+public:
+ Tree(string);
+ Tree(int);
+ Tree(); //to generate a tree from a file
+ ~Tree();
+
+ void getCopy(Tree*); //makes tree a copy of the one passed in.
+ void getSubTree(Tree*, vector<string>); //makes tree a that contains only the names 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 print(ostream&, string);
+ int findRoot(); //return index of root node
+
+ //this function takes the leaf info and populates the non leaf nodes
+ int assembleTree();
+ int assembleTree(string);
+
+ vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
+ map< string, vector<int> > groupNodeInfo; //maps group to indexes of leaf nodes with that group, different groups may contain same node because of names file.
+
+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 addNamesToCounts();
+ void randomTopology();
+ void randomBlengths();
+ void randomLabels(vector<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&);
+ int populateNewTree(vector<Node>&, int, int&);
+ void printBranch(int, ostream&, string, vector<Node>&);