char *
revcomp(char *comp, char *seq)
{
long bases;
char *bckp, *fwdp;
int idx;
long pos;
int c;
if (comp == NULL) return NULL;
if (seq == NULL) return NULL;
bases = strlen(seq);
fwdp = comp;
bckp = seq + bases -1;
for (pos = 0; pos < bases; pos++)
{
c = *bckp;
c = sre_toupper(c);
for (idx = 0; c != iupac[idx].sym && idx < IUPACSYMNUM; idx++);
if (idx == IUPACSYMNUM)
{
Warn("Can't reverse complement an %c, pal. Using N.", c);
*fwdp = 'N';
}
else
*fwdp = iupac[idx].symcomp;
if (islower((int) *bckp)) *fwdp = sre_tolower((int) *fwdp);
fwdp++;
bckp--;
}
*fwdp = '\0';
return comp;
}
int
GCGchecksum(char *seq, int seqlen)
{
int check = 0, count = 0, i;
for (i = 0; i < seqlen; i++) {
count++;
check += count * sre_toupper((int) seq[i]);
if (count == 57) count = 0;
}
return (check % 10000);
}
/* Function: GCGMultchecksum()
*
* Purpose: Simple modification of GCGchecksum(),
* to create a checksum for multiple sequences.
* Gaps count.
*
* Args: seqs - sequences to be checksummed
* nseq - number of sequences
*
* Return: the checksum, a number between 0 and 9999
*/
int
GCGMultchecksum(char **seqs, int nseq)
{
int check = 0;
int count = 0;
int idx;
char *sptr;
for (idx = 0; idx < nseq; idx++)
for (sptr = seqs[idx]; *sptr; sptr++)
{
count++;
check += count * sre_toupper((int) *sptr);
if (count == 57) count = 0;
}
return (check % 10000);
}
/* Function: Seqtype()
*
* Purpose: Returns a (very good) guess about type of sequence:
* kDNA, kRNA, kAmino, or kOtherSeq.
*
* Modified from, and replaces, Gilbert getseqtype().
*/
int
Seqtype(char *seq)
{
int saw; /* how many non-gap characters I saw */
char c;
int po = 0; /* count of protein-only */
int nt = 0; /* count of t's */
int nu = 0; /* count of u's */
int na = 0; /* count of nucleotides */
int aa = 0; /* count of amino acids */
int no = 0; /* count of others */
/* Look at the first 300 non-gap characters
*/
for (saw = 0; *seq != '\0' && saw < 300; seq++)
{
c = sre_toupper((int) *seq);
if (! isgap(c))
{
if (strchr(protonly, c)) po++;
else if (strchr(primenuc,c)) {
na++;
if (c == 'T') nt++;
else if (c == 'U') nu++;
}
else if (strchr(aminos,c)) aa++;
else if (isalpha(c)) no++;
saw++;
}
}
if (no > 0) return kOtherSeq;
else if (po > 0) return kAmino;
else if (na > aa) {
if (nu > nt) return kRNA;
else return kDNA;
}
else return kAmino;
}
