C++ SequenceTree::write方法代码示例

void write_partitions(std::ostream& o,const vector<Partition>& partitions)
{
  vector<Partition> full;
  vector<Partition> sub;
  for(int i=0;i<partitions.size();i++)
    if (partitions[i].full())
      full.push_back(partitions[i]);
    else
      sub.push_back(partitions[i]);

  if (full.size()) {
    SequenceTree consensus = get_mf_tree(partitions[0].names,full);
    o<<consensus.write(false)<<endl;
  }

  for(int i=0;i<sub.size();i++)
    o<<sub[i]<<endl;
}

int main(int argc,char* argv[]) { 
  Arguments args;
  args.read(argc,argv);

  unsigned long seed =0;
  if (args.set("seed")) {
    seed = convertTo<unsigned long>(args["seed"]);
    myrand_init(seed);
  }
  else
    seed = myrand_init();

  assert(args.set("names"));
  vector<string> names = split(args["names"],':');

  double branch_mean = 0.1;
  if (args.set("mean"))
    branch_mean = convertTo<double>(args["mean"]);

  SequenceTree T = RandomTree(names,branch_mean);

  std::cout<<T.write()<<std::endl;
}

int main(int argc,char* argv[]) 
{ 
  try {
    //----------- Parse command line  ----------//
    variables_map args = parse_cmd_line(argc,argv);

    int skip = args["skip"].as<int>();

    int max = -1;
    if (args.count("max"))
      max = args["max"].as<int>();

    int subsample = args["sub-sample"].as<int>();

    vector<string> prune;
    if (args.count("prune")) {
      string p = args["prune"].as<string>();
      prune = split(p,',');
    }
      

    //----------- Read the topology -----------//
    SequenceTree Q = load_T(args);
    standardize(Q);
    const int B = Q.n_branches();
    const int N = Q.n_nodes();
    vector<double> bf(B);
    for(int b=0;b<bf.size();b++)
      bf[b] = Q.branch(b).length();

    //-------- Read in the tree samples --------//
    if ( args.count("simple") ) {
      accum_branch_lengths_ignore_topology A(Q);
      scan_trees(std::cin,skip,subsample,max,prune,A);
      for(int b=0;b<B;b++)
	Q.branch(b).set_length(A.m1[b]);
      cout<<Q.write_with_bootstrap_fraction(bf,true)<<endl;
      exit(0);
    }

    accum_branch_lengths_same_topology A(Q);

    try {
      scan_trees(std::cin,skip,subsample,max,prune,A);
    }
    catch (std::exception& e) 
    {
      if (args.count("safe"))
	cout<<Q.write(false)<<endl;
      std::cerr<<"tree-mean-lengths: Error! "<<e.what()<<endl;
      exit(0);
    }

    if (log_verbose) std::cerr<<A.n_matches<<" out of "<<A.n_samples<<" trees matched the topology";
    if (log_verbose) std::cerr<<" ("<<double(A.n_matches)/A.n_samples*100<<"%)"<<std::endl;

    //------- Merge lengths and topology -------//
    if (args.count("var")) {
      for(int b=0;b<B;b++)
	Q.branch(b).set_length(A.m2[b]);
      cout<<Q;
      exit(0);
    }
    else {
      for(int b=0;b<B;b++)
	Q.branch(b).set_length(A.m1[b]);

      if (not args.count("no-node-lengths") and 
	  not args.count("show-node-lengths")) {
	for(int n=0;n<N;n++) {
	  int degree = Q[n].neighbors().size();
	  for(out_edges_iterator b = Q[n].branches_out();b;b++)
	    (*b).set_length((*b).length() + A.n1[n]/degree);
	}
      }

      //------- Print Tree and branch lengths -------//
      cout<<Q.write_with_bootstrap_fraction(bf,true)<<endl;

      //------------ Print node lengths -------------//
      if (args.count("show-node-lengths"))
	for(int n=0;n<Q.n_nodes();n++) {
	  if (A.n1[n] > 0) {
	    cout<<"node "<<A.n1[n]<<endl;
	    int b = (*Q[n].branches_in()).name();
	    cout<<partition_from_branch(Q,b)<<endl;
	  }
	}

    }
  }
  catch (std::exception& e) {
    std::cerr<<"tree-mean-lengths: Error! "<<e.what()<<endl;
    exit(1);
  }
  return 0;
}

string topology(const string& t) {
    SequenceTree T = standardized(t);
    return T.write(false);
}

int main(int argc,char* argv[]) 
{ 
  try {

    std::cout.precision(3);
    std::cout.setf(ios::fixed);

    //---------- Parse command line  -------//
    variables_map args = parse_cmd_line(argc,argv);

    //--------------------- Initialize ---------------------//
    if (args.count("seed")) {
      unsigned long seed = args["seed"].as<unsigned long>();
      myrand_init(seed);
    }
    else
      myrand_init();

    int skip = args["skip"].as<int>();

    int subsample=args["sub-sample"].as<int>();

    int max = -1;
    if (args.count("max"))
      max = args["max"].as<int>();

    double min_support = args["min-support"].as<double>();

    // leaf taxa to ignore
    vector<string> ignore;
    if (args.count("ignore") and args["ignore"].as<string>().size() > 0)
      ignore = split(args["ignore"].as<string>(),',');

    // consensus levels 
    string c_levels = args.count("consensus") ? args["consensus"].as<string>() : "";
    vector<double> consensus_levels = get_consensus_levels(c_levels);

    double report_ratio = args["odds-ratio"].as<double>();

    bool show_sub = args.count("sub-partitions");

    //-------------- Read in tree distributions --------------//
    string filename = args["file"].as<string>();
    ifstream file(filename.c_str());
    if (not file)
      throw myexception()<<"Couldn't open file "<<filename;
      
    tree_sample tree_dist(file,skip,subsample,max,ignore);
    const unsigned N = tree_dist.size();

    dynamic_bitset<> ignore_mask = group_from_names(tree_dist.names(),vector<string>());

    //------ Compute Ml partitions or sub-partitions --------//
    vector< pair<Partition,unsigned> > all_partitions;

    if (show_sub)
    {
      int depth = args["depth"].as<int>();

      double min_rooting = args["rooting"].as<double>();

      all_partitions = get_Ml_sub_partitions_and_counts(tree_dist,min_support, ~ignore_mask,min_rooting,depth);
      //      std::cerr<<"n_sub_partitions = "<<all_partitions.size()<<"\n";
    }
    else
      all_partitions = get_Ml_partitions_and_counts(tree_dist,min_support, ~ignore_mask);

    vector<int> which_topology;
    vector<int> topology_counts;
    std::map<tree_record,int> topologies_index;

    for(int i=0;i<tree_dist.size();i++)
    {
      std::map<tree_record,int>::iterator record = topologies_index.find(tree_dist[i]);
      if (record == topologies_index.end())
      {
	which_topology.push_back(i);
	topology_counts.push_back(0);

	topologies_index[tree_dist[i]] = which_topology.size()-1;
	record = topologies_index.find(tree_dist[i]);
      }
      topology_counts[record->second]++;
    }
    vector<int> order = iota<int>(topology_counts.size());

    std::sort(order.begin(),order.end(),sequence_order<int>(topology_counts));
    std::reverse(order.begin(), order.end());

    //------  Topologies to analyze -----//
    vector<string> topologies;

    cout<<"# n_trees = "<<tree_dist.size()<<"   n_topologies = "<<topology_counts.size()<<endl;
    cout<<"\nTopology support: \n\n";
    for(int i=0;i < args["map-trees"].as<int>() ;i++) 
    {
      if (i >= order.size()) continue;

      string t = tree_dist.T(which_topology[order[i]]).write(false);

//.........这里部分代码省略.........