added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 102d56546c24d427616b0388fcf80b869312b694..2d9d4f815f90bd889c10b886853ca415840060f5 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -11,16 +11,14 @@
  */
 
 #include "treenode.h"
-#include "globaldata.hpp"
-
-class GlobalData;
+#include "treemap.h"
 /* This class represents the treefile. */
 
 class Tree {
 public: 
-       Tree(string); 
-       Tree(int); 
-       Tree();         //to generate a tree from a file
+       Tree(string);  //do not use tree generated by this constructor its just to extract the treenames, its a chicken before the egg thing that needs to be revisited.
+       Tree(int, TreeMap*); 
+       Tree(TreeMap*);         //to generate a tree from a file
        ~Tree();
        
        void getCopy(Tree*);  //makes tree a copy of the one passed in.
@@ -47,7 +45,7 @@ public:
        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;
+       TreeMap* tmap;
        int numNodes, numLeaves;
        ofstream out;
        string filename;
@@ -68,6 +66,7 @@ private:
                                                        //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;