/* File autogenerated by gengetopt version 2.22.4 generated with the following command: gengetopt -isemphy.ggo -Fsemphy_cmdline 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 #include #include #ifndef FIX_UNUSED #define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */ #endif #include #include "semphy_cmdline.h" const char *gengetopt_args_info_purpose = "structural EM based Phylogeny"; const char *gengetopt_args_info_usage = "Usage: semphy [OPTIONS]..."; const char *gengetopt_args_info_description = ""; const char *gengetopt_args_info_full_help[] = { " -h, --help Print help and exit", " --full-help Print help, including hidden options, and exit", " -V, --version Print version and exit", "\nWhich algorithm to run:", " -S, --SEMPHY Do SEMPHY step (default=off)", " -n, --bbl Only optimize branch length (default=off)", " -L, --likelihood Compute likelihood for fixed tree \n (default=off)", " -P, --PerPosLike Compute likelihood per position for a fixed \n tree (default=off)", " -B, --PerPosPosterior Compute likelihood per position and Bayesian \n posterior (default=off)", " -R, --rate optimize rate of gene (default=off)", "\nAdvanced Algorithm Options:", " -M, --max-semphy-iter=INT Max number of SEM iterations (default=`100')", " --epsilonLikelihoodImprovement4iterNJ=FLOAT\n The threshold for optimization of likelihood of \n the tree, in iterative distance-based tree \n reconstruction (default=`0.01')", " --epsilonLikelihoodImprovement4pairwiseDistance=FLOAT\n The threshold for optimization of likelihood of \n a pair of sequences, in pairwise distance \n optimization (default=`0.0001')", " --epsilonLikelihoodImprovement4alphaOptimiz=FLOAT\n The threshold for optimization of likelihood of \n the tree, in alpha optimization (also used \n for Nu optimization when using --ssrv) \n (default=`0.01')", " --epsilonLikelihoodImprovement4BBL=FLOAT\n The threshold for optimization of likelihood of \n the tree, in branch-lengths optimization \n (default=`0.01')", " --maxNumOfBBLIter=INT Number of BBL iterations in BBL+ALPHA \n optimization (default=`10')", " --consurf version for use in consurf (default=off)", "\nNon Iterative methods:", "\n Group: DistanceTableEstimationMethod\n Method used for computing the distance table for the initial tree NJ \n construction", " -J, --NJ 'classic' Neighbor Joining (same as \n homogeneousRates)", " --homogeneousRatesDTME homogeneous rates MLE distance", " --pairwiseGammaDTME Gamma-ASRV with alpha optimized for each pair. \n (must give either --alpha or --optimizeAlpha)", "\nIterative distance-based tree reconstruction, with distance estimation methods \nthat utilize side information from the tree of the previous iteration:", " --commonAlphaDTME Side information is the alpha parameter.(must \n use --optimizeAlpha; may give an initial \n alpha value in --alpha)", " --rate4siteDTME Side information is the ML rate for each site", " --posteriorDTME Side information is the posterior probabilities \n of the rates at each site. (must use \n --optimizeAlpha; may give an initial alpha \n value in --alpha)", "\nBootstrap:", " --BPrepeats=INT Use bootstrap and set number of repeats", " --BPconsensus=INT Use bootstrap and compute a Consensus tree", " --BPonUserTree Use compute support for user provided tree \n (default=off)", "\nBasic Options:", " -s, --sequence=FILENAME Sequence file name (default=`-')", " -t, --tree=FILENAME Tree file name", " -c, --constraint=FILENAME Constraint Tree file name", " -o, --outputfile=FILENAME Output file (default=`-')", " -T, --treeoutputfile=FILENAME Tree output file (default=`-')", " -g, --gaps Remove positions with gaps (default=off)", " -r, --seed=LONG Seed random number generator", "\nModel Options:", " -a, --alphabet=4|20|61|64 Alphabet Size (default=`20')", " -z, --ratio=FLOAT Transition/Transversion ratio (default=`2.0')", " -p, --ACGprob=A,C,G User input nucleotide frequencies. String \n separated list for A,C,G \n (default=`0.25,0.25,0.25')", " --inputRate=FLOAT Set External globalRate (default=`1.0')", "\nAmong Site Rate Variation (ASRV):", " -H, --homogeneous Don't use Gamma ASRV (default=off)", " -A, --alpha=Alpha Set alpha for Gamma ASRV", " -O, --optimizeAlpha Optimize alpha for Gamma ASRV (default=off)", " -C, --categories=INT Number of categories to use with descrete Gamma \n ASRV (default=`8')", " --laguerre Use Laguerre approximation of Gamma - CURRENTLY \n NOT IMPLIMENTED (default=off)", " --ssrv Use a Site-Specific Rate Variation model (SSRV) \n (default=off)", " --nu=Nu Set Nu for the SSRV model (default=`1.0')", " --posteriorRates=FILENAME File with posterior distribution of the rate \n for each sequence site - for ASRV", "\n Group: Model\n Model type", " --day Use 'day' model", " --jtt Use 'jtt' model (default)", " --rev Use 'rev' model", " --wag Use 'wag' model", " --cprev Use 'cprev' model", " --nucjc Use nucleic acid JC model", " --aaJC Use amino acid JC model", " --k2p Use 'k2p' model", " --hky Use 'hky' model", " --tamura92 Use 'tamura92' model", " --gtr Use 'gtr' model (general reversible model)", " --modelfile=NAME Read replacement matrix from user input file", "\nLog Options:", " -v, --verbose=INT Log report level (verbose) (default=`1')", " -l, --Logfile=FILENAME Log output file name (default=`-')", 0 }; static void init_help_array(void) { gengetopt_args_info_help[0] = gengetopt_args_info_full_help[0]; gengetopt_args_info_help[1] = gengetopt_args_info_full_help[1]; gengetopt_args_info_help[2] = gengetopt_args_info_full_help[2]; gengetopt_args_info_help[3] = gengetopt_args_info_full_help[3]; gengetopt_args_info_help[4] = gengetopt_args_info_full_help[4]; gengetopt_args_info_help[5] = gengetopt_args_info_full_help[5]; gengetopt_args_info_help[6] = gengetopt_args_info_full_help[6]; gengetopt_args_info_help[7] = gengetopt_args_info_full_help[7]; gengetopt_args_info_help[8] = gengetopt_args_info_full_help[8]; gengetopt_args_info_help[9] = gengetopt_args_info_full_help[9]; gengetopt_args_info_help[10] = gengetopt_args_info_full_help[18]; gengetopt_args_info_help[11] = gengetopt_args_info_full_help[19]; gengetopt_args_info_help[12] = gengetopt_args_info_full_help[20]; gengetopt_args_info_help[13] = gengetopt_args_info_full_help[21]; gengetopt_args_info_help[14] = gengetopt_args_info_full_help[22]; gengetopt_args_info_help[15] = gengetopt_args_info_full_help[23]; gengetopt_args_info_help[16] = gengetopt_args_info_full_help[24]; gengetopt_args_info_help[17] = gengetopt_args_info_full_help[25]; gengetopt_args_info_help[18] = gengetopt_args_info_full_help[26]; gengetopt_args_info_help[19] = gengetopt_args_info_full_help[27]; gengetopt_args_info_help[20] = gengetopt_args_info_full_help[28]; gengetopt_args_info_help[21] = gengetopt_args_info_full_help[29]; gengetopt_args_info_help[22] = gengetopt_args_info_full_help[30]; gengetopt_args_info_help[23] = gengetopt_args_info_full_help[31]; gengetopt_args_info_help[24] = gengetopt_args_info_full_help[32]; gengetopt_args_info_help[25] = gengetopt_args_info_full_help[33]; gengetopt_args_info_help[26] = gengetopt_args_info_full_help[34]; gengetopt_args_info_help[27] = gengetopt_args_info_full_help[35]; gengetopt_args_info_help[28] = gengetopt_args_info_full_help[36]; gengetopt_args_info_help[29] = gengetopt_args_info_full_help[37]; gengetopt_args_info_help[30] = gengetopt_args_info_full_help[38]; gengetopt_args_info_help[31] = gengetopt_args_info_full_help[39]; gengetopt_args_info_help[32] = gengetopt_args_info_full_help[40]; gengetopt_args_info_help[33] = gengetopt_args_info_full_help[41]; gengetopt_args_info_help[34] = gengetopt_args_info_full_help[42]; gengetopt_args_info_help[35] = gengetopt_args_info_full_help[43]; gengetopt_args_info_help[36] = gengetopt_args_info_full_help[44]; gengetopt_args_info_help[37] = gengetopt_args_info_full_help[45]; gengetopt_args_info_help[38] = gengetopt_args_info_full_help[46]; gengetopt_args_info_help[39] = gengetopt_args_info_full_help[47]; gengetopt_args_info_help[40] = gengetopt_args_info_full_help[48]; gengetopt_args_info_help[41] = gengetopt_args_info_full_help[49]; gengetopt_args_info_help[42] = gengetopt_args_info_full_help[50]; gengetopt_args_info_help[43] = gengetopt_args_info_full_help[51]; gengetopt_args_info_help[44] = gengetopt_args_info_full_help[52]; gengetopt_args_info_help[45] = gengetopt_args_info_full_help[53]; gengetopt_args_info_help[46] = gengetopt_args_info_full_help[54]; gengetopt_args_info_help[47] = gengetopt_args_info_full_help[55]; gengetopt_args_info_help[48] = gengetopt_args_info_full_help[56]; gengetopt_args_info_help[49] = gengetopt_args_info_full_help[57]; gengetopt_args_info_help[50] = gengetopt_args_info_full_help[58]; gengetopt_args_info_help[51] = gengetopt_args_info_full_help[59]; gengetopt_args_info_help[52] = gengetopt_args_info_full_help[60]; gengetopt_args_info_help[53] = gengetopt_args_info_full_help[61]; gengetopt_args_info_help[54] = gengetopt_args_info_full_help[62]; gengetopt_args_info_help[55] = gengetopt_args_info_full_help[63]; gengetopt_args_info_help[56] = gengetopt_args_info_full_help[64]; gengetopt_args_info_help[57] = gengetopt_args_info_full_help[65]; gengetopt_args_info_help[58] = gengetopt_args_info_full_help[66]; gengetopt_args_info_help[59] = gengetopt_args_info_full_help[67]; gengetopt_args_info_help[60] = gengetopt_args_info_full_help[68]; gengetopt_args_info_help[61] = 0; } const char *gengetopt_args_info_help[62]; typedef enum {ARG_NO , ARG_FLAG , ARG_STRING , ARG_INT , ARG_LONG , ARG_FLOAT } 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 char * gengetopt_strdup (const char *s); static void clear_given (struct gengetopt_args_info *args_info) { args_info->help_given = 0 ; args_info->full_help_given = 0 ; args_info->version_given = 0 ; args_info->SEMPHY_given = 0 ; args_info->bbl_given = 0 ; args_info->likelihood_given = 0 ; args_info->PerPosLike_given = 0 ; args_info->PerPosPosterior_given = 0 ; args_info->rate_given = 0 ; args_info->max_semphy_iter_given = 0 ; args_info->epsilonLikelihoodImprovement4iterNJ_given = 0 ; args_info->epsilonLikelihoodImprovement4pairwiseDistance_given = 0 ; args_info->epsilonLikelihoodImprovement4alphaOptimiz_given = 0 ; args_info->epsilonLikelihoodImprovement4BBL_given = 0 ; args_info->maxNumOfBBLIter_given = 0 ; args_info->consurf_given = 0 ; args_info->NJ_given = 0 ; args_info->homogeneousRatesDTME_given = 0 ; args_info->pairwiseGammaDTME_given = 0 ; args_info->commonAlphaDTME_given = 0 ; args_info->rate4siteDTME_given = 0 ; args_info->posteriorDTME_given = 0 ; args_info->BPrepeats_given = 0 ; args_info->BPconsensus_given = 0 ; args_info->BPonUserTree_given = 0 ; args_info->sequence_given = 0 ; args_info->tree_given = 0 ; args_info->constraint_given = 0 ; args_info->outputfile_given = 0 ; args_info->treeoutputfile_given = 0 ; args_info->gaps_given = 0 ; args_info->seed_given = 0 ; args_info->alphabet_given = 0 ; args_info->ratio_given = 0 ; args_info->ACGprob_given = 0 ; args_info->inputRate_given = 0 ; args_info->homogeneous_given = 0 ; args_info->alpha_given = 0 ; args_info->optimizeAlpha_given = 0 ; args_info->categories_given = 0 ; args_info->laguerre_given = 0 ; args_info->ssrv_given = 0 ; args_info->nu_given = 0 ; args_info->posteriorRates_given = 0 ; args_info->day_given = 0 ; args_info->jtt_given = 0 ; args_info->rev_given = 0 ; args_info->wag_given = 0 ; args_info->cprev_given = 0 ; args_info->nucjc_given = 0 ; args_info->aaJC_given = 0 ; args_info->k2p_given = 0 ; args_info->hky_given = 0 ; args_info->tamura92_given = 0 ; args_info->gtr_given = 0 ; args_info->modelfile_given = 0 ; args_info->verbose_given = 0 ; args_info->Logfile_given = 0 ; args_info->DistanceTableEstimationMethod_group_counter = 0 ; args_info->Model_group_counter = 0 ; } static void clear_args (struct gengetopt_args_info *args_info) { FIX_UNUSED (args_info); args_info->SEMPHY_flag = 0; args_info->bbl_flag = 0; args_info->likelihood_flag = 0; args_info->PerPosLike_flag = 0; args_info->PerPosPosterior_flag = 0; args_info->rate_flag = 0; args_info->max_semphy_iter_arg = 100; args_info->max_semphy_iter_orig = NULL; args_info->epsilonLikelihoodImprovement4iterNJ_arg = 0.01; args_info->epsilonLikelihoodImprovement4iterNJ_orig = NULL; args_info->epsilonLikelihoodImprovement4pairwiseDistance_arg = 0.0001; args_info->epsilonLikelihoodImprovement4pairwiseDistance_orig = NULL; args_info->epsilonLikelihoodImprovement4alphaOptimiz_arg = 0.01; args_info->epsilonLikelihoodImprovement4alphaOptimiz_orig = NULL; args_info->epsilonLikelihoodImprovement4BBL_arg = 0.01; args_info->epsilonLikelihoodImprovement4BBL_orig = NULL; args_info->maxNumOfBBLIter_arg = 10; args_info->maxNumOfBBLIter_orig = NULL; args_info->consurf_flag = 0; args_info->BPrepeats_orig = NULL; args_info->BPconsensus_orig = NULL; args_info->BPonUserTree_flag = 0; args_info->sequence_arg = gengetopt_strdup ("-"); args_info->sequence_orig = NULL; args_info->tree_arg = NULL; args_info->tree_orig = NULL; args_info->constraint_arg = NULL; args_info->constraint_orig = NULL; args_info->outputfile_arg = gengetopt_strdup ("-"); args_info->outputfile_orig = NULL; args_info->treeoutputfile_arg = gengetopt_strdup ("-"); args_info->treeoutputfile_orig = NULL; args_info->gaps_flag = 0; args_info->seed_orig = NULL; args_info->alphabet_arg = 20; args_info->alphabet_orig = NULL; args_info->ratio_arg = 2.0; args_info->ratio_orig = NULL; args_info->ACGprob_arg = gengetopt_strdup ("0.25,0.25,0.25"); args_info->ACGprob_orig = NULL; args_info->inputRate_arg = 1.0; args_info->inputRate_orig = NULL; args_info->homogeneous_flag = 0; args_info->alpha_orig = NULL; args_info->optimizeAlpha_flag = 0; args_info->categories_arg = 8; args_info->categories_orig = NULL; args_info->laguerre_flag = 0; args_info->ssrv_flag = 0; args_info->nu_arg = 1.0; args_info->nu_orig = NULL; args_info->posteriorRates_arg = NULL; args_info->posteriorRates_orig = NULL; args_info->modelfile_arg = NULL; args_info->modelfile_orig = NULL; args_info->verbose_arg = 1; args_info->verbose_orig = NULL; args_info->Logfile_arg = gengetopt_strdup ("-"); args_info->Logfile_orig = NULL; } static void init_args_info(struct gengetopt_args_info *args_info) { init_help_array(); args_info->help_help = gengetopt_args_info_full_help[0] ; args_info->full_help_help = gengetopt_args_info_full_help[1] ; args_info->version_help = gengetopt_args_info_full_help[2] ; args_info->SEMPHY_help = gengetopt_args_info_full_help[4] ; args_info->bbl_help = gengetopt_args_info_full_help[5] ; args_info->likelihood_help = gengetopt_args_info_full_help[6] ; args_info->PerPosLike_help = gengetopt_args_info_full_help[7] ; args_info->PerPosPosterior_help = gengetopt_args_info_full_help[8] ; args_info->rate_help = gengetopt_args_info_full_help[9] ; args_info->max_semphy_iter_help = gengetopt_args_info_full_help[11] ; args_info->epsilonLikelihoodImprovement4iterNJ_help = gengetopt_args_info_full_help[12] ; args_info->epsilonLikelihoodImprovement4pairwiseDistance_help = gengetopt_args_info_full_help[13] ; args_info->epsilonLikelihoodImprovement4alphaOptimiz_help = gengetopt_args_info_full_help[14] ; args_info->epsilonLikelihoodImprovement4BBL_help = gengetopt_args_info_full_help[15] ; args_info->maxNumOfBBLIter_help = gengetopt_args_info_full_help[16] ; args_info->consurf_help = gengetopt_args_info_full_help[17] ; args_info->NJ_help = gengetopt_args_info_full_help[20] ; args_info->homogeneousRatesDTME_help = gengetopt_args_info_full_help[21] ; args_info->pairwiseGammaDTME_help = gengetopt_args_info_full_help[22] ; args_info->commonAlphaDTME_help = gengetopt_args_info_full_help[24] ; args_info->rate4siteDTME_help = gengetopt_args_info_full_help[25] ; args_info->posteriorDTME_help = gengetopt_args_info_full_help[26] ; args_info->BPrepeats_help = gengetopt_args_info_full_help[28] ; args_info->BPconsensus_help = gengetopt_args_info_full_help[29] ; args_info->BPonUserTree_help = gengetopt_args_info_full_help[30] ; args_info->sequence_help = gengetopt_args_info_full_help[32] ; args_info->tree_help = gengetopt_args_info_full_help[33] ; args_info->constraint_help = gengetopt_args_info_full_help[34] ; args_info->outputfile_help = gengetopt_args_info_full_help[35] ; args_info->treeoutputfile_help = gengetopt_args_info_full_help[36] ; args_info->gaps_help = gengetopt_args_info_full_help[37] ; args_info->seed_help = gengetopt_args_info_full_help[38] ; args_info->alphabet_help = gengetopt_args_info_full_help[40] ; args_info->ratio_help = gengetopt_args_info_full_help[41] ; args_info->ACGprob_help = gengetopt_args_info_full_help[42] ; args_info->inputRate_help = gengetopt_args_info_full_help[43] ; args_info->homogeneous_help = gengetopt_args_info_full_help[45] ; args_info->alpha_help = gengetopt_args_info_full_help[46] ; args_info->optimizeAlpha_help = gengetopt_args_info_full_help[47] ; args_info->categories_help = gengetopt_args_info_full_help[48] ; args_info->laguerre_help = gengetopt_args_info_full_help[49] ; args_info->ssrv_help = gengetopt_args_info_full_help[50] ; args_info->nu_help = gengetopt_args_info_full_help[51] ; args_info->posteriorRates_help = gengetopt_args_info_full_help[52] ; args_info->day_help = gengetopt_args_info_full_help[54] ; args_info->jtt_help = gengetopt_args_info_full_help[55] ; args_info->rev_help = gengetopt_args_info_full_help[56] ; args_info->wag_help = gengetopt_args_info_full_help[57] ; args_info->cprev_help = gengetopt_args_info_full_help[58] ; args_info->nucjc_help = gengetopt_args_info_full_help[59] ; args_info->aaJC_help = gengetopt_args_info_full_help[60] ; args_info->k2p_help = gengetopt_args_info_full_help[61] ; args_info->hky_help = gengetopt_args_info_full_help[62] ; args_info->tamura92_help = gengetopt_args_info_full_help[63] ; args_info->gtr_help = gengetopt_args_info_full_help[64] ; args_info->modelfile_help = gengetopt_args_info_full_help[65] ; args_info->verbose_help = gengetopt_args_info_full_help[67] ; args_info->Logfile_help = gengetopt_args_info_full_help[68] ; } 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); } 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_print_full_help (void) { int i = 0; print_help_common(); while (gengetopt_args_info_full_help[i]) printf("%s\n", gengetopt_args_info_full_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->max_semphy_iter_orig)); free_string_field (&(args_info->epsilonLikelihoodImprovement4iterNJ_orig)); free_string_field (&(args_info->epsilonLikelihoodImprovement4pairwiseDistance_orig)); free_string_field (&(args_info->epsilonLikelihoodImprovement4alphaOptimiz_orig)); free_string_field (&(args_info->epsilonLikelihoodImprovement4BBL_orig)); free_string_field (&(args_info->maxNumOfBBLIter_orig)); free_string_field (&(args_info->BPrepeats_orig)); free_string_field (&(args_info->BPconsensus_orig)); free_string_field (&(args_info->sequence_arg)); free_string_field (&(args_info->sequence_orig)); free_string_field (&(args_info->tree_arg)); free_string_field (&(args_info->tree_orig)); free_string_field (&(args_info->constraint_arg)); free_string_field (&(args_info->constraint_orig)); free_string_field (&(args_info->outputfile_arg)); free_string_field (&(args_info->outputfile_orig)); free_string_field (&(args_info->treeoutputfile_arg)); free_string_field (&(args_info->treeoutputfile_orig)); free_string_field (&(args_info->seed_orig)); free_string_field (&(args_info->alphabet_orig)); free_string_field (&(args_info->ratio_orig)); free_string_field (&(args_info->ACGprob_arg)); free_string_field (&(args_info->ACGprob_orig)); free_string_field (&(args_info->inputRate_orig)); free_string_field (&(args_info->alpha_orig)); free_string_field (&(args_info->categories_orig)); free_string_field (&(args_info->nu_orig)); free_string_field (&(args_info->posteriorRates_arg)); free_string_field (&(args_info->posteriorRates_orig)); free_string_field (&(args_info->modelfile_arg)); free_string_field (&(args_info->modelfile_orig)); free_string_field (&(args_info->verbose_orig)); free_string_field (&(args_info->Logfile_arg)); free_string_field (&(args_info->Logfile_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->full_help_given) write_into_file(outfile, "full-help", 0, 0 ); if (args_info->version_given) write_into_file(outfile, "version", 0, 0 ); if (args_info->SEMPHY_given) write_into_file(outfile, "SEMPHY", 0, 0 ); if (args_info->bbl_given) write_into_file(outfile, "bbl", 0, 0 ); if (args_info->likelihood_given) write_into_file(outfile, "likelihood", 0, 0 ); if (args_info->PerPosLike_given) write_into_file(outfile, "PerPosLike", 0, 0 ); if (args_info->PerPosPosterior_given) write_into_file(outfile, "PerPosPosterior", 0, 0 ); if (args_info->rate_given) write_into_file(outfile, "rate", 0, 0 ); if (args_info->max_semphy_iter_given) write_into_file(outfile, "max-semphy-iter", args_info->max_semphy_iter_orig, 0); if (args_info->epsilonLikelihoodImprovement4iterNJ_given) write_into_file(outfile, "epsilonLikelihoodImprovement4iterNJ", args_info->epsilonLikelihoodImprovement4iterNJ_orig, 0); if (args_info->epsilonLikelihoodImprovement4pairwiseDistance_given) write_into_file(outfile, "epsilonLikelihoodImprovement4pairwiseDistance", args_info->epsilonLikelihoodImprovement4pairwiseDistance_orig, 0); if (args_info->epsilonLikelihoodImprovement4alphaOptimiz_given) write_into_file(outfile, "epsilonLikelihoodImprovement4alphaOptimiz", args_info->epsilonLikelihoodImprovement4alphaOptimiz_orig, 0); if (args_info->epsilonLikelihoodImprovement4BBL_given) write_into_file(outfile, "epsilonLikelihoodImprovement4BBL", args_info->epsilonLikelihoodImprovement4BBL_orig, 0); if (args_info->maxNumOfBBLIter_given) write_into_file(outfile, "maxNumOfBBLIter", args_info->maxNumOfBBLIter_orig, 0); if (args_info->consurf_given) write_into_file(outfile, "consurf", 0, 0 ); if (args_info->NJ_given) write_into_file(outfile, "NJ", 0, 0 ); if (args_info->homogeneousRatesDTME_given) write_into_file(outfile, "homogeneousRatesDTME", 0, 0 ); if (args_info->pairwiseGammaDTME_given) write_into_file(outfile, "pairwiseGammaDTME", 0, 0 ); if (args_info->commonAlphaDTME_given) write_into_file(outfile, "commonAlphaDTME", 0, 0 ); if (args_info->rate4siteDTME_given) write_into_file(outfile, "rate4siteDTME", 0, 0 ); if (args_info->posteriorDTME_given) write_into_file(outfile, "posteriorDTME", 0, 0 ); if (args_info->BPrepeats_given) write_into_file(outfile, "BPrepeats", args_info->BPrepeats_orig, 0); if (args_info->BPconsensus_given) write_into_file(outfile, "BPconsensus", args_info->BPconsensus_orig, 0); if (args_info->BPonUserTree_given) write_into_file(outfile, "BPonUserTree", 0, 0 ); if (args_info->sequence_given) write_into_file(outfile, "sequence", args_info->sequence_orig, 0); if (args_info->tree_given) write_into_file(outfile, "tree", args_info->tree_orig, 0); if (args_info->constraint_given) write_into_file(outfile, "constraint", args_info->constraint_orig, 0); if (args_info->outputfile_given) write_into_file(outfile, "outputfile", args_info->outputfile_orig, 0); if (args_info->treeoutputfile_given) write_into_file(outfile, "treeoutputfile", args_info->treeoutputfile_orig, 0); if (args_info->gaps_given) write_into_file(outfile, "gaps", 0, 0 ); if (args_info->seed_given) write_into_file(outfile, "seed", args_info->seed_orig, 0); if (args_info->alphabet_given) write_into_file(outfile, "alphabet", args_info->alphabet_orig, 0); if (args_info->ratio_given) write_into_file(outfile, "ratio", args_info->ratio_orig, 0); if (args_info->ACGprob_given) write_into_file(outfile, "ACGprob", args_info->ACGprob_orig, 0); if (args_info->inputRate_given) write_into_file(outfile, "inputRate", args_info->inputRate_orig, 0); if (args_info->homogeneous_given) write_into_file(outfile, "homogeneous", 0, 0 ); if (args_info->alpha_given) write_into_file(outfile, "alpha", args_info->alpha_orig, 0); if (args_info->optimizeAlpha_given) write_into_file(outfile, "optimizeAlpha", 0, 0 ); if (args_info->categories_given) write_into_file(outfile, "categories", args_info->categories_orig, 0); if (args_info->laguerre_given) write_into_file(outfile, "laguerre", 0, 0 ); if (args_info->ssrv_given) write_into_file(outfile, "ssrv", 0, 0 ); if (args_info->nu_given) write_into_file(outfile, "nu", args_info->nu_orig, 0); if (args_info->posteriorRates_given) write_into_file(outfile, "posteriorRates", args_info->posteriorRates_orig, 0); if (args_info->day_given) write_into_file(outfile, "day", 0, 0 ); if (args_info->jtt_given) write_into_file(outfile, "jtt", 0, 0 ); if (args_info->rev_given) write_into_file(outfile, "rev", 0, 0 ); if (args_info->wag_given) write_into_file(outfile, "wag", 0, 0 ); if (args_info->cprev_given) write_into_file(outfile, "cprev", 0, 0 ); if (args_info->nucjc_given) write_into_file(outfile, "nucjc", 0, 0 ); if (args_info->aaJC_given) write_into_file(outfile, "aaJC", 0, 0 ); if (args_info->k2p_given) write_into_file(outfile, "k2p", 0, 0 ); if (args_info->hky_given) write_into_file(outfile, "hky", 0, 0 ); if (args_info->tamura92_given) write_into_file(outfile, "tamura92", 0, 0 ); if (args_info->gtr_given) write_into_file(outfile, "gtr", 0, 0 ); if (args_info->modelfile_given) write_into_file(outfile, "modelfile", args_info->modelfile_orig, 0); if (args_info->verbose_given) write_into_file(outfile, "verbose", args_info->verbose_orig, 0); if (args_info->Logfile_given) write_into_file(outfile, "Logfile", args_info->Logfile_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_DistanceTableEstimationMethod(struct gengetopt_args_info *args_info) { if (! args_info->DistanceTableEstimationMethod_group_counter) return; args_info->NJ_given = 0 ; args_info->homogeneousRatesDTME_given = 0 ; args_info->pairwiseGammaDTME_given = 0 ; args_info->commonAlphaDTME_given = 0 ; args_info->rate4siteDTME_given = 0 ; args_info->posteriorDTME_given = 0 ; args_info->DistanceTableEstimationMethod_group_counter = 0; } static void reset_group_Model(struct gengetopt_args_info *args_info) { if (! args_info->Model_group_counter) return; args_info->day_given = 0 ; args_info->jtt_given = 0 ; args_info->rev_given = 0 ; args_info->wag_given = 0 ; args_info->cprev_given = 0 ; args_info->nucjc_given = 0 ; args_info->aaJC_given = 0 ; args_info->k2p_given = 0 ; args_info->hky_given = 0 ; args_info->tamura92_given = 0 ; args_info->gtr_given = 0 ; args_info->Model_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) { FIX_UNUSED (args_info); FIX_UNUSED (prog_name); return EXIT_SUCCESS; } 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_LONG: if (val) *((long *)field) = (long)strtol (val, &stop_char, 0); break; case ARG_FLOAT: if (val) *((float *)field) = (float)strtod (val, &stop_char); 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: case ARG_LONG: case ARG_FLOAT: 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 = 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' }, { "full-help", 0, NULL, 0 }, { "version", 0, NULL, 'V' }, { "SEMPHY", 0, NULL, 'S' }, { "bbl", 0, NULL, 'n' }, { "likelihood", 0, NULL, 'L' }, { "PerPosLike", 0, NULL, 'P' }, { "PerPosPosterior", 0, NULL, 'B' }, { "rate", 0, NULL, 'R' }, { "max-semphy-iter", 1, NULL, 'M' }, { "epsilonLikelihoodImprovement4iterNJ", 1, NULL, 0 }, { "epsilonLikelihoodImprovement4pairwiseDistance", 1, NULL, 0 }, { "epsilonLikelihoodImprovement4alphaOptimiz", 1, NULL, 0 }, { "epsilonLikelihoodImprovement4BBL", 1, NULL, 0 }, { "maxNumOfBBLIter", 1, NULL, 0 }, { "consurf", 0, NULL, 0 }, { "NJ", 0, NULL, 'J' }, { "homogeneousRatesDTME", 0, NULL, 0 }, { "pairwiseGammaDTME", 0, NULL, 0 }, { "commonAlphaDTME", 0, NULL, 0 }, { "rate4siteDTME", 0, NULL, 0 }, { "posteriorDTME", 0, NULL, 0 }, { "BPrepeats", 1, NULL, 0 }, { "BPconsensus", 1, NULL, 0 }, { "BPonUserTree", 0, NULL, 0 }, { "sequence", 1, NULL, 's' }, { "tree", 1, NULL, 't' }, { "constraint", 1, NULL, 'c' }, { "outputfile", 1, NULL, 'o' }, { "treeoutputfile", 1, NULL, 'T' }, { "gaps", 0, NULL, 'g' }, { "seed", 1, NULL, 'r' }, { "alphabet", 1, NULL, 'a' }, { "ratio", 1, NULL, 'z' }, { "ACGprob", 1, NULL, 'p' }, { "inputRate", 1, NULL, 0 }, { "homogeneous", 0, NULL, 'H' }, { "alpha", 1, NULL, 'A' }, { "optimizeAlpha", 0, NULL, 'O' }, { "categories", 1, NULL, 'C' }, { "laguerre", 0, NULL, 0 }, { "ssrv", 0, NULL, 0 }, { "nu", 1, NULL, 0 }, { "posteriorRates", 1, NULL, 0 }, { "day", 0, NULL, 0 }, { "jtt", 0, NULL, 0 }, { "rev", 0, NULL, 0 }, { "wag", 0, NULL, 0 }, { "cprev", 0, NULL, 0 }, { "nucjc", 0, NULL, 0 }, { "aaJC", 0, NULL, 0 }, { "k2p", 0, NULL, 0 }, { "hky", 0, NULL, 0 }, { "tamura92", 0, NULL, 0 }, { "gtr", 0, NULL, 0 }, { "modelfile", 1, NULL, 0 }, { "verbose", 1, NULL, 'v' }, { "Logfile", 1, NULL, 'l' }, { 0, 0, 0, 0 } }; c = getopt_long (argc, argv, "hVSnLPBRM:Js:t:c:o:T:gr:a:z:p:HA:OC:v:l:", 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 'S': /* Do SEMPHY step. */ if (update_arg((void *)&(args_info->SEMPHY_flag), 0, &(args_info->SEMPHY_given), &(local_args_info.SEMPHY_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "SEMPHY", 'S', additional_error)) goto failure; break; case 'n': /* Only optimize branch length. */ if (update_arg((void *)&(args_info->bbl_flag), 0, &(args_info->bbl_given), &(local_args_info.bbl_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "bbl", 'n', additional_error)) goto failure; break; case 'L': /* Compute likelihood for fixed tree. */ if (update_arg((void *)&(args_info->likelihood_flag), 0, &(args_info->likelihood_given), &(local_args_info.likelihood_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "likelihood", 'L', additional_error)) goto failure; break; case 'P': /* Compute likelihood per position for a fixed tree. */ if (update_arg((void *)&(args_info->PerPosLike_flag), 0, &(args_info->PerPosLike_given), &(local_args_info.PerPosLike_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "PerPosLike", 'P', additional_error)) goto failure; break; case 'B': /* Compute likelihood per position and Bayesian posterior. */ if (update_arg((void *)&(args_info->PerPosPosterior_flag), 0, &(args_info->PerPosPosterior_given), &(local_args_info.PerPosPosterior_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "PerPosPosterior", 'B', additional_error)) goto failure; break; case 'R': /* optimize rate of gene. */ if (update_arg((void *)&(args_info->rate_flag), 0, &(args_info->rate_given), &(local_args_info.rate_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "rate", 'R', additional_error)) goto failure; break; case 'M': /* Max number of SEM iterations. */ if (update_arg( (void *)&(args_info->max_semphy_iter_arg), &(args_info->max_semphy_iter_orig), &(args_info->max_semphy_iter_given), &(local_args_info.max_semphy_iter_given), optarg, 0, "100", ARG_INT, check_ambiguity, override, 0, 0, "max-semphy-iter", 'M', additional_error)) goto failure; break; case 'J': /* 'classic' Neighbor Joining (same as homogeneousRates). */ if (args_info->DistanceTableEstimationMethod_group_counter && override) reset_group_DistanceTableEstimationMethod (args_info); args_info->DistanceTableEstimationMethod_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->NJ_given), &(local_args_info.NJ_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "NJ", 'J', additional_error)) goto failure; break; case 's': /* Sequence file name. */ if (update_arg( (void *)&(args_info->sequence_arg), &(args_info->sequence_orig), &(args_info->sequence_given), &(local_args_info.sequence_given), optarg, 0, "-", ARG_STRING, check_ambiguity, override, 0, 0, "sequence", 's', additional_error)) goto failure; break; case 't': /* Tree file name. */ if (update_arg( (void *)&(args_info->tree_arg), &(args_info->tree_orig), &(args_info->tree_given), &(local_args_info.tree_given), optarg, 0, 0, ARG_STRING, check_ambiguity, override, 0, 0, "tree", 't', additional_error)) goto failure; break; case 'c': /* Constraint Tree file name. */ if (update_arg( (void *)&(args_info->constraint_arg), &(args_info->constraint_orig), &(args_info->constraint_given), &(local_args_info.constraint_given), optarg, 0, 0, ARG_STRING, check_ambiguity, override, 0, 0, "constraint", 'c', additional_error)) goto failure; break; case 'o': /* Output file. */ if (update_arg( (void *)&(args_info->outputfile_arg), &(args_info->outputfile_orig), &(args_info->outputfile_given), &(local_args_info.outputfile_given), optarg, 0, "-", ARG_STRING, check_ambiguity, override, 0, 0, "outputfile", 'o', additional_error)) goto failure; break; case 'T': /* Tree output file. */ if (update_arg( (void *)&(args_info->treeoutputfile_arg), &(args_info->treeoutputfile_orig), &(args_info->treeoutputfile_given), &(local_args_info.treeoutputfile_given), optarg, 0, "-", ARG_STRING, check_ambiguity, override, 0, 0, "treeoutputfile", 'T', additional_error)) goto failure; break; case 'g': /* Remove positions with gaps. */ if (update_arg((void *)&(args_info->gaps_flag), 0, &(args_info->gaps_given), &(local_args_info.gaps_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "gaps", 'g', additional_error)) goto failure; break; case 'r': /* Seed random number generator. */ if (update_arg( (void *)&(args_info->seed_arg), &(args_info->seed_orig), &(args_info->seed_given), &(local_args_info.seed_given), optarg, 0, 0, ARG_LONG, check_ambiguity, override, 0, 0, "seed", 'r', additional_error)) goto failure; break; case 'a': /* Alphabet Size. */ if (update_arg( (void *)&(args_info->alphabet_arg), &(args_info->alphabet_orig), &(args_info->alphabet_given), &(local_args_info.alphabet_given), optarg, 0, "20", ARG_INT, check_ambiguity, override, 0, 0, "alphabet", 'a', additional_error)) goto failure; break; case 'z': /* Transition/Transversion ratio. */ if (update_arg( (void *)&(args_info->ratio_arg), &(args_info->ratio_orig), &(args_info->ratio_given), &(local_args_info.ratio_given), optarg, 0, "2.0", ARG_FLOAT, check_ambiguity, override, 0, 0, "ratio", 'z', additional_error)) goto failure; break; case 'p': /* User input nucleotide frequencies. String separated list for A,C,G. */ if (update_arg( (void *)&(args_info->ACGprob_arg), &(args_info->ACGprob_orig), &(args_info->ACGprob_given), &(local_args_info.ACGprob_given), optarg, 0, "0.25,0.25,0.25", ARG_STRING, check_ambiguity, override, 0, 0, "ACGprob", 'p', additional_error)) goto failure; break; case 'H': /* Don't use Gamma ASRV. */ if (update_arg((void *)&(args_info->homogeneous_flag), 0, &(args_info->homogeneous_given), &(local_args_info.homogeneous_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "homogeneous", 'H', additional_error)) goto failure; break; case 'A': /* Set alpha for Gamma ASRV. */ if (update_arg( (void *)&(args_info->alpha_arg), &(args_info->alpha_orig), &(args_info->alpha_given), &(local_args_info.alpha_given), optarg, 0, 0, ARG_FLOAT, check_ambiguity, override, 0, 0, "alpha", 'A', additional_error)) goto failure; break; case 'O': /* Optimize alpha for Gamma ASRV. */ if (update_arg((void *)&(args_info->optimizeAlpha_flag), 0, &(args_info->optimizeAlpha_given), &(local_args_info.optimizeAlpha_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "optimizeAlpha", 'O', additional_error)) goto failure; break; case 'C': /* Number of categories to use with descrete Gamma ASRV. */ if (update_arg( (void *)&(args_info->categories_arg), &(args_info->categories_orig), &(args_info->categories_given), &(local_args_info.categories_given), optarg, 0, "8", ARG_INT, check_ambiguity, override, 0, 0, "categories", 'C', additional_error)) goto failure; break; case 'v': /* Log report level (verbose). */ if (update_arg( (void *)&(args_info->verbose_arg), &(args_info->verbose_orig), &(args_info->verbose_given), &(local_args_info.verbose_given), optarg, 0, "1", ARG_INT, check_ambiguity, override, 0, 0, "verbose", 'v', additional_error)) goto failure; break; case 'l': /* Log output file name. */ if (update_arg( (void *)&(args_info->Logfile_arg), &(args_info->Logfile_orig), &(args_info->Logfile_given), &(local_args_info.Logfile_given), optarg, 0, "-", ARG_STRING, check_ambiguity, override, 0, 0, "Logfile", 'l', additional_error)) goto failure; break; case 0: /* Long option with no short option */ if (strcmp (long_options[option_index].name, "full-help") == 0) { cmdline_parser_print_full_help (); cmdline_parser_free (&local_args_info); exit (EXIT_SUCCESS); } /* The threshold for optimization of likelihood of the tree, in iterative distance-based tree reconstruction. */ if (strcmp (long_options[option_index].name, "epsilonLikelihoodImprovement4iterNJ") == 0) { if (update_arg( (void *)&(args_info->epsilonLikelihoodImprovement4iterNJ_arg), &(args_info->epsilonLikelihoodImprovement4iterNJ_orig), &(args_info->epsilonLikelihoodImprovement4iterNJ_given), &(local_args_info.epsilonLikelihoodImprovement4iterNJ_given), optarg, 0, "0.01", ARG_FLOAT, check_ambiguity, override, 0, 0, "epsilonLikelihoodImprovement4iterNJ", '-', additional_error)) goto failure; } /* The threshold for optimization of likelihood of a pair of sequences, in pairwise distance optimization. */ else if (strcmp (long_options[option_index].name, "epsilonLikelihoodImprovement4pairwiseDistance") == 0) { if (update_arg( (void *)&(args_info->epsilonLikelihoodImprovement4pairwiseDistance_arg), &(args_info->epsilonLikelihoodImprovement4pairwiseDistance_orig), &(args_info->epsilonLikelihoodImprovement4pairwiseDistance_given), &(local_args_info.epsilonLikelihoodImprovement4pairwiseDistance_given), optarg, 0, "0.0001", ARG_FLOAT, check_ambiguity, override, 0, 0, "epsilonLikelihoodImprovement4pairwiseDistance", '-', additional_error)) goto failure; } /* The threshold for optimization of likelihood of the tree, in alpha optimization (also used for Nu optimization when using --ssrv). */ else if (strcmp (long_options[option_index].name, "epsilonLikelihoodImprovement4alphaOptimiz") == 0) { if (update_arg( (void *)&(args_info->epsilonLikelihoodImprovement4alphaOptimiz_arg), &(args_info->epsilonLikelihoodImprovement4alphaOptimiz_orig), &(args_info->epsilonLikelihoodImprovement4alphaOptimiz_given), &(local_args_info.epsilonLikelihoodImprovement4alphaOptimiz_given), optarg, 0, "0.01", ARG_FLOAT, check_ambiguity, override, 0, 0, "epsilonLikelihoodImprovement4alphaOptimiz", '-', additional_error)) goto failure; } /* The threshold for optimization of likelihood of the tree, in branch-lengths optimization. */ else if (strcmp (long_options[option_index].name, "epsilonLikelihoodImprovement4BBL") == 0) { if (update_arg( (void *)&(args_info->epsilonLikelihoodImprovement4BBL_arg), &(args_info->epsilonLikelihoodImprovement4BBL_orig), &(args_info->epsilonLikelihoodImprovement4BBL_given), &(local_args_info.epsilonLikelihoodImprovement4BBL_given), optarg, 0, "0.01", ARG_FLOAT, check_ambiguity, override, 0, 0, "epsilonLikelihoodImprovement4BBL", '-', additional_error)) goto failure; } /* Number of BBL iterations in BBL+ALPHA optimization. */ else if (strcmp (long_options[option_index].name, "maxNumOfBBLIter") == 0) { if (update_arg( (void *)&(args_info->maxNumOfBBLIter_arg), &(args_info->maxNumOfBBLIter_orig), &(args_info->maxNumOfBBLIter_given), &(local_args_info.maxNumOfBBLIter_given), optarg, 0, "10", ARG_INT, check_ambiguity, override, 0, 0, "maxNumOfBBLIter", '-', additional_error)) goto failure; } /* version for use in consurf. */ else if (strcmp (long_options[option_index].name, "consurf") == 0) { if (update_arg((void *)&(args_info->consurf_flag), 0, &(args_info->consurf_given), &(local_args_info.consurf_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "consurf", '-', additional_error)) goto failure; } /* homogeneous rates MLE distance. */ else if (strcmp (long_options[option_index].name, "homogeneousRatesDTME") == 0) { if (args_info->DistanceTableEstimationMethod_group_counter && override) reset_group_DistanceTableEstimationMethod (args_info); args_info->DistanceTableEstimationMethod_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->homogeneousRatesDTME_given), &(local_args_info.homogeneousRatesDTME_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "homogeneousRatesDTME", '-', additional_error)) goto failure; } /* Gamma-ASRV with alpha optimized for each pair. (must give either --alpha or --optimizeAlpha). */ else if (strcmp (long_options[option_index].name, "pairwiseGammaDTME") == 0) { if (args_info->DistanceTableEstimationMethod_group_counter && override) reset_group_DistanceTableEstimationMethod (args_info); args_info->DistanceTableEstimationMethod_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->pairwiseGammaDTME_given), &(local_args_info.pairwiseGammaDTME_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "pairwiseGammaDTME", '-', additional_error)) goto failure; } /* Side information is the alpha parameter.(must use --optimizeAlpha; may give an initial alpha value in --alpha). */ else if (strcmp (long_options[option_index].name, "commonAlphaDTME") == 0) { if (args_info->DistanceTableEstimationMethod_group_counter && override) reset_group_DistanceTableEstimationMethod (args_info); args_info->DistanceTableEstimationMethod_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->commonAlphaDTME_given), &(local_args_info.commonAlphaDTME_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "commonAlphaDTME", '-', additional_error)) goto failure; } /* Side information is the ML rate for each site. */ else if (strcmp (long_options[option_index].name, "rate4siteDTME") == 0) { if (args_info->DistanceTableEstimationMethod_group_counter && override) reset_group_DistanceTableEstimationMethod (args_info); args_info->DistanceTableEstimationMethod_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->rate4siteDTME_given), &(local_args_info.rate4siteDTME_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "rate4siteDTME", '-', additional_error)) goto failure; } /* Side information is the posterior probabilities of the rates at each site. (must use --optimizeAlpha; may give an initial alpha value in --alpha). */ else if (strcmp (long_options[option_index].name, "posteriorDTME") == 0) { if (args_info->DistanceTableEstimationMethod_group_counter && override) reset_group_DistanceTableEstimationMethod (args_info); args_info->DistanceTableEstimationMethod_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->posteriorDTME_given), &(local_args_info.posteriorDTME_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "posteriorDTME", '-', additional_error)) goto failure; } /* Use bootstrap and set number of repeats. */ else if (strcmp (long_options[option_index].name, "BPrepeats") == 0) { if (update_arg( (void *)&(args_info->BPrepeats_arg), &(args_info->BPrepeats_orig), &(args_info->BPrepeats_given), &(local_args_info.BPrepeats_given), optarg, 0, 0, ARG_INT, check_ambiguity, override, 0, 0, "BPrepeats", '-', additional_error)) goto failure; } /* Use bootstrap and compute a Consensus tree. */ else if (strcmp (long_options[option_index].name, "BPconsensus") == 0) { if (update_arg( (void *)&(args_info->BPconsensus_arg), &(args_info->BPconsensus_orig), &(args_info->BPconsensus_given), &(local_args_info.BPconsensus_given), optarg, 0, 0, ARG_INT, check_ambiguity, override, 0, 0, "BPconsensus", '-', additional_error)) goto failure; } /* Use compute support for user provided tree. */ else if (strcmp (long_options[option_index].name, "BPonUserTree") == 0) { if (update_arg((void *)&(args_info->BPonUserTree_flag), 0, &(args_info->BPonUserTree_given), &(local_args_info.BPonUserTree_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "BPonUserTree", '-', additional_error)) goto failure; } /* Set External globalRate. */ else if (strcmp (long_options[option_index].name, "inputRate") == 0) { if (update_arg( (void *)&(args_info->inputRate_arg), &(args_info->inputRate_orig), &(args_info->inputRate_given), &(local_args_info.inputRate_given), optarg, 0, "1.0", ARG_FLOAT, check_ambiguity, override, 0, 0, "inputRate", '-', additional_error)) goto failure; } /* Use Laguerre approximation of Gamma - CURRENTLY NOT IMPLIMENTED. */ else if (strcmp (long_options[option_index].name, "laguerre") == 0) { if (update_arg((void *)&(args_info->laguerre_flag), 0, &(args_info->laguerre_given), &(local_args_info.laguerre_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "laguerre", '-', additional_error)) goto failure; } /* Use a Site-Specific Rate Variation model (SSRV). */ else if (strcmp (long_options[option_index].name, "ssrv") == 0) { if (update_arg((void *)&(args_info->ssrv_flag), 0, &(args_info->ssrv_given), &(local_args_info.ssrv_given), optarg, 0, 0, ARG_FLAG, check_ambiguity, override, 1, 0, "ssrv", '-', additional_error)) goto failure; } /* Set Nu for the SSRV model. */ else if (strcmp (long_options[option_index].name, "nu") == 0) { if (update_arg( (void *)&(args_info->nu_arg), &(args_info->nu_orig), &(args_info->nu_given), &(local_args_info.nu_given), optarg, 0, "1.0", ARG_FLOAT, check_ambiguity, override, 0, 0, "nu", '-', additional_error)) goto failure; } /* File with posterior distribution of the rate for each sequence site - for ASRV. */ else if (strcmp (long_options[option_index].name, "posteriorRates") == 0) { if (update_arg( (void *)&(args_info->posteriorRates_arg), &(args_info->posteriorRates_orig), &(args_info->posteriorRates_given), &(local_args_info.posteriorRates_given), optarg, 0, 0, ARG_STRING, check_ambiguity, override, 0, 0, "posteriorRates", '-', additional_error)) goto failure; } /* Use 'day' model. */ else if (strcmp (long_options[option_index].name, "day") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->day_given), &(local_args_info.day_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "day", '-', additional_error)) goto failure; } /* Use 'jtt' model (default). */ else if (strcmp (long_options[option_index].name, "jtt") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->jtt_given), &(local_args_info.jtt_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "jtt", '-', additional_error)) goto failure; } /* Use 'rev' model. */ else if (strcmp (long_options[option_index].name, "rev") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->rev_given), &(local_args_info.rev_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "rev", '-', additional_error)) goto failure; } /* Use 'wag' model. */ else if (strcmp (long_options[option_index].name, "wag") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->wag_given), &(local_args_info.wag_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "wag", '-', additional_error)) goto failure; } /* Use 'cprev' model. */ else if (strcmp (long_options[option_index].name, "cprev") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->cprev_given), &(local_args_info.cprev_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "cprev", '-', additional_error)) goto failure; } /* Use nucleic acid JC model. */ else if (strcmp (long_options[option_index].name, "nucjc") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->nucjc_given), &(local_args_info.nucjc_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "nucjc", '-', additional_error)) goto failure; } /* Use amino acid JC model. */ else if (strcmp (long_options[option_index].name, "aaJC") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->aaJC_given), &(local_args_info.aaJC_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "aaJC", '-', additional_error)) goto failure; } /* Use 'k2p' model. */ else if (strcmp (long_options[option_index].name, "k2p") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->k2p_given), &(local_args_info.k2p_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "k2p", '-', additional_error)) goto failure; } /* Use 'hky' model. */ else if (strcmp (long_options[option_index].name, "hky") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->hky_given), &(local_args_info.hky_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "hky", '-', additional_error)) goto failure; } /* Use 'tamura92' model. */ else if (strcmp (long_options[option_index].name, "tamura92") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->tamura92_given), &(local_args_info.tamura92_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "tamura92", '-', additional_error)) goto failure; } /* Use 'gtr' model (general reversible model). */ else if (strcmp (long_options[option_index].name, "gtr") == 0) { if (args_info->Model_group_counter && override) reset_group_Model (args_info); args_info->Model_group_counter += 1; if (update_arg( 0 , 0 , &(args_info->gtr_given), &(local_args_info.gtr_given), optarg, 0, 0, ARG_NO, check_ambiguity, override, 0, 0, "gtr", '-', additional_error)) goto failure; } /* Read replacement matrix from user input file. */ else if (strcmp (long_options[option_index].name, "modelfile") == 0) { if (update_arg( (void *)&(args_info->modelfile_arg), &(args_info->modelfile_orig), &(args_info->modelfile_given), &(local_args_info.modelfile_given), optarg, 0, 0, ARG_STRING, check_ambiguity, override, 0, 0, "modelfile", '-', 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->DistanceTableEstimationMethod_group_counter > 1) { fprintf (stderr, "%s: %d options of group DistanceTableEstimationMethod were given. At most one is required%s.\n", argv[0], args_info->DistanceTableEstimationMethod_group_counter, (additional_error ? additional_error : "")); error = 1; } if (args_info->Model_group_counter > 1) { fprintf (stderr, "%s: %d options of group Model were given. At most one is required%s.\n", argv[0], args_info->Model_group_counter, (additional_error ? additional_error : "")); error = 1; } cmdline_parser_release (&local_args_info); if ( error ) return (EXIT_FAILURE); return 0; failure: cmdline_parser_release (&local_args_info); return (EXIT_FAILURE); }