Exemple #1
0
  void NEXUS::initialize()
  {
    // Check #NEXUS
    getline(*file,line);
    if (line != "#NEXUS")
      throw myexception()<<"NEXUS trees reader: File does not begin with '#NEXUS' and may not be a NEXUS file.";
  
    // [ and ] do not break words

    string word;

    bool in_trees_block=false;

    while(get_NEXUS_command(*file,line))
    {
      //    cerr<<"line: "<<line<<endl;
      int pos=0;
      
      if (not get_word_NEXUS(word,pos,line)) continue;

      //      cerr<<"NEXUS: command = :"<<word<<":"<<"     in_trees_block = "<<in_trees_block<<endl;
      
      // Parse BEGIN TREES
      if (uppercase(word) == "BEGIN") {
	if (not get_word_NEXUS(word,pos,line)) continue;
	if (uppercase(word) == "TREES")
	  in_trees_block = true;
      }
      
      if (not in_trees_block) continue;
      
      // Parse TRANSLATE ...
      if (uppercase(word) == "TRANSLATE") {
	parse_translate_command(line.substr(pos,line.size()-pos));
	//      cerr<<"leaf names = "<<join(leaf_names,',')<<endl;
	line.clear();
	return;
      }
      else if (uppercase(word) == "TREE") {
	try {
	  get_word_NEXUS(word,pos,line);
	  if (not (word == "="))
	    get_word_NEXUS(word,pos,line);
	  NEXUS_skip_ws(pos,line);
	  SequenceTree T;
	  string t = strip_NEXUS_comments(line.substr(pos,line.size()-pos));
	  T.parse(t);
	  leaf_names = T.get_sequences();
	  std::sort(leaf_names.begin(),leaf_names.end());
	  return;
	}
	catch (std::exception& e) {
	  cerr<<" Error! "<<e.what()<<endl;
	  cerr<<" Quitting read of tree file."<<endl;
	  file->setstate(std::ios::badbit);
	}
      }
    }
  }
Exemple #2
0
 void Newick::initialize()
 {
   SequenceTree T;
   getline(*file,line);
   T.parse(line);
   leaf_names = T.get_sequences();
   std::sort(leaf_names.begin(),leaf_names.end());
   
   //FIXME - this loses the first line!
 }