unsigned long distanceofshortstringsbytearray(unsigned long *eqsvector,
unsigned int alphasize,
const GtUchar *useq,
unsigned long ulen,
const GtUchar *vseq,
unsigned long vlen)
{
DECLARELOCALVARS;
const GtUchar *vptr;
initeqsvector(eqsvector,(unsigned long) alphasize,useq,ulen);
for (vptr = vseq; vptr < vseq + vlen; vptr++)
{
COMPUTENEWDIST(*vptr);
}
return distval;
}
static void pms_initdfsconstinfo(Limdfsconstinfo *mti,
unsigned int alphasize,
...)
/* Variable argument list is as follows:
unsigned int alphasize
const GtUchar *pattern,
unsigned long patternlength
*/
{
va_list ap;
const GtUchar *pattern;
va_start(ap,alphasize);
pattern = va_arg(ap, const GtUchar *);
mti->patternlength = va_arg(ap, unsigned long);
va_end(ap);
initeqsvector(mti->eqsvector,(unsigned long) alphasize,
pattern,mti->patternlength);
}
unsigned long distanceofshortstringsencseq(unsigned long *eqsvector,
unsigned int alphasize,
const GtUchar *useq,
unsigned long ulen,
const Encodedsequence *encseq,
Seqpos vstartpos,
Seqpos vlen)
{
DECLARELOCALVARS;
GtUchar cc;
Seqpos pos;
initeqsvector(eqsvector,(unsigned long) alphasize,useq,ulen);
for (pos = vstartpos; pos < vstartpos + vlen; pos++)
{
cc = getencodedchar(encseq,pos,Forwardmode);
COMPUTENEWDIST(cc);
}
return distval;
}
Definedunsignedlong forwardprefixmatch(const Encodedsequence *encseq,
unsigned int alphasize,
Seqpos startpos,
bool nowildcards,
unsigned long *eqsvector,
const GtUchar *useq,
unsigned long ulen,
unsigned long maxdistance)
{
DECLARELOCALVARS;
Seqpos pos, totallength = getencseqtotallength(encseq);
GtUchar cc;
Definedunsignedlong result;
initeqsvector(eqsvector,(unsigned long) alphasize,useq,ulen);
gt_assert(maxdistance > 0);
for (pos = startpos; /* Nothing */; pos++)
{
gt_assert(pos - startpos <= (Seqpos) (ulen + maxdistance));
cc = getencodedchar(encseq,pos,Forwardmode);
if (nowildcards && cc == (GtUchar) WILDCARD)
{
result.defined = false;
result.valueunsignedlong = 0;
return result;
}
COMPUTENEWDIST(cc);
if (distval <= maxdistance || pos == totallength-1)
{
break;
}
}
result.defined = true;
result.valueunsignedlong = (unsigned long) (pos - startpos + 1);
return result;
}