X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=1c44d8c919805c24072e0f6ab314789393ed63ce;hb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;hp=a076cef8eb30e3cda0efd8d74fcb680ae007cb24;hpb=5f44783e6d74a9c207492ac244210c915cadc272;p=mothur.git

diff --git a/tree.h b/tree.h
index a076cef..1c44d8c 100644
--- a/tree.h
+++ b/tree.h
@@ -18,6 +18,7 @@ class GlobalData;
 
 class Tree {
 public: 
+	Tree(string); 
 	Tree();		//to generate a tree from a file
 	~Tree();
 	
@@ -37,10 +38,12 @@ public:
 	int findRoot();  //return index of root node
 	
 	//this function takes the leaf info and populates the non leaf nodes
-	void assembleTree();	
+	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;
@@ -55,14 +58,16 @@ private:
 	void randomTopology();
 	void randomBlengths();
 	void randomLabels(vector<string>);
-	void randomLabels(string, 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&);
-	
+		
+	MothurOut* m;
+		
 };
 
 #endif