removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 0b316c3042f01cbb000a3aed975a778f8af5f9fc..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;