X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=0b316c3042f01cbb000a3aed975a778f8af5f9fc;hb=1916dd65829d6bb5b8bef74eddc61ea38fccf63a;hp=99cd68fa7f4b71dfeebffc90ad649a1f01c6564e;hpb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;p=mothur.git

diff --git a/tree.h b/tree.h
index 99cd68f..0b316c3 100644
--- a/tree.h
+++ b/tree.h
@@ -18,10 +18,13 @@ class GlobalData;
 
 class Tree {
 public: 
+	Tree(string); 
+	Tree(int); 
 	Tree();		//to generate a tree from a file
 	~Tree();
 	
 	void getCopy(Tree*);  //makes tree a copy of the one passed in.
+	void getSubTree(Tree*, vector<string>);  //makes tree a that contains only the names passed in.
 	void assembleRandomTree();
 	void assembleRandomUnifracTree(vector<string>);
 	void assembleRandomUnifracTree(string, string);
@@ -33,14 +36,16 @@ public:
 	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&);
+	void print(ostream&, string);
 	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;
@@ -62,12 +67,11 @@ private:
 							//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&);
-	
+	int populateNewTree(vector<Node>&, int, int&);
+	void printBranch(int, ostream&, string, vector<Node>&);
+		
 	MothurOut* m;
-	
+		
 };
 
 #endif