static int feature_visitor_region_node(GtNodeVisitor *gv, GtRegionNode *rn,
GtError *err)
{
GtFeatureVisitor *v = feature_visitor_cast(gv);
gt_error_check(err);
return gt_feature_index_add_region_node(v->feature_index, rn, err);
}
static GtFeatureIndex *in_stream_test_data(GtError *error)
{
GtFeatureIndex *fi;
GtFeatureNode *fn;
GtGenomeNode *gn;
GtRegionNode *rn;
GtStr *seqid;
fi = gt_feature_index_memory_new();
seqid = gt_str_new_cstr("chr1");
gn = gt_region_node_new(seqid, 1, 100000);
rn = gt_region_node_cast(gn);
gt_feature_index_add_region_node(fi, rn, error);
gt_genome_node_delete(gn);
gn = gt_feature_node_new(seqid, "region", 500, 5000, GT_STRAND_BOTH);
fn = gt_feature_node_cast(gn);
gt_feature_index_add_feature_node(fi, fn, error);
gt_genome_node_delete(gn);
gn = gt_feature_node_new(seqid, "region", 50000, 75000, GT_STRAND_BOTH);
fn = gt_feature_node_cast(gn);
gt_feature_index_add_feature_node(fi, fn, error);
gt_genome_node_delete(gn);
gt_str_delete(seqid);
seqid = gt_str_new_cstr("scf0001");
gn = gt_region_node_new(seqid, 1, 10000);
rn = gt_region_node_cast(gn);
gt_feature_index_add_region_node(fi, rn, error);
gt_genome_node_delete(gn);
gn = gt_feature_node_new(seqid, "mRNA", 4000, 6000, GT_STRAND_REVERSE);
fn = gt_feature_node_cast(gn);
gt_feature_index_add_feature_node(fi, fn, error);
gt_genome_node_delete(gn);
gn = gt_feature_node_new(seqid, "mRNA", 7000, 9500, GT_STRAND_FORWARD);
fn = gt_feature_node_cast(gn);
gt_feature_index_add_feature_node(fi, fn, error);
gt_genome_node_delete(gn);
gt_str_delete(seqid);
return fi;
}
static int feature_index_lua_add_region_node(lua_State *L)
{
GtFeatureIndex **fi;
GtGenomeNode **gn;
GtRegionNode *rn;
gt_assert(L);
fi = check_feature_index(L, 1);
gn = check_genome_node(L, 2);
rn = gt_region_node_try_cast(*gn);
luaL_argcheck(L, rn, 2, "not a region node");
gt_feature_index_add_region_node(*fi, rn);
return 0;
}
static int feature_index_lua_add_region_node(lua_State *L)
{
GtFeatureIndex **fi;
GtGenomeNode **gn;
GtRegionNode *rn;
GtError *err;
gt_assert(L);
fi = check_feature_index(L, 1);
gn = check_genome_node(L, 2);
rn = gt_region_node_try_cast(*gn);
luaL_argcheck(L, rn, 2, "not a region node");
err = gt_error_new();
if (gt_feature_index_add_region_node(*fi, rn, err))
return gt_lua_error(L, err);
gt_error_delete(err);
return 0;
}
/* 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;
}
