X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=55d3c92aabca1083fd300896a813f41374eca860;hb=010638fc7580c18a51f5ed650e9ee7589c8fb2d4;hp=9dee24d2eec051428b9cbb977042a91195cca5f5;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1;p=mothur.git

diff --git a/tree.h b/tree.h
index 9dee24d..55d3c92 100644
--- a/tree.h
+++ b/tree.h
@@ -12,43 +12,48 @@
 
 using namespace std;
 
-#include <string>
-#include <iostream>
-#include <vector>
-
-struct Node  {
-		string	name;
-		string	group;
-		float	branchLength;
-		Node*	parent;
-		Node*	lchild;
-		Node*	rchild;
-};		
-
+#include "treenode.h"
+#include "globaldata.hpp"
 
+/* This class represents the treefile. */
 
 class Tree {
 	public: 
-		Tree();
-		~Tree();
+		Tree();		//to generate a tree from a file
+		~Tree() {};
 		
-		Node* getParent(Node);
-		Node* getLChild(Node);
-		Node* getRChild(Node);
 		
-		void setParent(Node);
-		void setLChild(Node);
-		void setRChild(Node);
+		void getCopy(Tree*);  //makes tree a copy of the one passed in.
+		void assembleRandomTree();
+		void assembleRandomUnifracTree();
+		void createNewickFile();
+		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
 		
+		//this function takes the leaf info and populates the non leaf nodes
+		void assembleTree();		
 		
-		Tree generateRandomTree();
-		
-		vector<Node> leaves;		//gives you easy access to the leaves of the tree to generate the parsimony score
+		vector<Node> tree;		//the first n nodes are the leaves, where n is the number of sequences.
 		
 	private:
+		GlobalData* globaldata;
+		int numNodes, numLeaves;
+		ofstream out;
+		string filename;
+		
+		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);
+		void randomTopology();
+		void randomBlengths();
+		void randomLabels();
+		int findRoot();  //return index of root node
+		void printBranch(int);  //recursively print out tree
+		void setGroups();
 };
 
-
-
-
-#endif
\ No newline at end of file
+#endif