void gt_ma_clean(void)
{
gt_assert(ma);
gt_mutex_lock(bookkeeping_lock);
ma->bookkeeping = false;
gt_hashmap_delete(ma->allocated_pointer);
gt_mutex_unlock(bookkeeping_lock);
gt_mutex_delete(bookkeeping_lock);
free(ma);
ma = NULL;
}
void gt_alphabet_delete(GtAlphabet *alphabet)
{
if (!alphabet) return;
gt_mutex_lock(alphabet->refmutex);
if (alphabet->reference_count) {
alphabet->reference_count--;
gt_mutex_unlock(alphabet->refmutex);
return;
}
gt_mutex_unlock(alphabet->refmutex);
gt_free(alphabet->mapdomain);
gt_free(alphabet->characters);
if (alphabet->alphadef != NULL)
gt_str_delete(alphabet->alphadef);
gt_mutex_delete(alphabet->refmutex);
gt_free(alphabet);
}
void gt_spacepeak_clean()
{
if (!peaklogger) return;
gt_mutex_delete(peaklogger->mutex);
free(peaklogger);
}
/* to be called from implementing class! */
int gt_feature_index_unit_test(GtFeatureIndex *fi, GtError *err)
{
int had_err = 0, i, rval;
GtFeatureIndexTestShared sh;
GtStrArray *seqids;
GtStr *seqid;
GtRange check_range;
GtRegionNode *rn;
bool has_seqid;
gt_error_check(err);
sh.mutex = gt_mutex_new();
sh.nodes = gt_array_new(sizeof (GtFeatureNode*));
sh.error_count = 0;
sh.next_node_idx = 0;
sh.fi = fi;
sh.err = gt_error_new();
/* create region */
seqid = gt_str_new_cstr(GT_FI_TEST_SEQID);
rn = (GtRegionNode*) gt_region_node_new(seqid, GT_FI_TEST_START,
GT_FI_TEST_END);
/* test seqid is not supposed to exist */
gt_ensure(gt_feature_index_has_seqid(sh.fi, &has_seqid,
GT_FI_TEST_SEQID, err) == 0);
gt_ensure(!has_seqid);
/* add a sequence region directly and check if it has been added */
rval = gt_feature_index_add_region_node(sh.fi, rn, err);
gt_ensure(rval == 0);
gt_genome_node_delete((GtGenomeNode*) rn);
gt_ensure(gt_feature_index_has_seqid(sh.fi, &has_seqid,
GT_FI_TEST_SEQID, err) == 0);
gt_ensure(has_seqid);
gt_feature_index_get_range_for_seqid(sh.fi, &check_range, GT_FI_TEST_SEQID,
err);
gt_ensure(check_range.start == GT_FI_TEST_START
&& check_range.end == GT_FI_TEST_END);
/* set up nodes to store */
for (i=0;i<GT_FI_TEST_FEATURES_PER_THREAD*gt_jobs;i++) {
GtUword start, end;
GtFeatureNode *fn;
start = random() % (GT_FI_TEST_END - GT_FI_TEST_FEATURE_WIDTH);
end = start + random() % (GT_FI_TEST_FEATURE_WIDTH);
fn = gt_feature_node_cast(gt_feature_node_new(seqid, "gene", start, end,
GT_STRAND_FORWARD));
gt_array_add(sh.nodes, fn);
}
/* test parallel addition */
gt_multithread(gt_feature_index_unit_test_add, &sh, err);
seqids = gt_feature_index_get_seqids(fi, err);
gt_ensure(seqids);
gt_ensure(gt_feature_index_has_seqid(fi, &has_seqid,GT_FI_TEST_SEQID,
err) == 0);
gt_ensure(has_seqid);
gt_ensure(gt_str_array_size(seqids) == 1);
/* test parallel query */
if (!had_err)
gt_multithread(gt_feature_index_unit_test_query, &sh, err);
gt_ensure(sh.error_count == 0);
gt_mutex_delete(sh.mutex);
gt_error_delete(sh.err);
gt_str_array_delete(seqids);
gt_array_delete(sh.nodes);
gt_str_delete(seqid);
return had_err;
}
void gt_symbol_clean(void)
{
gt_cstr_table_delete(symbols);
gt_mutex_delete(symbol_mutex);
}
void gt_ya_rand_clean(void)
{
if (!mutex) return;
gt_mutex_delete(mutex);
mutex = NULL;
}