X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=4f77e50578bad8c234ae4711adf69a612175b088;hb=bede5752eaeedb5a7e339439b6ba2f6670bca2b9;hp=6404db784eec791783e609dfc8ff8d8a971c61aa;hpb=9099173ea17b13be96563c7579ecc8dc2ef65d20;p=mothur.git

diff --git a/tree.h b/tree.h
index 6404db7..4f77e50 100644
--- a/tree.h
+++ b/tree.h
@@ -10,8 +10,6 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
@@ -20,19 +18,23 @@ using namespace std;
 class Tree {
 public: 
 	Tree();		//to generate a tree from a file
-	~Tree() {};
+	~Tree();
 	
 	
 	void getCopy(Tree*);  //makes tree a copy of the one passed in.
 	void assembleRandomTree();
-	void assembleRandomUnifracTree();
-	void createNewickFile();
+	void assembleRandomUnifracTree(vector<string>);
+	void assembleRandomUnifracTree(string, string);
+	void createNewickFile(string);
 	int getIndex(string);
 	void setIndex(string, int);
 	int getNumNodes() { return numNodes; }
 	int getNumLeaves(){	return numLeaves; }
-	map<string, int> mergeUserGroups(int);  //returns a map with a groupname and the number of times that group was seen in the children
+	map<string, int> mergeUserGroups(int, vector<string>);  //returns a map with a groupname and the number of times that group was seen in the children
 	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();		
@@ -47,13 +49,12 @@ 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> Tree::mergeGcounts(int);
+	map<string,int> mergeGcounts(int);
 	void randomTopology();
 	void randomBlengths();
-	void randomLabels();
-	int findRoot();  //return index of root node
-	void printBranch(int);  //recursively print out tree
-	void setGroups();
+	void randomLabels(vector<string>);
+	void randomLabels(string, string);
+	void printBranch(int, ostream&, string);  //recursively print out tree
 };
 
 #endif