X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=23ddf5dd87ed6d901d8db793861e34cb92b43e2d;hb=44b464979e91c2a1f144ac45ca12c14fcf6579f0;hp=a5259552d8fa09f18d1e81b1776ef94f84724748;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/tree.h b/tree.h
index a525955..23ddf5d 100644
--- a/tree.h
+++ b/tree.h
@@ -37,9 +37,10 @@ public:
 	int findRoot();  //return index of root node
 	
 	//this function takes the leaf info and populates the non leaf nodes
-	void assembleTree();		
+	int assembleTree();	
 	
 	vector<Node> tree;		//the first n nodes are the leaves, where n is the number of sequences.
+		
 private:
 	GlobalData* globaldata;
 	int numNodes, numLeaves;
@@ -48,18 +49,21 @@ 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.
-	void readTreeString(ifstream&);
+	int readTreeString(ifstream&);
+	MothurOut* m;
+	
 };
 
 #endif