void assembleRandomTree();
void assembleRandomUnifracTree(vector<string>);
void assembleRandomUnifracTree(string, string);
void assembleRandomTree();
void assembleRandomUnifracTree(vector<string>);
void assembleRandomUnifracTree(string, string);
map<string, int> mergeUserGroups(int, vector<string>); //returns a map with a groupname and the number of times that group was seen in the children
void printTree();
void print(ostream&);
map<string, int> mergeUserGroups(int, vector<string>); //returns a map with a groupname and the number of times that group was seen in the children
void printTree();
void print(ostream&);
int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
int numNodes, numLeaves;
ofstream out;
string filename;
map<string, int>::iterator it, it2;
map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
int numNodes, numLeaves;
ofstream out;
string filename;
map<string, int>::iterator it, it2;
map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
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.
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.
- void readTreeString(ifstream&);
+ int readTreeString(ifstream&);
+ int populateNewTree(vector<Node>&, int, int&);
+ void printBranch(int, ostream&, string, vector<Node>&);
+
+ MothurOut* m;
+