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/*****************************************************************
* @LICENSE@
*****************************************************************/
/* seqencode.c
*
* Routines for creating and manipulating encoded sequence strings.
* CVS $Id: seqencode.c,v 1.4 2003/04/14 16:00:16 eddy Exp $
*/
#include "squidconf.h"
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include "squid.h"
/* seqcmp()
returns 0 if s1 == s2
mismatch number otherwise */
int
seqcmp(char *s1, char *s2, int allow)
{
int mmat = 0;
while ((*s1 != NTEND) && (*s2 != NTEND) && (mmat <= allow))
{
if (!(ntmatch(*s1, *s2)))
mmat++;;
s1++;
s2++;
}
while ((*s1++ != NTEND) && (mmat <= allow))
mmat++;
return(mmat);
}
/* seqncmp()
same as seqcmp but it looks at,
at most, n positions */
int
seqncmp(char *s1, char *s2, int n, int allow)
{
int mmat = 0;
while ((*s2 != NTEND) &&
(n-- != 0))
{
if ((!(ntmatch(*s1, *s2))) &&
(++mmat > allow))
return(mmat);
s1++;
s2++;
}
while ((n-- != 0) && (*s1++ != NTEND) && (mmat <= allow))
mmat++;
return (mmat);
}
/* seqencode()
given a character text string str (A,C,G,T),
convert to an encoded seq string;
return 1 for success, 0 if fail */
int
seqencode(char *codeseq, /* pre-allocated space for answer */
char *str) /* character string to convert */
{
char *ptr;
int idx;
ptr = codeseq;
while (*str != '\0')
{
if (islower((int) (*str))) *str = (char) toupper((int) (*str));
for (idx = 0; *str != iupac[idx].sym && idx <= IUPACSYMNUM; idx++)
;
if (idx > IUPACSYMNUM)
{
*ptr = (char) NTEND;
return 0;
}
else
*ptr = iupac[idx].code;
ptr++;
str++;
}
*ptr = NTEND;
return 1;
}
int
coded_revcomp(char *comp, char *seq)
{
long bases;
char *bckp, *fwdp;
int idx;
long pos;
bases = strlen(seq);
fwdp = comp;
bckp = seq + bases -1;
for (pos = 0; pos < bases; pos++)
{
for (idx = 0; *bckp != iupac[idx].code && idx < IUPACSYMNUM; idx++);
if (idx > IUPACSYMNUM)
{
*fwdp = NTEND;
return 0;
}
else
*fwdp = iupac[idx].comp;
fwdp++;
bckp--;
}
*fwdp = NTEND;
return(1);
}
int
seqdecode(char *str, char *codeseq)
{
int idx;
int pos;
pos = 0;
while (*codeseq != NTEND)
{
for (idx = 0; *codeseq != iupac[idx].code && idx < IUPACSYMNUM; idx++)
;
if (idx > IUPACSYMNUM)
{
str[pos] = 'X';
return 0;
}
else
str[pos] = iupac[idx].sym;
codeseq++;
pos++;
}
str[pos] = '\0';
return 1;
}
int
seqndecode(
char *str, /* pre-allocated string to write into */
char *codeseq, /* sequence to decode */
int n) /* how many bases to decode */
{
int idx;
int pos = 0;
while (--n >= 0)
{
for (idx = 0; *codeseq != iupac[idx].code && idx < IUPACSYMNUM; idx++);
if (idx > IUPACSYMNUM)
{
str[pos] = 'X';
return 0;
}
else
str[pos] = iupac[idx].sym;
codeseq++;
pos++;
}
str[pos] = '\0';
return 1;
}
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