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#include "libc.h"
#include "types.h"
#include "misc.h"
#include "args.h"
#include "seq.h"
#include "dna.h"
#include "discrim.h"
#ifndef __lint
static const char rcsid[] =
"$Id: discrim.c,v 1.2 2000/06/05 22:48:19 florea Exp $";
#endif
/* DNA characters */
const uchar dchars[] = "ABCDGHKMNRSTVWXY";
static int is_dchar(int ch);
bool is_DNA(uchar *s, int len)
{
int ACGT, i;
for (ACGT = i = 0; i < len; ++i)
if (strchr("ACGTNXacgtnx", s[i]))
++ACGT;
if (10*ACGT < 9*len) /* ACGT < 90% of len */
return 0;
for (i = 0; i < len; ++i)
if (!is_dchar(s[i])) {
fatalf("Illegal character '%c' in sequence file.\n", s[i]);
exit(1);
}
return 1;
}
static int is_dchar(int ch)
{
return !!strchr((const char*)dchars, toupper(ch));
}
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