added name option to read.tree for use in unifrac and parimony commands

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index c90f51a451461ceca068f743ecefe8fd3e7cba5f..a076cef8eb30e3cda0efd8d74fcb680ae007cb24 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -37,9 +37,10 @@ public:
        int findRoot();  //return index of root node
        
        //this function takes the leaf info and populates the non leaf nodes
-       void assembleTree();            
+       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;
@@ -48,8 +49,9 @@ private:
        
        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>);
@@ -60,6 +62,7 @@ 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&);
+       
 };
 
 #endif