int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
- void assembleTree();
+ void assembleTree();
vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
+
private:
GlobalData* globaldata;
int numNodes, numLeaves;
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
-
map<string,int> mergeGcounts(int);
+
+ void addNamesToCounts();
void randomTopology();
void randomBlengths();
void randomLabels(vector<string>);
//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&);
+
};
#endif