class Tree {
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);
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&);
+ void print(ostream&, string);
int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
- void assembleTree();
+ 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;
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 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>&);
+
+ MothurOut* m;
+
};
#endif