int gt_feature_index_add_gff3file(GtFeatureIndex *feature_index,
const char *gff3file, GtError *err)
{
GtNodeStream *gff3_in_stream;
GtGenomeNode *gn;
GtArray *tmp;
int had_err = 0;
GtUword i;
gt_error_check(err);
gt_assert(feature_index && gff3file);
tmp = gt_array_new(sizeof (GtGenomeNode*));
gff3_in_stream = gt_gff3_in_stream_new_unsorted(1, &gff3file);
while (!(had_err = gt_node_stream_next(gff3_in_stream, &gn, err)) && gn)
gt_array_add(tmp, gn);
if (!had_err) {
GtNodeVisitor *feature_visitor = gt_feature_visitor_new(feature_index);
for (i=0;i<gt_array_size(tmp);i++) {
gn = *(GtGenomeNode**) gt_array_get(tmp, i);
/* no need to lock, add_*_node() is synchronized */
had_err = gt_genome_node_accept(gn, feature_visitor, NULL);
gt_assert(!had_err); /* cannot happen */
}
gt_node_visitor_delete(feature_visitor);
}
gt_node_stream_delete(gff3_in_stream);
for (i=0;i<gt_array_size(tmp);i++)
gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(tmp, i));
gt_array_delete(tmp);
return had_err;
}
GtNodeStream* gt_feature_stream_new(GtNodeStream *in_stream, GtFeatureIndex *fi)
{
GtNodeStream *gs;
GtFeatureStream *feature_stream;
gs = gt_node_stream_create(gt_feature_stream_class(), false);
feature_stream = feature_stream_cast(gs);
feature_stream->in_stream = gt_node_stream_ref(in_stream);
feature_stream->feature_visitor = gt_feature_visitor_new(fi);
return gs;
}
static int feature_visitor_lua_new(lua_State *L)
{
GtNodeVisitor **feature_visitor;
GtFeatureIndex **feature_index;
feature_visitor = lua_newuserdata(L, sizeof (GtNodeVisitor*));
gt_assert(feature_visitor);
feature_index = check_feature_index(L, 1);
*feature_visitor = gt_feature_visitor_new(*feature_index);
luaL_getmetatable(L, GENOME_VISITOR_METATABLE);
lua_setmetatable(L, -2);
return 1;
}