void gt_alignment_set_multieop_list(GtAlignment *alignment, GtMultieoplist *eoplist) { gt_assert(alignment != NULL && eoplist != NULL); gt_multieoplist_delete(alignment->eops); alignment->eops = gt_multieoplist_ref(eoplist); alignment->alilen = gt_multieoplist_get_length(eoplist); }
void gt_alignment_delete(GtAlignment *alignment) { if (!alignment) return; gt_multieoplist_delete(alignment->eops); gt_free(alignment); }
int gt_xdrop_unit_test(GT_UNUSED GtError *err) { int had_err = 0, i, j, s; const GtUchar *strings[GT_XDROP_NUM_OF_TESTS] = {(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCCAAAGGGTTTCCCTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTTTTTGGGGCCCCAAAATTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTNNNNTTTTGGGGCCCCAAAATTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCGCAAAGGGTTTCCCTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCAAAGGGTTTCCCCTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCTCAAAGGGTTTCCTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAACAGATCACCCGCTTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAACGGGTTTCTCAAAGGGTTCCCTTTTTTTTTTTTTTT"}; GtUword lengths[GT_XDROP_NUM_OF_TESTS] = {54UL, 46UL, 50UL, 54UL, 54UL, 54UL, 46UL, 54UL}, eval_scores[GT_XDROP_NUM_OF_TESTS * GT_XDROP_NUM_OF_TESTS * GT_XDROP_NUM_OF_TESTS] = {0, 13UL, 0, 1UL, 4UL, 1UL, 0, 7UL, 13UL, 0, 0, 14UL, 15UL, 14UL, 0, 15UL, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 14UL, 0, 0, 1UL, 2UL, 0, 1UL, 4UL, 15UL, 0, 1UL, 0, 8UL, 0, 1UL, 1UL, 14UL, 0, 2UL, 8UL, 0, 0, 4UL, 0, 0, 0, 0, 0, 0, 0, 0, 7UL, 15UL, 0, 1UL, 1UL, 4UL, 0, 0, 0, 13UL, 0, 1UL, 4UL, 5UL, 14UL, 7UL, 13UL, 0, 0, 14UL, 15UL, 14UL, 12UL, 15UL, 0, 0, 0, 20UL, 0, 19UL, 17UL, 0, 1UL, 14UL, 20UL, 0, 5UL, 6UL, 15UL, 8UL, 4UL, 15UL, 0, 5UL, 0, 8UL, 15UL, 10UL, 5UL, 14UL, 19UL, 6UL, 8UL, 0, 14UL, 4UL, 14UL, 12UL, 17UL, 15UL, 15UL, 14UL, 0, 14UL, 7UL, 15UL, 0, 8UL, 10UL, 4UL, 14UL, 0, 0, 13UL, 19UL, 1UL, 2UL, 2UL, 13UL, 3UL, 13UL, 0, 9UL, 14UL, 14UL, 13UL, 12UL, 14UL, 17UL, 4UL, 0, 18UL, 19UL, 16UL, 16UL, 18UL, 1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL, 2UL, 14UL, 18UL, 2UL, 0, 4UL, 13UL, 4UL, 2UL, 13UL, 19UL, 3UL, 4UL, 0, 13UL, 3UL, 14UL, 12UL, 17UL, 13UL, 13UL, 14UL, 0, 14UL, 3UL, 14UL, 18UL, 3UL, 4UL, 3UL, 13UL, 0, 0, 13UL, 17UL, 1UL, 2UL, 2UL, 14UL, 3UL, 13UL, 0, 4UL, 14UL, 15UL, 13UL, 12UL, 14UL, 19UL, 9UL, 0, 18UL, 18UL, 19UL, 17UL, 18UL, 1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL, 2UL, 14UL, 19UL, 2UL, 0, 4UL, 13UL, 4UL, 2UL, 13UL, 16UL, 3UL, 4UL, 0, 14UL, 3UL, 13UL, 12UL, 16UL, 13UL, 13UL, 13UL, 0, 13UL, 3UL, 14UL, 18UL, 3UL, 4UL, 3UL, 14UL, 0, 0, 0, 0, 1UL, 1UL, 1UL, 0, 1UL, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 0, 1UL, 0, 0, 1UL, 1UL, 0, 0, 1UL, 0, 0, 0, 1UL, 1UL, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 1UL, 1UL, 1UL, 0, 0, 0, 0, 0, 1UL, 1UL, 1UL, 0, 1UL, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 0, 1UL, 2UL, 0, 1UL, 1UL, 0, 0, 1UL, 0, 0, 0, 1UL, 1UL, 0, 0, 2UL, 0, 0, 0, 1UL, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 1UL, 1UL, 1UL, 0, 0, 0, 13UL, 17UL, 1UL, 2UL, 2UL, 13UL, 3UL, 13UL, 0, 4UL, 14UL, 14UL, 13UL, 12UL, 14UL, 17UL, 4UL, 0, 18UL, 19UL, 16UL, 16UL, 19UL, 1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL, 2UL, 14UL, 19UL, 2UL, 0, 4UL, 13UL, 4UL, 2UL, 13UL, 16UL, 3UL, 4UL, 0, 13UL, 3UL, 13UL, 12UL, 16UL, 13UL, 13UL, 13UL, 0, 13UL, 3UL, 14UL, 19UL, 3UL, 4UL, 3UL, 13UL, 0, 0, 13UL, 0, 1UL, 2UL, 2UL, 5UL, 3UL, 13UL, 0, 0, 14UL, 15UL, 13UL, 0, 14UL, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 14UL, 0, 0, 2UL, 3UL, 5UL, 3UL, 2UL, 15UL, 0, 2UL, 0, 4UL, 5UL, 4UL, 2UL, 13UL, 0, 3UL, 4UL, 0, 6UL, 3UL, 5UL, 0, 0, 5UL, 5UL, 6UL, 0, 5UL, 3UL, 14UL, 0, 3UL, 4UL, 3UL, 5UL, 0}; GtSeqabstract *useq, *vseq; GtXdropArbitraryscores score[GT_XDROP_NUM_OF_TESTS] = {{2, -2, -2, -2}, {2, -1, -1, -1}, {2, -1, -5, -2}, {2, -1, -2, -5}, {3, -2, -3, -3}, {3, -1, -1, -1}, {4, -1, -3, -3}, {10, -3, -8, -8}}; GtXdropresources *resources; GtXdropbest best; GtXdropscore dropscore = (GtXdropscore) 12; GtMultieoplist *edit_ops = NULL; GtAlignment *alignment; bool rightextension = true; gt_error_check(err); for (s = 0; s < GT_XDROP_NUM_OF_TESTS; ++s) { resources = gt_xdrop_resources_new(&score[s]); for (i = 0; i < GT_XDROP_NUM_OF_TESTS && !had_err; ++i) { for (j = 0; j < GT_XDROP_NUM_OF_TESTS; ++j) { useq = gt_seqabstract_new_gtuchar(rightextension,GT_READMODE_FORWARD, strings[i], lengths[i], 0,lengths[i]); vseq = gt_seqabstract_new_gtuchar(rightextension, GT_READMODE_FORWARD, strings[j], lengths[j], 0,lengths[j]); gt_evalxdroparbitscoresextend(true, &best, resources, useq, vseq, dropscore); edit_ops = gt_xdrop_backtrack(resources, &best); gt_ensure(edit_ops != NULL); alignment = gt_alignment_new_with_seqs(strings[i], best.ivalue, strings[j], best.jvalue); gt_alignment_set_multieop_list(alignment, edit_ops); gt_ensure(eval_scores[s*64+i*8+j] == gt_alignment_eval(alignment)); gt_multieoplist_delete(edit_ops); gt_alignment_delete(alignment); if (i == j) { gt_evalxdroparbitscoresextend(false, &best, resources, useq, vseq, dropscore); edit_ops = gt_xdrop_backtrack(resources, &best); alignment = gt_alignment_new_with_seqs(strings[i], best.ivalue, strings[j], best.jvalue); gt_alignment_set_multieop_list(alignment, edit_ops); gt_ensure(eval_scores[s*64+i*8+j] == gt_alignment_eval(alignment)); gt_multieoplist_delete(edit_ops); gt_alignment_delete(alignment); } gt_seqabstract_delete(useq); gt_seqabstract_delete(vseq); } } gt_xdrop_resources_delete(resources); } return had_err; }