X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=99cd68fa7f4b71dfeebffc90ad649a1f01c6564e;hb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;hp=9dee24d2eec051428b9cbb977042a91195cca5f5;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1;p=mothur.git

diff --git a/tree.h b/tree.h
index 9dee24d..99cd68f 100644
--- a/tree.h
+++ b/tree.h
@@ -10,45 +10,64 @@
  *
  */
 
-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"
 
+class GlobalData;
+/* 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);
-		
+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
+	int assembleTree();	
+	
+	vector<Node> tree;		//the first n nodes are the leaves, where n is the number of sequences.
 		
-		Tree generateRandomTree();
-		
-		vector<Node> leaves;		//gives you easy access to the leaves of the tree to generate the parsimony score
-		
-	private:
+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&);
+	string readLabel(ifstream&);
+	string readName(ifstream&);
+	string readBranchLength(ifstream&);
+	
+	MothurOut* m;
+	
 };
 
-
-
-
-#endif
\ No newline at end of file
+#endif