fixed some bugs and added scriptengine

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 8b77d3ddbed48dddb5de57dfa44394118c7a1920..a5259552d8fa09f18d1e81b1776ef94f84724748 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -10,11 +10,10 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
+class GlobalData;
 /* This class represents the treefile. */
 
 class Tree {
@@ -22,7 +21,6 @@ public:
        Tree();         //to generate a tree from a file
        ~Tree();
        
-       
        void getCopy(Tree*);  //makes tree a copy of the one passed in.
        void assembleRandomTree();
        void assembleRandomUnifracTree(vector<string>);
@@ -36,6 +34,7 @@ public:
        void printTree();
        void print(ostream&);
        void printForBoot(ostream&);
+       int findRoot();  //return index of root node
        
        //this function takes the leaf info and populates the non leaf nodes
        void assembleTree();            
@@ -55,8 +54,12 @@ private:
        void randomBlengths();
        void randomLabels(vector<string>);
        void randomLabels(string, string);
-       int findRoot();  //return index of root node
        void printBranch(int, ostream&, string);  //recursively print out tree
+       void parseTreeFile();   //parses through tree file to find names of nodes and number of them
+                                                       //this is required in case user has sequences in the names file that are
+                                                       //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.
+       void readTreeString(ifstream&);
 };
 
 #endif