const char *gt_condenseq_description(const GtCondenseq *condenseq,
GtUword *desclen,
GtUword seqnum)
{
gt_assert(condenseq != NULL);
gt_assert(condenseq->orig_num_seq != 0);
gt_assert(seqnum < condenseq->orig_num_seq);
if (condenseq->id_len == GT_UNDEF_UWORD) {
GtUword this = gt_intset_get(condenseq->sdstab, seqnum), previous;
if (seqnum == 0) {
*desclen = this;
return condenseq->orig_ids;
}
previous = gt_intset_get(condenseq->sdstab, seqnum - 1);
*desclen = this - previous;
return condenseq->orig_ids + previous;
}
else {
const char *id = condenseq->orig_ids + seqnum * condenseq->id_len;
*desclen = condenseq->id_len;
while (id[*desclen - 1] == '\0')
(*desclen)--;
return condenseq->orig_ids + seqnum * condenseq->id_len;
}
}
static GtUword condenseq_next_sep(const GtCondenseq *ces, GtUword pos)
{
GtUword seqidx = gt_condenseq_pos2seqnum(ces, pos);
if (seqidx < ces->orig_num_seq - 1)
return gt_intset_get(ces->ssptab, seqidx);
return 0;
}
GtUword gt_condenseq_seqlength(const GtCondenseq *condenseq, GtUword seqnum)
{
GtUword start = 0;
if (seqnum != 0)
start = gt_intset_get(condenseq->ssptab, seqnum - 1) + 1;
return condenseq_seqlength_help(condenseq, seqnum, start);
}
GtUword gt_condenseq_seqstartpos(const GtCondenseq *condenseq, GtUword seqnum)
{
GtUword ret = 0;
if (seqnum != 0)
ret = gt_intset_get(condenseq->ssptab, seqnum - 1) + 1;
return ret;
}
static inline GtUword condenseq_seqlength_help(const GtCondenseq *condenseq,
GtUword seqnum,
GtUword seqstart)
{
GtUword end = condenseq->orig_length;
if (seqnum < condenseq->orig_num_seq - 1)
end = gt_intset_get(condenseq->ssptab, seqnum);
return end - seqstart;
}
