X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=6404db784eec791783e609dfc8ff8d8a971c61aa;hb=3c5c4e255ee8c36feb9e97aebc4e792e6ff8c440;hp=55d3c92aabca1083fd300896a813f41374eca860;hpb=010638fc7580c18a51f5ed650e9ee7589c8fb2d4;p=mothur.git

diff --git a/tree.h b/tree.h
index 55d3c92..6404db7 100644
--- a/tree.h
+++ b/tree.h
@@ -18,42 +18,42 @@ using namespace std;
 /* This class represents the treefile. */
 
 class Tree {
-	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();
-		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();		
-		
-		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();
+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();
+	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
+	void printTree();
+	
+	//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> 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