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http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 05:10:26 +08:00
373 lines
12 KiB
C
373 lines
12 KiB
C
/*
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File autogenerated by gengetopt version 2.13
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generated with the following command:
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gengetopt -ibootstrap_prog.ggo -Fbootstrap_prog_cmdline -f bootstrap_prog_cmdline_parser --arg-struct-name=bootstrap_prog_args_info
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The developers of gengetopt consider the fixed text that goes in all
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gengetopt output files to be in the public domain:
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we make no copyright claims on it.
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*/
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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>
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#include <stdlib.h>
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#include <string.h>
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#include "getopt.h"
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#include "bootstrap_prog_cmdline.h"
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static
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void clear_given (struct bootstrap_prog_args_info *args_info);
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static
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void clear_args (struct bootstrap_prog_args_info *args_info);
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static int
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bootstrap_prog_cmdline_parser_internal (int argc, char * const *argv, struct bootstrap_prog_args_info *args_info, int override, int initialize, int check_required, const char *additional_error);
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static int
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bootstrap_prog_cmdline_parser_required2 (struct bootstrap_prog_args_info *args_info, const char *prog_name, const char *additional_error);
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static char *
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gengetopt_strdup (const char *s);
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static
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void clear_given (struct bootstrap_prog_args_info *args_info)
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{
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args_info->help_given = 0 ;
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args_info->version_given = 0 ;
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args_info->treesList_given = 0 ;
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args_info->reftree_given = 0 ;
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args_info->outputfile_given = 0 ;
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args_info->Logfile_given = 0 ;
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args_info->verbose_given = 0 ;
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args_info->ConsensusLevel_given = 0 ;
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args_info->noBranchLen_given = 0 ;
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}
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static
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void clear_args (struct bootstrap_prog_args_info *args_info)
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{
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args_info->treesList_arg = NULL;
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args_info->reftree_arg = NULL;
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args_info->outputfile_arg = gengetopt_strdup ("-");
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args_info->Logfile_arg = gengetopt_strdup ("-");
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args_info->verbose_arg = 0 ;
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args_info->ConsensusLevel_arg = 0.5 ;
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args_info->noBranchLen_flag = 0;
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}
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void
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bootstrap_prog_cmdline_parser_print_version (void)
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{
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printf ("%s %s\n", BOOTSTRAP_PROG_CMDLINE_PARSER_PACKAGE, BOOTSTRAP_PROG_CMDLINE_PARSER_VERSION);
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}
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void
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bootstrap_prog_cmdline_parser_print_help (void)
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{
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bootstrap_prog_cmdline_parser_print_version ();
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printf("\n%s\n", "compute bootstrap values and consensus trees from a list of trees");
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printf("\nUsage: bootstrap [OPTIONS]...\n\n");
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printf("%s\n"," -h, --help Print help and exit");
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printf("%s\n"," -V, --version Print version and exit");
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printf("%s\n"," -t, --treesList=STRING filename of list of input trees");
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printf("%s\n"," -r, --reftree=STRING Refremce Tree file name");
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printf("%s\n"," -o, --outputfile=STRING Output tree file (default=`-')");
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printf("%s\n"," -l, --Logfile=STRING Log file output name (default=`-')");
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printf("%s\n"," -v, --verbose=INT Log report level (verbose) (default=`0')");
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printf("%s\n"," -c, --ConsensusLevel=FLOAT use only branches with sport above this \n (default=`0.5')");
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printf("%s\n"," -b, --noBranchLen Do not output branch lengths in output tree \n (default=off)");
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}
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void
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bootstrap_prog_cmdline_parser_init (struct bootstrap_prog_args_info *args_info)
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{
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clear_given (args_info);
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clear_args (args_info);
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}
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void
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bootstrap_prog_cmdline_parser_free (struct bootstrap_prog_args_info *args_info)
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{
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if (args_info->treesList_arg)
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{
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free (args_info->treesList_arg); /* free previous argument */
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args_info->treesList_arg = 0;
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}
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if (args_info->reftree_arg)
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{
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free (args_info->reftree_arg); /* free previous argument */
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args_info->reftree_arg = 0;
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}
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if (args_info->outputfile_arg)
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{
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free (args_info->outputfile_arg); /* free previous argument */
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args_info->outputfile_arg = 0;
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}
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if (args_info->Logfile_arg)
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{
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free (args_info->Logfile_arg); /* free previous argument */
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args_info->Logfile_arg = 0;
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}
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clear_given (args_info);
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}
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/* gengetopt_strdup() */
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/* strdup.c replacement of strdup, which is not standard */
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char *
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gengetopt_strdup (const char *s)
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{
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char *result = NULL;
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if (!s)
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return result;
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result = (char*)malloc(strlen(s) + 1);
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if (result == (char*)0)
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return (char*)0;
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strcpy(result, s);
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return result;
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}
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int
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bootstrap_prog_cmdline_parser (int argc, char * const *argv, struct bootstrap_prog_args_info *args_info)
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{
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return bootstrap_prog_cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
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}
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int
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bootstrap_prog_cmdline_parser2 (int argc, char * const *argv, struct bootstrap_prog_args_info *args_info, int override, int initialize, int check_required)
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{
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int result;
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result = bootstrap_prog_cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
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if (result == EXIT_FAILURE)
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{
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bootstrap_prog_cmdline_parser_free (args_info);
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exit (EXIT_FAILURE);
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}
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return result;
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}
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int
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bootstrap_prog_cmdline_parser_required (struct bootstrap_prog_args_info *args_info, const char *prog_name)
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{
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int result = EXIT_SUCCESS;
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if (bootstrap_prog_cmdline_parser_required2(args_info, prog_name, NULL) > 0)
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result = EXIT_FAILURE;
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if (result == EXIT_FAILURE)
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{
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bootstrap_prog_cmdline_parser_free (args_info);
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exit (EXIT_FAILURE);
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}
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return result;
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}
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int
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bootstrap_prog_cmdline_parser_required2 (struct bootstrap_prog_args_info *args_info, const char *prog_name, const char *additional_error)
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{
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int error = 0;
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if (! args_info->treesList_given)
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{
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fprintf (stderr, "%s: '--treesList' ('-t') option required%s\n", prog_name, (additional_error ? additional_error : ""));
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error = 1;
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}
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return error;
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}
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int
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bootstrap_prog_cmdline_parser_internal (int argc, char * const *argv, struct bootstrap_prog_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
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{
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int c; /* Character of the parsed option. */
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int error = 0;
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struct bootstrap_prog_args_info local_args_info;
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if (initialize)
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bootstrap_prog_cmdline_parser_init (args_info);
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bootstrap_prog_cmdline_parser_init (&local_args_info);
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optarg = 0;
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optind = 1;
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opterr = 1;
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optopt = '?';
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while (1)
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{
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int option_index = 0;
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char *stop_char;
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static struct option long_options[] = {
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{ "help", 0, NULL, 'h' },
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{ "version", 0, NULL, 'V' },
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{ "treesList", 1, NULL, 't' },
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{ "reftree", 1, NULL, 'r' },
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{ "outputfile", 1, NULL, 'o' },
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{ "Logfile", 1, NULL, 'l' },
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{ "verbose", 1, NULL, 'v' },
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{ "ConsensusLevel", 1, NULL, 'c' },
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{ "noBranchLen", 0, NULL, 'b' },
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{ NULL, 0, NULL, 0 }
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};
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stop_char = 0;
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c = getopt_long (argc, argv, "hVt:r:o:l:v:c:b", long_options, &option_index);
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if (c == -1) break; /* Exit from `while (1)' loop. */
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switch (c)
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{
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case 'h': /* Print help and exit. */
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bootstrap_prog_cmdline_parser_print_help ();
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exit (EXIT_SUCCESS);
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case 'V': /* Print version and exit. */
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bootstrap_prog_cmdline_parser_print_version ();
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exit (EXIT_SUCCESS);
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case 't': /* filename of list of input trees. */
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if (local_args_info.treesList_given)
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{
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fprintf (stderr, "%s: `--treesList' (`-t') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
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goto failure;
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}
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if (args_info->treesList_given && ! override)
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continue;
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local_args_info.treesList_given = 1;
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args_info->treesList_given = 1;
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if (args_info->treesList_arg)
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free (args_info->treesList_arg); /* free previous string */
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args_info->treesList_arg = gengetopt_strdup (optarg);
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break;
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case 'r': /* Refremce Tree file name. */
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if (local_args_info.reftree_given)
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{
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fprintf (stderr, "%s: `--reftree' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
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goto failure;
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}
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if (args_info->reftree_given && ! override)
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continue;
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local_args_info.reftree_given = 1;
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args_info->reftree_given = 1;
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if (args_info->reftree_arg)
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free (args_info->reftree_arg); /* free previous string */
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args_info->reftree_arg = gengetopt_strdup (optarg);
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break;
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case 'o': /* Output tree file. */
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if (local_args_info.outputfile_given)
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{
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fprintf (stderr, "%s: `--outputfile' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
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goto failure;
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}
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if (args_info->outputfile_given && ! override)
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continue;
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local_args_info.outputfile_given = 1;
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args_info->outputfile_given = 1;
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if (args_info->outputfile_arg)
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free (args_info->outputfile_arg); /* free previous string */
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args_info->outputfile_arg = gengetopt_strdup (optarg);
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break;
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case 'l': /* Log file output name. */
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if (local_args_info.Logfile_given)
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{
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fprintf (stderr, "%s: `--Logfile' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
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goto failure;
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}
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if (args_info->Logfile_given && ! override)
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continue;
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local_args_info.Logfile_given = 1;
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args_info->Logfile_given = 1;
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if (args_info->Logfile_arg)
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free (args_info->Logfile_arg); /* free previous string */
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args_info->Logfile_arg = gengetopt_strdup (optarg);
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break;
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case 'v': /* Log report level (verbose). */
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if (local_args_info.verbose_given)
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{
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fprintf (stderr, "%s: `--verbose' (`-v') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
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goto failure;
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}
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if (args_info->verbose_given && ! override)
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continue;
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local_args_info.verbose_given = 1;
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args_info->verbose_given = 1;
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args_info->verbose_arg = strtol (optarg,&stop_char,0);
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break;
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case 'c': /* use only branches with sport above this. */
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if (local_args_info.ConsensusLevel_given)
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{
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fprintf (stderr, "%s: `--ConsensusLevel' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
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goto failure;
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}
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if (args_info->ConsensusLevel_given && ! override)
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continue;
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local_args_info.ConsensusLevel_given = 1;
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args_info->ConsensusLevel_given = 1;
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args_info->ConsensusLevel_arg = (float)strtod (optarg, NULL);
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break;
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case 'b': /* Do not output branch lengths in output tree. */
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if (local_args_info.noBranchLen_given)
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{
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fprintf (stderr, "%s: `--noBranchLen' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
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goto failure;
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}
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if (args_info->noBranchLen_given && ! override)
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continue;
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local_args_info.noBranchLen_given = 1;
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args_info->noBranchLen_given = 1;
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args_info->noBranchLen_flag = !(args_info->noBranchLen_flag);
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break;
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case 0: /* Long option with no short option */
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case '?': /* Invalid option. */
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/* `getopt_long' already printed an error message. */
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goto failure;
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default: /* bug: option not considered. */
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fprintf (stderr, "%s: option unknown: %c%s\n", BOOTSTRAP_PROG_CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
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abort ();
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} /* switch */
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} /* while */
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if (check_required)
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{
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error += bootstrap_prog_cmdline_parser_required2 (args_info, argv[0], additional_error);
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}
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bootstrap_prog_cmdline_parser_free (&local_args_info);
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if ( error )
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return (EXIT_FAILURE);
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return 0;
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failure:
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bootstrap_prog_cmdline_parser_free (&local_args_info);
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return (EXIT_FAILURE);
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}
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