static int md5_to_seqid(GtGenomeNode *gn, GtRegionMapping *region_mapping,
GtError *err)
{
GtStr *seqid;
int had_err = 0;
gt_error_check(err);
gt_assert(gn && region_mapping);
seqid = gt_genome_node_get_seqid(gn);
if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) {
/* seqid is a MD5 seqid -> change id */
GtStr *desc = gt_str_new();
had_err = gt_region_mapping_get_description(region_mapping, desc, seqid,
err);
if (!had_err) {
GtStr *new_seqid = gt_str_new();
gt_regular_seqid_save(new_seqid, desc);
if (gt_feature_node_try_cast(gn)) {
M2IChangeSeqidInfo info;
info.new_seqid = new_seqid;
info.region_mapping = region_mapping;
had_err = gt_feature_node_traverse_children((GtFeatureNode*) gn, &info,
m2i_change_seqid, true,
err);
}
else
gt_genome_node_change_seqid(gn, new_seqid);
gt_str_delete(new_seqid);
}
gt_str_delete(desc);
}
return had_err;
}
static int change_sequence_id(GtGenomeNode *gn, void *data,
GT_UNUSED GtError *err)
{
GtStr *changed_seqid = data;
gt_error_check(err);
gt_assert(changed_seqid);
gt_genome_node_change_seqid(gn, changed_seqid);
return 0;
}
static int m2i_change_seqid(GtFeatureNode *fn, void *data, GtError *err)
{
const char *target;
M2IChangeSeqidInfo *info = (M2IChangeSeqidInfo*) data;
gt_error_check(err);
gt_assert(fn && info);
gt_genome_node_change_seqid((GtGenomeNode*) fn, info->new_seqid);
if ((target = gt_feature_node_get_attribute(fn, GT_GFF_TARGET)))
return m2i_change_target_seqids(fn, target, info->region_mapping, err);
return 0;
}
static int chseqids_stream_next(GtNodeStream *gs, GtGenomeNode **gn,
GtError *err)
{
GtChseqidsStream *cs;
GtGenomeNode *node, **gn_a, **gn_b;
GtFeatureNode *feature_node;
GtStr *changed_seqid;
unsigned long i;
int rval, had_err = 0;
gt_error_check(err);
cs = chseqids_stream_cast(gs);
if (!cs->sequence_regions_processed) {
while (!had_err) {
if (!(had_err = gt_node_stream_next(cs->in_stream, &node, err))) {
if (node)
gt_array_add(cs->gt_genome_node_buffer, node);
else
break;
if (!gt_region_node_try_cast(node))
break; /* no more sequence regions */
}
}
/* now the buffer contains only sequence regions (except the last entry)
-> change sequence ids */
for (i = 0; !had_err && i < gt_array_size(cs->gt_genome_node_buffer); i++) {
node = *(GtGenomeNode**) gt_array_get(cs->gt_genome_node_buffer, i);
if (gt_genome_node_get_seqid(node)) {
if ((changed_seqid = gt_mapping_map_string(cs->chseqids_mapping,
gt_str_get(gt_genome_node_get_seqid(node)),
err))) {
if ((feature_node = gt_feature_node_try_cast(node))) {
rval = gt_genome_node_traverse_children(node, changed_seqid,
change_sequence_id, true,
err);
gt_assert(!rval); /* change_sequence_id() is sane */
}
else
gt_genome_node_change_seqid(node, changed_seqid);
gt_str_delete(changed_seqid);
}
else
had_err = -1;
}
}
/* sort them */
if (!had_err)
gt_genome_nodes_sort(cs->gt_genome_node_buffer);
/* consolidate them */
for (i = 1; !had_err && i + 1 < gt_array_size(cs->gt_genome_node_buffer);
i++) {
gn_a = gt_array_get(cs->gt_genome_node_buffer, i-1);
gn_b = gt_array_get(cs->gt_genome_node_buffer, i);
if (gt_genome_nodes_are_equal_region_nodes(*gn_a, *gn_b)) {
gt_region_node_consolidate(gt_region_node_cast(*gn_b),
gt_region_node_cast(*gn_a));
gt_genome_node_delete(*gn_a);
*gn_a = NULL;
}
}
cs->sequence_regions_processed = true;
}
/* return non-null nodes from buffer */
while (!had_err &&
cs->buffer_index < gt_array_size(cs->gt_genome_node_buffer)) {
node = *(GtGenomeNode**) gt_array_get(cs->gt_genome_node_buffer,
cs->buffer_index);
cs->buffer_index++;
if (node) {
*gn = node;
return had_err;
}
}
if (!had_err)
had_err = gt_node_stream_next(cs->in_stream, gn, err);
if (!had_err && *gn) {
if (gt_genome_node_get_seqid(*gn)) {
changed_seqid = gt_mapping_map_string(cs->chseqids_mapping,
gt_str_get(gt_genome_node_get_seqid(*gn)),
err);
gt_assert(changed_seqid); /* is always defined, because an undefined
mapping would be catched earlier */
if ((feature_node = gt_feature_node_try_cast(*gn))) {
rval = gt_genome_node_traverse_children(*gn, changed_seqid,
change_sequence_id, true, err);
gt_assert(!rval); /* change_sequence_id() is sane */
}
else
gt_genome_node_change_seqid(*gn, changed_seqid);
gt_str_delete(changed_seqid);
}
}
return had_err;
}
