void
checkKmers(DnaString const & kmer,
TVertexDescriptor const & starting_vertex,
TVertexDescriptor const & source_vertex,
TGraph const & graph,
std::vector<VertexLabels> & vertex_vector,
boost::unordered_set<TVertexDescriptor> const & free_nodes,
boost::unordered_map< std::pair<TVertexDescriptor, TVertexDescriptor>, boost::dynamic_bitset<> > & edge_ids,
boost::dynamic_bitset<> const & id_bits,
TKmerMap & kmer_map,
std::size_t const & kmer_size
)
{
if (id_bits.none())
return;
if (length(kmer) == kmer_size)
{
KmerLabels new_kmer_label =
{
starting_vertex,
source_vertex,
id_bits
};
if (kmer_map.count(kmer) == 0)
{
std::vector<KmerLabels> new_vector(1, new_kmer_label);
kmer_map[kmer] = new_vector;
}
else
{
kmer_map[kmer].push_back(new_kmer_label);
}
return;
}
for (Iterator<TGraph, OutEdgeIterator>::Type out_edge_iterator (graph, source_vertex) ; !atEnd(out_edge_iterator) ; ++out_edge_iterator)
{
DnaString new_kmer(kmer);
TVertexDescriptor const & target_vertex = targetVertex(out_edge_iterator);
boost::dynamic_bitset<> new_id_bits(id_bits);
if (free_nodes.count(target_vertex) == 0)
{
seqan::appendValue(new_kmer, vertex_vector[target_vertex].dna);
std::pair<TVertexDescriptor, TVertexDescriptor> edge_pair(source_vertex, target_vertex);
if (edge_ids.count(edge_pair) == 1)
{
new_id_bits = id_bits & edge_ids[edge_pair];
}
}
checkKmers(new_kmer, starting_vertex, target_vertex, graph, vertex_vector, free_nodes, edge_ids, new_id_bits, kmer_map, kmer_size);
}
}
void
check_kmers_simple(DnaString const & kmer,
TGraph const & graph,
TVertexDescriptor const & source_vertex,
std::vector<VertexLabels> & vertex_vector,
boost::unordered_set<TVertexDescriptor> const & free_nodes,
boost::unordered_map< std::pair<TVertexDescriptor, TVertexDescriptor>, boost::dynamic_bitset<> > & edge_ids,
boost::dynamic_bitset<> const & id_bits,
TKmerMapSimple & kmer_map,
std::size_t const & kmer_size
)
{
if (id_bits.none())
return;
if (length(kmer) == kmer_size)
{
if (id_bits.all())
return;
if (kmer_map.count(kmer) == 0)
{
kmer_map[kmer] = id_bits;
}
else
{
kmer_map[kmer] |= id_bits;
}
return;
}
for (Iterator<TGraph, OutEdgeIterator>::Type out_edge_iterator (graph, source_vertex) ; !atEnd(out_edge_iterator) ; ++out_edge_iterator)
{
DnaString new_kmer(kmer);
TVertexDescriptor const & target_vertex = targetVertex(out_edge_iterator);
// std::cout << source_vertex << " -> " << target_vertex << std::endl;
boost::dynamic_bitset<> new_id_bits(id_bits);
if (free_nodes.count(target_vertex) == 0)
{
seqan::appendValue(new_kmer, vertex_vector[target_vertex].dna);
std::pair<TVertexDescriptor, TVertexDescriptor> edge_pair(source_vertex, target_vertex);
if (edge_ids.count(edge_pair) == 1)
{
new_id_bits = id_bits & edge_ids[edge_pair];
}
}
check_kmers_simple(new_kmer, graph, target_vertex, vertex_vector, free_nodes, edge_ids, new_id_bits, kmer_map, kmer_size);
}
}