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355 lines
23 KiB
C
355 lines
23 KiB
C
/** @file semphy_cmdline.h
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* @brief The header file for the command line option parser
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* generated by GNU Gengetopt version 2.22.4
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* http://www.gnu.org/software/gengetopt.
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* DO NOT modify this file, since it can be overwritten
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* @author GNU Gengetopt by Lorenzo Bettini */
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#ifndef SEMPHY_CMDLINE_H
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#define SEMPHY_CMDLINE_H
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/* If we use autoconf. */
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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#include <stdio.h> /* for FILE */
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#ifdef __cplusplus
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extern "C" {
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#endif /* __cplusplus */
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#ifndef CMDLINE_PARSER_PACKAGE
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/** @brief the program name (used for printing errors) */
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#define CMDLINE_PARSER_PACKAGE "semphy"
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#endif
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#ifndef CMDLINE_PARSER_PACKAGE_NAME
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/** @brief the complete program name (used for help and version) */
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#define CMDLINE_PARSER_PACKAGE_NAME "semphy"
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#endif
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#ifndef CMDLINE_PARSER_VERSION
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/** @brief the program version */
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#define CMDLINE_PARSER_VERSION "1.0.b1"
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#endif
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/** @brief Where the command line options are stored */
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struct gengetopt_args_info
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{
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const char *help_help; /**< @brief Print help and exit help description. */
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const char *full_help_help; /**< @brief Print help, including hidden options, and exit help description. */
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const char *version_help; /**< @brief Print version and exit help description. */
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int SEMPHY_flag; /**< @brief Do SEMPHY step (default=off). */
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const char *SEMPHY_help; /**< @brief Do SEMPHY step help description. */
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int bbl_flag; /**< @brief Only optimize branch length (default=off). */
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const char *bbl_help; /**< @brief Only optimize branch length help description. */
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int likelihood_flag; /**< @brief Compute likelihood for fixed tree (default=off). */
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const char *likelihood_help; /**< @brief Compute likelihood for fixed tree help description. */
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int PerPosLike_flag; /**< @brief Compute likelihood per position for a fixed tree (default=off). */
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const char *PerPosLike_help; /**< @brief Compute likelihood per position for a fixed tree help description. */
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int PerPosPosterior_flag; /**< @brief Compute likelihood per position and Bayesian posterior (default=off). */
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const char *PerPosPosterior_help; /**< @brief Compute likelihood per position and Bayesian posterior help description. */
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int rate_flag; /**< @brief optimize rate of gene (default=off). */
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const char *rate_help; /**< @brief optimize rate of gene help description. */
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int max_semphy_iter_arg; /**< @brief Max number of SEM iterations (default='100'). */
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char * max_semphy_iter_orig; /**< @brief Max number of SEM iterations original value given at command line. */
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const char *max_semphy_iter_help; /**< @brief Max number of SEM iterations help description. */
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float epsilonLikelihoodImprovement4iterNJ_arg; /**< @brief The threshold for optimization of likelihood of the tree, in iterative distance-based tree reconstruction (default='0.01'). */
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char * epsilonLikelihoodImprovement4iterNJ_orig; /**< @brief The threshold for optimization of likelihood of the tree, in iterative distance-based tree reconstruction original value given at command line. */
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const char *epsilonLikelihoodImprovement4iterNJ_help; /**< @brief The threshold for optimization of likelihood of the tree, in iterative distance-based tree reconstruction help description. */
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float epsilonLikelihoodImprovement4pairwiseDistance_arg; /**< @brief The threshold for optimization of likelihood of a pair of sequences, in pairwise distance optimization (default='0.0001'). */
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char * epsilonLikelihoodImprovement4pairwiseDistance_orig; /**< @brief The threshold for optimization of likelihood of a pair of sequences, in pairwise distance optimization original value given at command line. */
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const char *epsilonLikelihoodImprovement4pairwiseDistance_help; /**< @brief The threshold for optimization of likelihood of a pair of sequences, in pairwise distance optimization help description. */
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float epsilonLikelihoodImprovement4alphaOptimiz_arg; /**< @brief The threshold for optimization of likelihood of the tree, in alpha optimization (also used for Nu optimization when using --ssrv) (default='0.01'). */
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char * epsilonLikelihoodImprovement4alphaOptimiz_orig; /**< @brief The threshold for optimization of likelihood of the tree, in alpha optimization (also used for Nu optimization when using --ssrv) original value given at command line. */
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const char *epsilonLikelihoodImprovement4alphaOptimiz_help; /**< @brief The threshold for optimization of likelihood of the tree, in alpha optimization (also used for Nu optimization when using --ssrv) help description. */
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float epsilonLikelihoodImprovement4BBL_arg; /**< @brief The threshold for optimization of likelihood of the tree, in branch-lengths optimization (default='0.01'). */
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char * epsilonLikelihoodImprovement4BBL_orig; /**< @brief The threshold for optimization of likelihood of the tree, in branch-lengths optimization original value given at command line. */
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const char *epsilonLikelihoodImprovement4BBL_help; /**< @brief The threshold for optimization of likelihood of the tree, in branch-lengths optimization help description. */
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int maxNumOfBBLIter_arg; /**< @brief Number of BBL iterations in BBL+ALPHA optimization (default='10'). */
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char * maxNumOfBBLIter_orig; /**< @brief Number of BBL iterations in BBL+ALPHA optimization original value given at command line. */
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const char *maxNumOfBBLIter_help; /**< @brief Number of BBL iterations in BBL+ALPHA optimization help description. */
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int consurf_flag; /**< @brief version for use in consurf (default=off). */
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const char *consurf_help; /**< @brief version for use in consurf help description. */
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const char *NJ_help; /**< @brief 'classic' Neighbor Joining (same as homogeneousRates) help description. */
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const char *homogeneousRatesDTME_help; /**< @brief homogeneous rates MLE distance help description. */
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const char *pairwiseGammaDTME_help; /**< @brief Gamma-ASRV with alpha optimized for each pair. (must give either --alpha or --optimizeAlpha) help description. */
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const char *commonAlphaDTME_help; /**< @brief Side information is the alpha parameter.(must use --optimizeAlpha; may give an initial alpha value in --alpha) help description. */
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const char *rate4siteDTME_help; /**< @brief Side information is the ML rate for each site help description. */
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const char *posteriorDTME_help; /**< @brief Side information is the posterior probabilities of the rates at each site. (must use --optimizeAlpha; may give an initial alpha value in --alpha) help description. */
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int BPrepeats_arg; /**< @brief Use bootstrap and set number of repeats. */
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char * BPrepeats_orig; /**< @brief Use bootstrap and set number of repeats original value given at command line. */
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const char *BPrepeats_help; /**< @brief Use bootstrap and set number of repeats help description. */
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int BPconsensus_arg; /**< @brief Use bootstrap and compute a Consensus tree. */
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char * BPconsensus_orig; /**< @brief Use bootstrap and compute a Consensus tree original value given at command line. */
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const char *BPconsensus_help; /**< @brief Use bootstrap and compute a Consensus tree help description. */
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int BPonUserTree_flag; /**< @brief Use compute support for user provided tree (default=off). */
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const char *BPonUserTree_help; /**< @brief Use compute support for user provided tree help description. */
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char * sequence_arg; /**< @brief Sequence file name (default='-'). */
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char * sequence_orig; /**< @brief Sequence file name original value given at command line. */
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const char *sequence_help; /**< @brief Sequence file name help description. */
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char * tree_arg; /**< @brief Tree file name. */
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char * tree_orig; /**< @brief Tree file name original value given at command line. */
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const char *tree_help; /**< @brief Tree file name help description. */
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char * constraint_arg; /**< @brief Constraint Tree file name. */
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char * constraint_orig; /**< @brief Constraint Tree file name original value given at command line. */
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const char *constraint_help; /**< @brief Constraint Tree file name help description. */
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char * outputfile_arg; /**< @brief Output file (default='-'). */
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char * outputfile_orig; /**< @brief Output file original value given at command line. */
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const char *outputfile_help; /**< @brief Output file help description. */
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char * treeoutputfile_arg; /**< @brief Tree output file (default='-'). */
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char * treeoutputfile_orig; /**< @brief Tree output file original value given at command line. */
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const char *treeoutputfile_help; /**< @brief Tree output file help description. */
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int gaps_flag; /**< @brief Remove positions with gaps (default=off). */
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const char *gaps_help; /**< @brief Remove positions with gaps help description. */
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long seed_arg; /**< @brief Seed random number generator. */
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char * seed_orig; /**< @brief Seed random number generator original value given at command line. */
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const char *seed_help; /**< @brief Seed random number generator help description. */
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int alphabet_arg; /**< @brief Alphabet Size (default='20'). */
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char * alphabet_orig; /**< @brief Alphabet Size original value given at command line. */
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const char *alphabet_help; /**< @brief Alphabet Size help description. */
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float ratio_arg; /**< @brief Transition/Transversion ratio (default='2.0'). */
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char * ratio_orig; /**< @brief Transition/Transversion ratio original value given at command line. */
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const char *ratio_help; /**< @brief Transition/Transversion ratio help description. */
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char * ACGprob_arg; /**< @brief User input nucleotide frequencies. String separated list for A,C,G (default='0.25,0.25,0.25'). */
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char * ACGprob_orig; /**< @brief User input nucleotide frequencies. String separated list for A,C,G original value given at command line. */
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const char *ACGprob_help; /**< @brief User input nucleotide frequencies. String separated list for A,C,G help description. */
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float inputRate_arg; /**< @brief Set External globalRate (default='1.0'). */
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char * inputRate_orig; /**< @brief Set External globalRate original value given at command line. */
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const char *inputRate_help; /**< @brief Set External globalRate help description. */
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int homogeneous_flag; /**< @brief Don't use Gamma ASRV (default=off). */
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const char *homogeneous_help; /**< @brief Don't use Gamma ASRV help description. */
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float alpha_arg; /**< @brief Set alpha for Gamma ASRV. */
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char * alpha_orig; /**< @brief Set alpha for Gamma ASRV original value given at command line. */
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const char *alpha_help; /**< @brief Set alpha for Gamma ASRV help description. */
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int optimizeAlpha_flag; /**< @brief Optimize alpha for Gamma ASRV (default=off). */
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const char *optimizeAlpha_help; /**< @brief Optimize alpha for Gamma ASRV help description. */
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int categories_arg; /**< @brief Number of categories to use with descrete Gamma ASRV (default='8'). */
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char * categories_orig; /**< @brief Number of categories to use with descrete Gamma ASRV original value given at command line. */
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const char *categories_help; /**< @brief Number of categories to use with descrete Gamma ASRV help description. */
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int laguerre_flag; /**< @brief Use Laguerre approximation of Gamma - CURRENTLY NOT IMPLIMENTED (default=off). */
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const char *laguerre_help; /**< @brief Use Laguerre approximation of Gamma - CURRENTLY NOT IMPLIMENTED help description. */
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int ssrv_flag; /**< @brief Use a Site-Specific Rate Variation model (SSRV) (default=off). */
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const char *ssrv_help; /**< @brief Use a Site-Specific Rate Variation model (SSRV) help description. */
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float nu_arg; /**< @brief Set Nu for the SSRV model (default='1.0'). */
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char * nu_orig; /**< @brief Set Nu for the SSRV model original value given at command line. */
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const char *nu_help; /**< @brief Set Nu for the SSRV model help description. */
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char * posteriorRates_arg; /**< @brief File with posterior distribution of the rate for each sequence site - for ASRV. */
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char * posteriorRates_orig; /**< @brief File with posterior distribution of the rate for each sequence site - for ASRV original value given at command line. */
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const char *posteriorRates_help; /**< @brief File with posterior distribution of the rate for each sequence site - for ASRV help description. */
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const char *day_help; /**< @brief Use 'day' model help description. */
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const char *jtt_help; /**< @brief Use 'jtt' model (default) help description. */
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const char *rev_help; /**< @brief Use 'rev' model help description. */
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const char *wag_help; /**< @brief Use 'wag' model help description. */
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const char *cprev_help; /**< @brief Use 'cprev' model help description. */
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const char *nucjc_help; /**< @brief Use nucleic acid JC model help description. */
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const char *aaJC_help; /**< @brief Use amino acid JC model help description. */
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const char *k2p_help; /**< @brief Use 'k2p' model help description. */
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const char *hky_help; /**< @brief Use 'hky' model help description. */
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const char *tamura92_help; /**< @brief Use 'tamura92' model help description. */
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const char *gtr_help; /**< @brief Use 'gtr' model (general reversible model) help description. */
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char * modelfile_arg; /**< @brief Read replacement matrix from user input file. */
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char * modelfile_orig; /**< @brief Read replacement matrix from user input file original value given at command line. */
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const char *modelfile_help; /**< @brief Read replacement matrix from user input file help description. */
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int verbose_arg; /**< @brief Log report level (verbose) (default='1'). */
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char * verbose_orig; /**< @brief Log report level (verbose) original value given at command line. */
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const char *verbose_help; /**< @brief Log report level (verbose) help description. */
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char * Logfile_arg; /**< @brief Log output file name (default='-'). */
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char * Logfile_orig; /**< @brief Log output file name original value given at command line. */
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const char *Logfile_help; /**< @brief Log output file name help description. */
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unsigned int help_given ; /**< @brief Whether help was given. */
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unsigned int full_help_given ; /**< @brief Whether full-help was given. */
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unsigned int version_given ; /**< @brief Whether version was given. */
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unsigned int SEMPHY_given ; /**< @brief Whether SEMPHY was given. */
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unsigned int bbl_given ; /**< @brief Whether bbl was given. */
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unsigned int likelihood_given ; /**< @brief Whether likelihood was given. */
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unsigned int PerPosLike_given ; /**< @brief Whether PerPosLike was given. */
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unsigned int PerPosPosterior_given ; /**< @brief Whether PerPosPosterior was given. */
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unsigned int rate_given ; /**< @brief Whether rate was given. */
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unsigned int max_semphy_iter_given ; /**< @brief Whether max-semphy-iter was given. */
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unsigned int epsilonLikelihoodImprovement4iterNJ_given ; /**< @brief Whether epsilonLikelihoodImprovement4iterNJ was given. */
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unsigned int epsilonLikelihoodImprovement4pairwiseDistance_given ; /**< @brief Whether epsilonLikelihoodImprovement4pairwiseDistance was given. */
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unsigned int epsilonLikelihoodImprovement4alphaOptimiz_given ; /**< @brief Whether epsilonLikelihoodImprovement4alphaOptimiz was given. */
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unsigned int epsilonLikelihoodImprovement4BBL_given ; /**< @brief Whether epsilonLikelihoodImprovement4BBL was given. */
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unsigned int maxNumOfBBLIter_given ; /**< @brief Whether maxNumOfBBLIter was given. */
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unsigned int consurf_given ; /**< @brief Whether consurf was given. */
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unsigned int NJ_given ; /**< @brief Whether NJ was given. */
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unsigned int homogeneousRatesDTME_given ; /**< @brief Whether homogeneousRatesDTME was given. */
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unsigned int pairwiseGammaDTME_given ; /**< @brief Whether pairwiseGammaDTME was given. */
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unsigned int commonAlphaDTME_given ; /**< @brief Whether commonAlphaDTME was given. */
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unsigned int rate4siteDTME_given ; /**< @brief Whether rate4siteDTME was given. */
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unsigned int posteriorDTME_given ; /**< @brief Whether posteriorDTME was given. */
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unsigned int BPrepeats_given ; /**< @brief Whether BPrepeats was given. */
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unsigned int BPconsensus_given ; /**< @brief Whether BPconsensus was given. */
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unsigned int BPonUserTree_given ; /**< @brief Whether BPonUserTree was given. */
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unsigned int sequence_given ; /**< @brief Whether sequence was given. */
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unsigned int tree_given ; /**< @brief Whether tree was given. */
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unsigned int constraint_given ; /**< @brief Whether constraint was given. */
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unsigned int outputfile_given ; /**< @brief Whether outputfile was given. */
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unsigned int treeoutputfile_given ; /**< @brief Whether treeoutputfile was given. */
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unsigned int gaps_given ; /**< @brief Whether gaps was given. */
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unsigned int seed_given ; /**< @brief Whether seed was given. */
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unsigned int alphabet_given ; /**< @brief Whether alphabet was given. */
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unsigned int ratio_given ; /**< @brief Whether ratio was given. */
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unsigned int ACGprob_given ; /**< @brief Whether ACGprob was given. */
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unsigned int inputRate_given ; /**< @brief Whether inputRate was given. */
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unsigned int homogeneous_given ; /**< @brief Whether homogeneous was given. */
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unsigned int alpha_given ; /**< @brief Whether alpha was given. */
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unsigned int optimizeAlpha_given ; /**< @brief Whether optimizeAlpha was given. */
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unsigned int categories_given ; /**< @brief Whether categories was given. */
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unsigned int laguerre_given ; /**< @brief Whether laguerre was given. */
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unsigned int ssrv_given ; /**< @brief Whether ssrv was given. */
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unsigned int nu_given ; /**< @brief Whether nu was given. */
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unsigned int posteriorRates_given ; /**< @brief Whether posteriorRates was given. */
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unsigned int day_given ; /**< @brief Whether day was given. */
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unsigned int jtt_given ; /**< @brief Whether jtt was given. */
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unsigned int rev_given ; /**< @brief Whether rev was given. */
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unsigned int wag_given ; /**< @brief Whether wag was given. */
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unsigned int cprev_given ; /**< @brief Whether cprev was given. */
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unsigned int nucjc_given ; /**< @brief Whether nucjc was given. */
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unsigned int aaJC_given ; /**< @brief Whether aaJC was given. */
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unsigned int k2p_given ; /**< @brief Whether k2p was given. */
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unsigned int hky_given ; /**< @brief Whether hky was given. */
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unsigned int tamura92_given ; /**< @brief Whether tamura92 was given. */
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unsigned int gtr_given ; /**< @brief Whether gtr was given. */
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unsigned int modelfile_given ; /**< @brief Whether modelfile was given. */
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unsigned int verbose_given ; /**< @brief Whether verbose was given. */
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unsigned int Logfile_given ; /**< @brief Whether Logfile was given. */
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int DistanceTableEstimationMethod_group_counter; /**< @brief Counter for group DistanceTableEstimationMethod */
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int Model_group_counter; /**< @brief Counter for group Model */
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} ;
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/** @brief The additional parameters to pass to parser functions */
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struct cmdline_parser_params
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{
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int override; /**< @brief whether to override possibly already present options (default 0) */
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int initialize; /**< @brief whether to initialize the option structure gengetopt_args_info (default 1) */
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int check_required; /**< @brief whether to check that all required options were provided (default 1) */
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int check_ambiguity; /**< @brief whether to check for options already specified in the option structure gengetopt_args_info (default 0) */
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int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
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} ;
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/** @brief the purpose string of the program */
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extern const char *gengetopt_args_info_purpose;
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/** @brief the usage string of the program */
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extern const char *gengetopt_args_info_usage;
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/** @brief all the lines making the help output */
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extern const char *gengetopt_args_info_help[];
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/** @brief all the lines making the full help output (including hidden options) */
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extern const char *gengetopt_args_info_full_help[];
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/**
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* The command line parser
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* @param argc the number of command line options
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* @param argv the command line options
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* @param args_info the structure where option information will be stored
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* @return 0 if everything went fine, NON 0 if an error took place
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*/
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int cmdline_parser (int argc, char **argv,
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struct gengetopt_args_info *args_info);
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/**
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* The command line parser (version with additional parameters - deprecated)
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* @param argc the number of command line options
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* @param argv the command line options
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* @param args_info the structure where option information will be stored
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* @param override whether to override possibly already present options
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* @param initialize whether to initialize the option structure my_args_info
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* @param check_required whether to check that all required options were provided
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* @return 0 if everything went fine, NON 0 if an error took place
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* @deprecated use cmdline_parser_ext() instead
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*/
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int cmdline_parser2 (int argc, char **argv,
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struct gengetopt_args_info *args_info,
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int override, int initialize, int check_required);
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/**
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* The command line parser (version with additional parameters)
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* @param argc the number of command line options
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* @param argv the command line options
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* @param args_info the structure where option information will be stored
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* @param params additional parameters for the parser
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* @return 0 if everything went fine, NON 0 if an error took place
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*/
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int cmdline_parser_ext (int argc, char **argv,
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struct gengetopt_args_info *args_info,
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struct cmdline_parser_params *params);
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/**
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* Save the contents of the option struct into an already open FILE stream.
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* @param outfile the stream where to dump options
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* @param args_info the option struct to dump
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* @return 0 if everything went fine, NON 0 if an error took place
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*/
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int cmdline_parser_dump(FILE *outfile,
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struct gengetopt_args_info *args_info);
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/**
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* Save the contents of the option struct into a (text) file.
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* This file can be read by the config file parser (if generated by gengetopt)
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* @param filename the file where to save
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* @param args_info the option struct to save
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* @return 0 if everything went fine, NON 0 if an error took place
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*/
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int cmdline_parser_file_save(const char *filename,
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struct gengetopt_args_info *args_info);
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/**
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* Print the help
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*/
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void cmdline_parser_print_help(void);
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/**
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* Print the full help (including hidden options)
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*/
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void cmdline_parser_print_full_help(void);
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/**
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* Print the version
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*/
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void cmdline_parser_print_version(void);
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/**
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* Initializes all the fields a cmdline_parser_params structure
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* to their default values
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* @param params the structure to initialize
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*/
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void cmdline_parser_params_init(struct cmdline_parser_params *params);
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/**
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* Allocates dynamically a cmdline_parser_params structure and initializes
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* all its fields to their default values
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* @return the created and initialized cmdline_parser_params structure
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*/
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struct cmdline_parser_params *cmdline_parser_params_create(void);
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/**
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* Initializes the passed gengetopt_args_info structure's fields
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* (also set default values for options that have a default)
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* @param args_info the structure to initialize
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*/
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void cmdline_parser_init (struct gengetopt_args_info *args_info);
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/**
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* Deallocates the string fields of the gengetopt_args_info structure
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* (but does not deallocate the structure itself)
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* @param args_info the structure to deallocate
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*/
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void cmdline_parser_free (struct gengetopt_args_info *args_info);
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/**
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* Checks that all the required options were specified
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* @param args_info the structure to check
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* @param prog_name the name of the program that will be used to print
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* possible errors
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* @return
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*/
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int cmdline_parser_required (struct gengetopt_args_info *args_info,
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const char *prog_name);
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#ifdef __cplusplus
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}
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#endif /* __cplusplus */
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#endif /* SEMPHY_CMDLINE_H */
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