static void split_cds_feature(GtFeatureNode *cds_feature, GtFeatureNode *fn)
{
GtArray *parents;
unsigned long i;
gt_assert(cds_feature && fn);
/* find parents */
parents = find_cds_parents(cds_feature, fn);
/* remove CDS feature */
gt_feature_node_remove_leaf(fn, cds_feature);
/* add CDS feature to all parents */
for (i = 0; i < gt_array_size(parents); i++) {
GtFeatureNode *parent = *(GtFeatureNode**) gt_array_get(parents, i);
const char *id = gt_feature_node_get_attribute(parent, GT_GFF_ID);
if (!i) {
gt_feature_node_set_attribute(cds_feature, GT_GFF_PARENT, id);
gt_feature_node_add_child(parent, cds_feature);
}
else {
GtFeatureNode *new_cds = gt_feature_node_clone(cds_feature);
gt_feature_node_set_attribute(new_cds, GT_GFF_PARENT, id);
gt_feature_node_add_child(parent, new_cds);
gt_genome_node_delete((GtGenomeNode*) cds_feature);
}
}
gt_array_delete(parents);
}
static int feature_node_lua_remove_leaf(lua_State *L)
{
GtGenomeNode **parent, **leaf;
GtFeatureNode *pf, *lf;
parent = check_genome_node(L, 1);
leaf = check_genome_node(L, 2);
pf = gt_feature_node_try_cast(*parent);
luaL_argcheck(L, pf, 1, "not a feature node");
lf = gt_feature_node_try_cast(*leaf);
luaL_argcheck(L, lf, 2, "not a feature node");
gt_feature_node_remove_leaf(pf, lf);
return 0;
}
static int gt_ltrdigest_pdom_visitor_choose_strand(GtLTRdigestPdomVisitor *lv)
{
int had_err = 0;
double log_eval_fwd = 0.0,
log_eval_rev = 0.0;
GtFeatureNodeIterator *fni;
GtStrand strand;
double score;
bool seen_fwd = false,
seen_rev = false;
GtFeatureNode *curnode = NULL;
GtUword i;
GtArray *to_delete;
fni = gt_feature_node_iterator_new(lv->ltr_retrotrans);
while (!had_err && (curnode = gt_feature_node_iterator_next(fni))) {
if (strcmp(gt_feature_node_get_type(curnode),
gt_ft_protein_match) == 0) {
strand = gt_feature_node_get_strand(curnode);
score = (double) gt_feature_node_get_score(curnode);
if (strand == GT_STRAND_FORWARD) {
log_eval_fwd += log(score);
seen_fwd = true;
} else if (strand == GT_STRAND_REVERSE) {
log_eval_rev += log(score);
seen_rev = true;
}
}
}
gt_feature_node_iterator_delete(fni);
if (seen_rev && !seen_fwd)
gt_feature_node_set_strand(lv->ltr_retrotrans, GT_STRAND_REVERSE);
else if (!seen_rev && seen_fwd)
gt_feature_node_set_strand(lv->ltr_retrotrans, GT_STRAND_FORWARD);
else if (!seen_rev && !seen_fwd)
return had_err;
else {
gt_assert(seen_rev && seen_fwd);
if (gt_double_compare(log_eval_fwd, log_eval_rev) < 0)
strand = GT_STRAND_FORWARD;
else
strand = GT_STRAND_REVERSE;
gt_feature_node_set_strand(lv->ltr_retrotrans, strand);
to_delete = gt_array_new(sizeof (GtFeatureNode*));
fni = gt_feature_node_iterator_new(lv->ltr_retrotrans);
while (!had_err && (curnode = gt_feature_node_iterator_next(fni))) {
if (strcmp(gt_feature_node_get_type(curnode),
gt_ft_protein_match) == 0) {
if (strand != gt_feature_node_get_strand(curnode)) {
gt_array_add(to_delete, curnode);
}
}
}
gt_feature_node_iterator_delete(fni);
gt_assert(gt_array_size(to_delete) > 0);
for (i = 0; i < gt_array_size(to_delete); i++) {
gt_feature_node_remove_leaf(lv->ltr_retrotrans,
*(GtFeatureNode**) gt_array_get(to_delete,
i));
}
gt_array_delete(to_delete);
}
return had_err;
}
