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#include "configuration.h"
#include <iostream>
#include <sstream>
#include <string>
#include <cstdlib> // std::exit()
#include <cassert>
#include <getopt.h>
using namespace std;
configuration::configuration(int argc, char **argv)
: prog(argv[0]), listfile(""), tmpfile(""), inputformat(input_reader::input_fasta),
minlength(9), maxlength(100), minfreq(1), minsupport(2), maxsupport(~0u),
verbose(false), debug(false), good(false)
{
assert (argc > 0);
good = parse(argc, argv);
}
int atoi_min(char const *value, int min, char const *parameter, char const *name)
{
istringstream iss(value);
int i;
char c;
if (!(iss >> i) || iss.get(c))
{
cerr << "error: argument of " << parameter << " must be of type <int>, and greater than or equal to " << min << endl
<< "Check " << name << " --help' for more information." << endl;
exit(1);
}
if (i < min)
{
cerr << "error: argument of " << parameter << " must be greater than or equal to " << min << endl
<< "Check `" << name << " --help' for more information." << endl;
exit(1);
}
return i;
}
void configuration::print_short_usage() const
{
cerr << "See " << prog << " --help for more information." << endl;
exit(1);
}
void configuration::print_usage() const
{
cerr << "usage: " << prog << " -l <file> -t <file> [options]" << endl
<< " -l,--list <file> Text file that lists all input files as whitespace-separated pairs "<< endl
<< " <data-name> <data-filename>" << endl
<< " where <data-name> is unique identifier (without whitespace)" << endl
<< " and <data-filename> is full path to each input file." << endl
<< " Default data file format is FASTA (uncompressed)." << endl
<< " -t,--tmp <file> Store temporary index data" << endl
<< "options:" << endl
<< " -m,--min <int> Minimum length to report (default 9)" << endl
<< " -M,--max <int> Maximum length to report (default 100)" << endl
<< " -f,--freq <int> Minimum frequency per input file to report (default 1)" << endl
<< " -s,--minsupp <int> Minimum number of input files with support to report (default 2)" << endl
<< " -S,--maxsupp <int> Maximum number of input files with support to report (default inf)" << endl
<< " -v,--verbose Verbose output" << endl;
exit(1);
}
bool configuration::parse(int argc, char **argv)
{
static struct option long_options[] =
{
{"list", required_argument, 0, 'l'},
{"tmp", required_argument, 0, 't'},
{"min", required_argument, 0, 'm'},
{"max", required_argument, 0, 'M'},
{"freq", required_argument, 0, 'f'},
{"minsupp", required_argument, 0, 's'},
{"maxsupp", required_argument, 0, 'S'},
{"verbose", no_argument, 0, 'v'},
{"debug", no_argument, 0, 'D'},
{"help", no_argument, 0, 'h'},
{0, 0, 0, 0}
};
int option_index = 0;
int c;
while ((c = getopt_long(argc, argv, "l:t:m:M:f:s:S:vDh",
long_options, &option_index)) != -1)
{
switch(c)
{
case 'l':
listfile = string(optarg); break;
case 't':
tmpfile = string(optarg); break;
case 'm':
minlength = atoi_min(optarg, 1, "-m,--min", argv[0]); break;
case 'M':
maxlength = atoi_min(optarg, 1, "-M,--max", argv[0]); break;
case 'f':
minfreq = atoi_min(optarg, 1, "-f,--freq", argv[0]); break;
case 's':
minsupport = atoi_min(optarg, 1, "-s,--minsupp", argv[0]); break;
case 'S':
maxsupport = atoi_min(optarg, 1, "-S,--maxsupp", argv[0]); break;
case 'v':
verbose = true; break;
case 'D':
debug = true; break;
case 'h':
print_usage(); return 1;
default:
cerr << "error: invalid parameter!" << endl;
return false;
}
}
if (listfile == "")
{
cerr << "error: -l,--list is a required parameter" << endl;
return false;
}
if (tmpfile == "")
{
cerr << "error: -t,--tmp is a required parameter" << endl;
return false;
}
if (minlength > maxlength)
{
cerr << "error: -m,--min must be smaller than or equal to -M,--max" << endl;
return false;
}
if (minsupport > maxsupport)
{
cerr << "error: -s,--minsupp must be smaller than or equal to -S,--maxsupp" << endl;
return false;
}
return true;
}
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