static int gt_sort_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *err)
{
GtSortStream *sort_stream;
GtGenomeNode *node, *eofn;
int had_err = 0;
gt_error_check(err);
sort_stream = gt_sort_stream_cast(ns);
if (!sort_stream->sorted) {
while (!(had_err = gt_node_stream_next(sort_stream->in_stream, &node,
err)) && node) {
if ((eofn = gt_eof_node_try_cast(node)))
gt_genome_node_delete(eofn); /* get rid of EOF nodes */
else
gt_array_add(sort_stream->nodes, node);
}
if (!had_err) {
gt_genome_nodes_sort_stable(sort_stream->nodes);
sort_stream->sorted = true;
}
}
if (!had_err) {
gt_assert(sort_stream->sorted);
if (sort_stream->idx < gt_array_size(sort_stream->nodes)) {
*gn = *(GtGenomeNode**) gt_array_get(sort_stream->nodes,
sort_stream->idx);
sort_stream->idx++;
/* join region nodes with the same sequence ID */
if (gt_region_node_try_cast(*gn)) {
GtRange range_a, range_b;
while (sort_stream->idx < gt_array_size(sort_stream->nodes)) {
node = *(GtGenomeNode**) gt_array_get(sort_stream->nodes,
sort_stream->idx);
if (!gt_region_node_try_cast(node) ||
gt_str_cmp(gt_genome_node_get_seqid(*gn),
gt_genome_node_get_seqid(node))) {
/* the next node is not a region node with the same ID */
break;
}
range_a = gt_genome_node_get_range(*gn);
range_b = gt_genome_node_get_range(node);
range_a = gt_range_join(&range_a, &range_b);
gt_genome_node_set_range(*gn, &range_a);
gt_genome_node_delete(node);
sort_stream->idx++;
}
}
return 0;
}
}
if (!had_err) {
gt_array_reset(sort_stream->nodes);
*gn = NULL;
}
return had_err;
}
static int stat_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
{
GtStatStream *stat_stream;
int had_err;
gt_error_check(err);
stat_stream = stat_stream_cast(ns);
had_err = gt_node_stream_next(stat_stream->in_stream, gn, err);
if (!had_err) {
gt_assert(stat_stream->stat_visitor);
if (*gn) {
if (!gt_eof_node_try_cast(*gn)) /* do not count EOF nodes */
stat_stream->number_of_DAGs++;
had_err = gt_genome_node_accept(*gn, stat_stream->stat_visitor, err);
gt_assert(!had_err); /* the status visitor is sane */
}
}
return had_err;
}
static int gt_load_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *err)
{
GtLoadStream *load_stream;
GtGenomeNode *node, *eofn;
int had_err = 0;
gt_error_check(err);
load_stream = gt_load_stream_cast(ns);
if (!load_stream->full) {
while (!(had_err = gt_node_stream_next(load_stream->in_stream, &node,
err)) && node) {
if ((eofn = gt_eof_node_try_cast(node)))
gt_genome_node_delete(eofn); /* get rid of EOF nodes */
else
gt_array_add(load_stream->nodes, node);
}
if (!had_err) {
load_stream->full = true;
}
}
if (!had_err) {
gt_assert(load_stream->full);
if (load_stream->idx < gt_array_size(load_stream->nodes)) {
*gn = *(GtGenomeNode**) gt_array_get(load_stream->nodes,
load_stream->idx);
load_stream->idx++;
return 0;
}
}
if (!had_err) {
gt_array_reset(load_stream->nodes);
*gn = NULL;
}
return had_err;
}
