X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=1c44d8c919805c24072e0f6ab314789393ed63ce;hb=d051154d778b77ba36dc603bbdb3c148a62a8e33;hp=55d3c92aabca1083fd300896a813f41374eca860;hpb=010638fc7580c18a51f5ed650e9ee7589c8fb2d4;p=mothur.git

diff --git a/tree.h b/tree.h
index 55d3c92..1c44d8c 100644
--- a/tree.h
+++ b/tree.h
@@ -10,50 +10,64 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
+class GlobalData;
 /* 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;
+public: 
+	Tree(string); 
+	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
+	int assembleTree();	
+	int assembleTree(string);	
+	
+	vector<Node> tree;		//the first n nodes are the leaves, where n is the number of sequences.
+	map< string, vector<int> > groupNodeInfo;	//maps group to indexes of leaf nodes with that group, different groups may contain same node because of names file.
+			
+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 addNamesToCounts();
+	void randomTopology();
+	void randomBlengths();
+	void randomLabels(vector<string>);
+	//void randomLabels(string, string);
+	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.
+	int readTreeString(ifstream&);
 		
-		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
+	MothurOut* m;
 		
-		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