+public:
+ Tree(); //to generate a tree from a file
+ ~Tree();
+
+
+ void getCopy(Tree*); //makes tree a copy of the one passed in.
+ void assembleRandomTree();
+ void assembleRandomUnifracTree(vector<string>);
+ void assembleRandomUnifracTree(string, string);
+ void createNewickFile(string);
+ int getIndex(string);
+ void setIndex(string, int);
+ int getNumNodes() { return numNodes; }
+ int getNumLeaves(){ return numLeaves; }
+ 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&);
+ void printForBoot(ostream&);
+ int findRoot(); //return index of root node
+
+ //this function takes the leaf info and populates the non leaf nodes
+ 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;
+ 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
+
+ map<string,int> mergeGcounts(int);
+ void randomTopology();
+ void randomBlengths();
+ void randomLabels(vector<string>);
+ void randomLabels(string, string);
+ void printBranch(int, ostream&, string); //recursively print out tree