static void gt_match_iterator_sw_free(GtMatchIterator *mi)
{
GtMatchIteratorSW *mis;
if (!mi) return;
mis = gt_match_iterator_sw_cast(mi);
gt_encseq_delete(mis->pvt->es1);
gt_encseq_delete(mis->pvt->es2);
gt_score_function_delete(mis->pvt->sf);
gt_free(mis->pvt);
}
GtPBSResults* gt_pbs_find(const char *seq,
const char *rev_seq,
GtLTRElement *element,
GtPBSOptions *o,
GtError *err)
{
GtSeq *seq_forward, *seq_rev;
GtPBSResults *results;
unsigned long j;
GtAlignment *ali;
GtAlphabet *a = gt_alphabet_new_dna();
GtScoreFunction *sf = gt_dna_scorefunc_new(a,
o->ali_score_match,
o->ali_score_mismatch,
o->ali_score_insertion,
o->ali_score_deletion);
gt_assert(seq && rev_seq && sf && a && element);
results = gt_pbs_results_new(element, o);
seq_forward = gt_seq_new(seq + (gt_ltrelement_leftltrlen(element))
- (o->radius),
2*o->radius + 1,
a);
seq_rev = gt_seq_new(rev_seq + (gt_ltrelement_rightltrlen(element))
- (o->radius),
2*o->radius + 1,
a);
for (j=0;j<gt_bioseq_number_of_sequences(o->trna_lib);j++)
{
GtSeq *trna_seq, *trna_from3;
char *trna_from3_full;
unsigned long trna_seqlen;
trna_seq = gt_bioseq_get_seq(o->trna_lib, j);
trna_seqlen = gt_seq_length(trna_seq);
trna_from3_full = gt_calloc(trna_seqlen, sizeof (char));
memcpy(trna_from3_full, gt_seq_get_orig(trna_seq),
sizeof (char)*trna_seqlen);
(void) gt_reverse_complement(trna_from3_full, trna_seqlen, err);
trna_from3 = gt_seq_new_own(trna_from3_full, trna_seqlen, a);
ali = gt_swalign(seq_forward, trna_from3, sf);
gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
gt_seq_get_description(trna_seq), GT_STRAND_FORWARD,
results);
gt_alignment_delete(ali);
ali = gt_swalign(seq_rev, trna_from3, sf);
gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
gt_seq_get_description(trna_seq), GT_STRAND_REVERSE,
results);
gt_alignment_delete(ali);
gt_seq_delete(trna_from3);
}
gt_seq_delete(seq_forward);
gt_seq_delete(seq_rev);
gt_score_function_delete(sf);
gt_alphabet_delete(a);
gt_array_sort(results->hits, gt_pbs_hit_compare);
return results;
}
