sped up unifrac weighted.

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 37028be57e90f3d5d38eeb3080b36a8538e8bf8e..1c44d8c919805c24072e0f6ab314789393ed63ce 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -18,6 +18,7 @@ class GlobalData;
 
 class Tree {
 public: 
+       Tree(string); 
        Tree();         //to generate a tree from a file
        ~Tree();
        
@@ -37,10 +38,12 @@ public:
        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;
@@ -62,7 +65,9 @@ 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&);
-       
+               
+       MothurOut* m;
+               
 };
 
 #endif