X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=7fc383806c946d8f22efab62c648f19095313feb;hb=825512fb96e5bb00e08665396d9fa6a8c4da5a68;hp=9dee24d2eec051428b9cbb977042a91195cca5f5;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1;p=mothur.git

diff --git a/tree.h b/tree.h
index 9dee24d..7fc3838 100644
--- a/tree.h
+++ b/tree.h
@@ -12,43 +12,51 @@
 
 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();
-		
-		Node* getParent(Node);
-		Node* getLChild(Node);
-		Node* getRChild(Node);
-		
-		void setParent(Node);
-		void setLChild(Node);
-		void setRChild(Node);
-		
-		
-		Tree generateRandomTree();
-		
-		vector<Node> leaves;		//gives you easy access to the leaves of the tree to generate the parsimony score
-		
-	private:
+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>);
+	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, 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();		
+	
+	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> mergeGcounts(int);
+	void randomTopology();
+	void randomBlengths();
+	void randomLabels(vector<string>);
+	void randomLabels(string, string);
+	void printBranch(int, ostream&, string);  //recursively print out tree
 };
 
-
-
-
-#endif
\ No newline at end of file
+#endif