int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
- void assembleTree();
+ int assembleTree();
vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
void randomTopology();
void randomBlengths();
void randomLabels(vector<string>);
- void randomLabels(string, string);
+ //void randomLabels(string, string);
void printBranch(int, ostream&, string); //recursively print out tree
void parseTreeFile(); //parses through tree file to find names of nodes and number of them
//this is required in case user has sequences in the names file that are
//not included in the tree.
//only takes names from the first tree in the tree file and assumes that all trees use the same names.
int readTreeString(ifstream&);
+ MothurOut* m;
};