X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=1c44d8c919805c24072e0f6ab314789393ed63ce;hb=f09bacac01a842a74c1c1b69070852cc969ff506;hp=c90f51a451461ceca068f743ecefe8fd3e7cba5f;hpb=ac1da2a793271cb67f2a2155c5558e1fabdd6aba;p=mothur.git

diff --git a/tree.h b/tree.h
index c90f51a..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();
 	
@@ -37,9 +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;
@@ -48,18 +52,22 @@ private:
 	
 	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 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