Example #1
0
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);
  }
}
Example #2
0
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);
  }
}