added indicator command

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 1c44d8c919805c24072e0f6ab314789393ed63ce..102d56546c24d427616b0388fcf80b869312b694 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -19,10 +19,12 @@ class GlobalData;
 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);
@@ -34,7 +36,7 @@ public:
        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
@@ -65,6 +67,7 @@ private:
                                                        //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&);
                
        MothurOut* m;