bool CdTreeStream::read(std::istream& is, SeqTree& seqTree)
{
if (!is.good())
return false;
char ch;
is.get(ch);
// skip to the first (
while((ch != '(') && (is.good()))
{
is.get(ch);
}
if (!is.good())
return false;
SeqItem item;
SeqTree::iterator top = seqTree.insert(seqTree.begin(),item);
SeqTree::iterator cursor = top;
std::string nameDist;
std::string distance;
std::string delimiters = "(),";
while(is.get(ch))
{
if (!isspace((unsigned char) ch))
{
SeqItem tmp1;
switch (ch)
{
case ';': //end seq tree data
return true;
//break;
case '(': // start a node
cursor = seqTree.append_child(cursor, tmp1);
break;
case ',':
// end a sibling, nothing needs done, skip it.
break;
case ')': //end a node; read and set the distance
readToDelimiter(is,distance);
if (distance.size() >0)
{
// allow interior nodes to be named
int colon_loc = distance.find_first_of(":");
if (colon_loc > 0) {
cursor->name = distance.substr(0, colon_loc);
distance = distance.erase(0, colon_loc);
}
//skip the leading :
//if not present, check if dealing w/ a final named internal node
if (distance[0] != ':') {
int semi_loc = distance.find_first_of(";");
if (semi_loc > 0) {
cursor->name = distance.substr(0, semi_loc);
is.putback(distance[semi_loc]);
// } else {
// std::cout<<"length missing; semi_loc = "<<semi_loc<<std::endl;
}
}
else
{
distance.erase(0,1);
double dist = atof(distance.c_str());
if (dist < 0.0) {
std::cout << "Warning: negative branch length! "
<< cursor->name << ", D = " << distance << std::endl;
}
//set distance
cursor->distance = dist;
if (cursor == top)
{
std::cout<<"Warning: already reached top before processing )";
return false;
}
else
cursor = seqTree.parent(cursor);
}
}
distance.erase();
break;
default: // non-delimiter starts a new leaf node
nameDist += ch;
readToDelimiter(is, nameDist);
tmp1 = SeqItem(nameDist);
seqTree.append_child(cursor,tmp1); //don't move cursor
//reset the word
nameDist.erase();
}
}
}
return true;
}
std::string readline(std::istream& in) {
return readToDelimiter(in, in.widen('\n'));
}
