vector<int> Vectorizer::alignment_to_a_hot(Alignment a){
int64_t entity_size = my_xg->node_count + my_xg->edge_count;
vector<int> ret(entity_size, 0);
Path path = a.path();
for (int i = 0; i < path.mapping_size(); i++){
Mapping mapping = path.mapping(i);
if(! mapping.has_position()){
continue;
}
Position pos = mapping.position();
int64_t node_id = pos.node_id();
int64_t key = my_xg->node_rank_as_entity(node_id);
// Okay, solved the previous out of range errors:
// We have to use an entity-space that is |nodes + edges + 1|
// as nodes are indexed from 1, not from 0.
//TODO: this means we may one day have to do the same bump up
// by one for edges, as I assume they are also indexed starting at 1.
//cerr << key << " - " << entity_size << endl;
//Find edge by current / previous node ID
// we can check the orientation, though it shouldn't **really** matter
// whether we catch them in the forward or reverse direction.
if (i > 0){
Mapping prev_mapping = path.mapping(i - 1);
Position prev_pos = prev_mapping.position();
int64_t prev_node_id = prev_pos.node_id();
if (my_xg->has_edge(prev_node_id, false, node_id, false)){
int64_t edge_key = my_xg->edge_rank_as_entity(prev_node_id, false, node_id, false);
vector<size_t> edge_paths = my_xg->paths_of_entity(edge_key);
if (edge_paths.size() > 0){
ret[edge_key - 1] = 1;
}
else{
ret[edge_key - 1] = 2;
}
}
}
//Check if the node of interest is on a path
vector<size_t> node_paths = my_xg->paths_of_node(node_id);
if (node_paths.size() > 0){
ret[key - 1] = 2;
}
else{
ret[key - 1] = 1;
}
}
return ret;
}
vector<double> Vectorizer::alignment_to_identity_hot(Alignment a){
int64_t entity_size = my_xg->node_count + my_xg->edge_count;
vector<double> ret(entity_size, 0.0);
Path path = a.path();
for (int i = 0; i < path.mapping_size(); i ++){
Mapping mapping = path.mapping(i);
if(! mapping.has_position()){
continue;
}
Position pos = mapping.position();
int64_t node_id = pos.node_id();
int64_t key = my_xg->node_rank_as_entity(node_id);
//Calculate % identity by walking the edits and counting matches.
double pct_id = 0.0;
double match_len = 0.0;
double total_len = 0.0;
for (int j = 0; j < mapping.edit_size(); j++){
Edit e = mapping.edit(j);
total_len += e.from_length();
if (e.from_length() == e.to_length() && e.sequence() == ""){
match_len += (double) e.to_length();
}
else if (e.from_length() == e.to_length() && e.sequence() != ""){
// TODO if we map but don't match exactly, add half the average length to match_length
//match_len += (double) (0.5 * ((double) e.to_length()));
}
else{
}
}
pct_id = (match_len == 0.0 && total_len == 0.0) ? 0.0 : (match_len / total_len);
ret[key - 1] = pct_id;
if (i > 0){
Mapping prev_mapping = path.mapping(i - 1);
Position prev_pos = prev_mapping.position();
int64_t prev_node_id = prev_pos.node_id();
if (my_xg->has_edge(prev_node_id, false, node_id, false)){
int64_t edge_key = my_xg->edge_rank_as_entity(prev_node_id, false, node_id, false);
ret[edge_key - 1] = 1.0;
}
}
}
return ret;
}
