ribosum Matrix instead of normal energy model. Matrixes to use should be 6x6 matrices, the order of the terms is AU, CG, GC, GU, UA, UG.
+
+ original value given at command line. */
+ const char *ribosum_file_help; /**< @brief use specified Ribosum Matrix instead of normal energy model. Matrixes to use should be 6x6 matrices, the order of the terms is AU, CG, GC, GU, UA, UG.
+
+ help description. */
+ int ribosum_scoring_flag; /**< @brief use ribosum scoring matrix. The matrix is chosen according to the minimal and maximal pairwise identities of the sequences in the file.
+
+ (default=off). */
+ const char *ribosum_scoring_help; /**< @brief use ribosum scoring matrix. The matrix is chosen according to the minimal and maximal pairwise identities of the sequences in the file.
+
+ help description. */
+ int old_flag; /**< @brief use old energy evaluation, treating gaps as characters.
+
+ (default=off). */
+ const char *old_help; /**< @brief use old energy evaluation, treating gaps as characters.
+
+ help description. */
+ char * paramFile_arg; /**< @brief Read energy parameters from paramfile, instead of using the default parameter set.
+. */
+ char * paramFile_orig; /**< @brief Read energy parameters from paramfile, instead of using the default parameter set.
+ original value given at command line. */
+ const char *paramFile_help; /**< @brief Read energy parameters from paramfile, instead of using the default parameter set.
+ help description. */
+ char * nsp_arg; /**< @brief Allow other pairs in addition to the usual AU,GC,and GU pairs.
+. */
+ char * nsp_orig; /**< @brief Allow other pairs in addition to the usual AU,GC,and GU pairs.
+ original value given at command line. */
+ const char *nsp_help; /**< @brief Allow other pairs in addition to the usual AU,GC,and GU pairs.
+ help description. */
+ int energyModel_arg; /**< @brief Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.
+
+. */
+ char * energyModel_orig; /**< @brief Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.
+
+ original value given at command line. */
+ const char *energyModel_help; /**< @brief Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.
+
+ help description. */
+ double betaScale_arg; /**< @brief Set the scaling of the Boltzmann factors
+ (default='1.'). */
+ char * betaScale_orig; /**< @brief Set the scaling of the Boltzmann factors
+ original value given at command line. */
+ const char *betaScale_help; /**< @brief Set the scaling of the Boltzmann factors
+ help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int detailed_help_given ; /**< @brief Whether detailed-help was given. */
+ unsigned int full_help_given ; /**< @brief Whether full-help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int constraint_given ; /**< @brief Whether constraint was given. */
+ unsigned int color_given ; /**< @brief Whether color was given. */
+ unsigned int aln_given ; /**< @brief Whether aln was given. */
+ unsigned int noPS_given ; /**< @brief Whether noPS was given. */
+ unsigned int partfunc_given ; /**< @brief Whether partfunc was given. */
+ unsigned int MEA_given ; /**< @brief Whether MEA was given. */
+ unsigned int mis_given ; /**< @brief Whether mis was given. */
+ unsigned int stochBT_given ; /**< @brief Whether stochBT was given. */
+ unsigned int stochBT_en_given ; /**< @brief Whether stochBT_en was given. */
+ unsigned int pfScale_given ; /**< @brief Whether pfScale was given. */
+ unsigned int circ_given ; /**< @brief Whether circ was given. */
+ unsigned int bppmThreshold_given ; /**< @brief Whether bppmThreshold was given. */
+ unsigned int gquad_given ; /**< @brief Whether gquad was given. */
+ unsigned int temp_given ; /**< @brief Whether temp was given. */
+ unsigned int noTetra_given ; /**< @brief Whether noTetra was given. */
+ unsigned int dangles_given ; /**< @brief Whether dangles was given. */
+ unsigned int noLP_given ; /**< @brief Whether noLP was given. */
+ unsigned int noGU_given ; /**< @brief Whether noGU was given. */
+ unsigned int noClosingGU_given ; /**< @brief Whether noClosingGU was given. */
+ unsigned int cfactor_given ; /**< @brief Whether cfactor was given. */
+ unsigned int nfactor_given ; /**< @brief Whether nfactor was given. */
+ unsigned int endgaps_given ; /**< @brief Whether endgaps was given. */
+ unsigned int ribosum_file_given ; /**< @brief Whether ribosum_file was given. */
+ unsigned int ribosum_scoring_given ; /**< @brief Whether ribosum_scoring was given. */
+ unsigned int old_given ; /**< @brief Whether old was given. */
+ unsigned int paramFile_given ; /**< @brief Whether paramFile was given. */
+ unsigned int nsp_given ; /**< @brief Whether nsp was given. */
+ unsigned int energyModel_given ; /**< @brief Whether energyModel was given. */
+ unsigned int betaScale_given ; /**< @brief Whether betaScale was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct RNAalifold_cmdline_parser_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure RNAalifold_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 RNAalifold_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 *RNAalifold_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *RNAalifold_args_info_usage;
+/** @brief all the lines making the help output */
+extern const char *RNAalifold_args_info_help[];
+/** @brief all the lines making the full help output (including hidden options) */
+extern const char *RNAalifold_args_info_full_help[];
+/** @brief all the lines making the detailed help output (including hidden options and details) */
+extern const char *RNAalifold_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 RNAalifold_cmdline_parser (int argc, char **argv,
+ struct RNAalifold_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 RNAalifold_cmdline_parser_ext() instead
+ */
+int RNAalifold_cmdline_parser2 (int argc, char **argv,
+ struct RNAalifold_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 RNAalifold_cmdline_parser_ext (int argc, char **argv,
+ struct RNAalifold_args_info *args_info,
+ struct RNAalifold_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 RNAalifold_cmdline_parser_dump(FILE *outfile,
+ struct RNAalifold_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 RNAalifold_cmdline_parser_file_save(const char *filename,
+ struct RNAalifold_args_info *args_info);
+
+/**
+ * Print the help
+ */
+void RNAalifold_cmdline_parser_print_help(void);
+/**
+ * Print the full help (including hidden options)
+ */
+void RNAalifold_cmdline_parser_print_full_help(void);
+/**
+ * Print the detailed help (including hidden options and details)
+ */
+void RNAalifold_cmdline_parser_print_detailed_help(void);
+/**
+ * Print the version
+ */
+void RNAalifold_cmdline_parser_print_version(void);
+
+/**
+ * Initializes all the fields a RNAalifold_cmdline_parser_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void RNAalifold_cmdline_parser_params_init(struct RNAalifold_cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a RNAalifold_cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized RNAalifold_cmdline_parser_params structure
+ */
+struct RNAalifold_cmdline_parser_params *RNAalifold_cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed RNAalifold_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void RNAalifold_cmdline_parser_init (struct RNAalifold_args_info *args_info);
+/**
+ * Deallocates the string fields of the RNAalifold_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void RNAalifold_cmdline_parser_free (struct RNAalifold_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 RNAalifold_cmdline_parser_required (struct RNAalifold_args_info *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* RNAALIFOLD_CMDL_H */
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