int gt_clustered_set_union_find_unit_test(GtError *err)
{
int had_err = 0, i = 0, j = 0;
GtClusteredSet *cs = NULL;
cs = gt_clustered_set_union_find_new(1, err);
gt_ensure(
gt_clustered_set_union_find_num_of_elements(cs, err) ==
gt_clustered_set_union_find_cluster_num(cs, 0, err));
gt_ensure(
gt_clustered_set_union_find_num_of_clusters(cs, err) == 0);
gt_clustered_set_union_find_delete(cs, err);
if (!had_err) {
cs = gt_clustered_set_union_find_new(2, err);
gt_clustered_set_union_find_merge_clusters(cs, 0, 1, err);
gt_ensure(
gt_clustered_set_union_find_num_of_clusters(cs, err) == 1);
gt_ensure(
gt_clustered_set_union_find_cluster_num(cs, 0, err) ==
gt_clustered_set_union_find_cluster_num(cs, 1, err));
gt_ensure(
gt_clustered_set_union_find_num_of_clusters(cs, err) == 1);
gt_clustered_set_union_find_delete(cs, err);
}
if (!had_err) {
cs = gt_clustered_set_union_find_new(3, err);
gt_clustered_set_union_find_merge_clusters(cs, 0, 1, err);
gt_clustered_set_union_find_merge_clusters(cs, 1, 2, err);
gt_ensure(
gt_clustered_set_union_find_num_of_clusters(cs, err) == 1);
gt_ensure(
gt_clustered_set_union_find_cluster_num(cs, 0, err) ==
gt_clustered_set_union_find_cluster_num(cs, 1, err));
gt_ensure(
gt_clustered_set_union_find_cluster_num(cs, 0, err) ==
gt_clustered_set_union_find_cluster_num(cs, 2, err));
gt_ensure(
gt_clustered_set_union_find_cluster_num(cs, 1, err) ==
gt_clustered_set_union_find_cluster_num(cs, 2, err));
gt_clustered_set_union_find_delete(cs, err);
}
if (!had_err) {
cs = gt_clustered_set_union_find_new(4, err);
gt_clustered_set_union_find_merge_clusters(cs, 0, 1, err);
gt_clustered_set_union_find_merge_clusters(cs, 2, 3, err);
gt_ensure(
gt_clustered_set_union_find_num_of_clusters(cs, err) == 2);
gt_clustered_set_union_find_merge_clusters(cs, 0, 2, err);
for (i = 0; i < 4 - 1; i++) {
for (j = i + 1; j < 4; j++) {
gt_ensure(
gt_clustered_set_union_find_cluster_num(cs, i, err) ==
gt_clustered_set_union_find_cluster_num(cs, j, err));
}
}
gt_clustered_set_union_find_delete(cs, err);
}
if (!had_err) {
cs = gt_clustered_set_union_find_new(CLUSTERED_SET_UNION_FIND_TEST_SIZE,
err);
for (i = 0; !had_err && i < CLUSTERED_SET_UNION_FIND_TEST_SIZE; i++) {
gt_ensure(
gt_clustered_set_union_find_num_of_elements(cs, err) ==
gt_clustered_set_union_find_cluster_num(cs, i, err));
}
for (i = 1;!had_err && i < CLUSTERED_SET_UNION_FIND_TEST_SIZE; i++) {
gt_clustered_set_union_find_merge_clusters(cs, 0, i, err);
}
for (i = 0; !had_err && i < CLUSTERED_SET_UNION_FIND_TEST_SIZE; i++) {
gt_ensure(
gt_clustered_set_union_find_cluster_num(cs, i, err) == 0);
}
gt_clustered_set_union_find_delete(cs, err);
}
return had_err;
}
static int process_feature(GtLTRClusterStream *lcs,
const char *feature,
GtError *err)
{
GtArray *matches;
GtMatchIterator *mi = NULL;
GtMatch *match = NULL;
GtMatchIteratorStatus status;
GtEncseq *encseq;
unsigned long i;
int had_err = 0;
if (lcs->current_state != NULL) {
char tmp[BUFSIZ];
gt_free(*lcs->current_state);
(void) snprintf(tmp, BUFSIZ, "Clustering feature: %s", feature);
*lcs->current_state = gt_cstr_dup(tmp);
}
matches = gt_array_new(sizeof(GtMatch*));
encseq = (GtEncseq*) gt_hashmap_get(lcs->feat_to_encseq, feature);
gt_log_log("found encseq %p for feature %s", encseq, feature);
if (!had_err) {
mi = gt_match_iterator_last_new(encseq, encseq, lcs->match_score,
lcs->mismatch_cost,
lcs->gap_open_cost,
lcs->gap_ext_cost,
lcs->xdrop,
lcs->ydrop,
lcs->zdrop,
lcs->k,
lcs->mscoregapped,
lcs->mscoregapless, err);
if (mi != NULL) {
while ((status = gt_match_iterator_next(mi, &match, err))
!= GT_MATCHER_STATUS_END) {
if (status == GT_MATCHER_STATUS_OK) {
gt_array_add(matches, match);
} else {
gt_assert(status == GT_MATCHER_STATUS_ERROR);
had_err = -1;
break;
}
}
} else
had_err = -1;
}
if (!had_err) {
GtClusteredSet *cs;
GtHashmap *seqdesc2seqnum;
GtMatch *tmp_match;
const char *description;
char *output;
unsigned long desclen,
num_of_seq;
seqdesc2seqnum = gt_hashmap_new(GT_HASH_STRING, free_hash, NULL);
num_of_seq = gt_encseq_num_of_sequences(encseq);
for (i = 0; i < num_of_seq; i++) {
description = gt_encseq_description(encseq, &desclen, i);
output = gt_calloc((size_t) (desclen + 1), sizeof (char));
strncpy(output, description, (size_t) desclen);
output[desclen] = '\0';
gt_hashmap_add(seqdesc2seqnum, (void*) gt_cstr_dup(output),
(void*) (i + 1));
gt_free(output);
}
cs = gt_clustered_set_union_find_new(num_of_seq, err);
if (cs != NULL) {
if (cluster_sequences(matches, cs, seqdesc2seqnum, (unsigned) lcs->psmall,
(unsigned) lcs->plarge, encseq, err) != 0) {
had_err = -1;
}
if (!had_err) {
(void) cluster_annotate_nodes(cs, encseq, feature, lcs->nodes, err);
}
} else
had_err = -1;
for (i = 0; i < gt_array_size(matches); i++) {
tmp_match = *(GtMatch**) gt_array_get(matches, i);
gt_match_delete(tmp_match);
}
gt_array_delete(matches);
matches = NULL;
gt_hashmap_delete(seqdesc2seqnum);
gt_clustered_set_delete(cs, err);
}
gt_match_iterator_delete(mi);
return had_err;
}
