void gt_inplace_reversecomplement(GtUchar *seq,GtUword len)
{
GtUchar tmp, *frontptr, *backptr;
for (frontptr = seq, backptr = seq + len - 1;
frontptr < backptr; frontptr++, backptr--)
{
tmp = *frontptr;
*frontptr = GT_COMPLEMENTBASE(*backptr);
*backptr = GT_COMPLEMENTBASE(tmp);
}
}
static GtUchar gt_mmsearch_accessquery(const GtQueryrepresentation *queryrep,
GtUword pos)
{
GtUword abspos, cc;
gt_assert(queryrep != NULL);
gt_assert(pos < queryrep->seqlen);
abspos = queryrep->startpos + (queryrep->readmode == GT_READMODE_FORWARD
? pos
: GT_REVERSEPOS(queryrep->seqlen,pos));
if (queryrep->sequence != NULL)
{
cc = queryrep->sequence[abspos];
} else
{
gt_assert(queryrep->encseq != NULL);
cc = gt_encseq_get_encoded_char(queryrep->encseq,abspos,
GT_READMODE_FORWARD);
}
if (GT_ISDIRCOMPLEMENT(queryrep->readmode))
{
if (ISSPECIAL(cc))
{
return cc;
}
return GT_COMPLEMENTBASE(cc);
} else
{
return cc;
}
}
void bare_encseq_convert(GtBareEncseq *bare_encseq,bool forward,bool direct)
{
GtUchar *leftptr, *rightptr;
if (forward)
{
gt_assert(!direct);
for (leftptr = bare_encseq->sequence;
leftptr < bare_encseq->sequence + bare_encseq->totallength;
leftptr++)
{
if (ISNOTSPECIAL(*leftptr))
{
*leftptr = GT_COMPLEMENTBASE(*leftptr);
}
}
} else
{
if (direct)
{
for (leftptr = bare_encseq->sequence,
rightptr = bare_encseq->sequence + bare_encseq->totallength - 1;
leftptr < rightptr; leftptr++, rightptr--)
{
GtUchar tmp = *leftptr;
*leftptr = *rightptr;
*rightptr = tmp;
}
} else
{
for (leftptr = bare_encseq->sequence,
rightptr = bare_encseq->sequence + bare_encseq->totallength - 1;
leftptr <= rightptr; leftptr++, rightptr--)
{
GtUchar tmp = *leftptr;
*leftptr = ISSPECIAL(*rightptr) ? *rightptr
: GT_COMPLEMENTBASE(*rightptr);
*rightptr = ISSPECIAL(tmp) ? tmp
: GT_COMPLEMENTBASE(tmp);
}
}
}
}
void gt_copy_reversecomplement(GtUchar *dest,const GtUchar *src,
GtUword len)
{
GtUchar *destptr;
const GtUchar *srcptr;
for (destptr = dest, srcptr = src + len - 1;
destptr < dest + len; destptr++, srcptr--)
{
*destptr = GT_COMPLEMENTBASE(*srcptr);
}
}
