X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.h;fp=phylodiversitycommand.h;h=52cd3e27953ebac12619df1148e0e9bf932c8261;hb=0c64d4590ecba2cb19475ca0af206d85bfb2195c;hp=5d0cccf249099ac51d86b58e41e5098793ef3f3c;hpb=72e0be6b9c80009d4dbee24e8d690ad9514dc6fb;p=mothur.git

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index 5d0cccf..52cd3e2 100644
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -39,10 +39,11 @@ private:
 		string groups, outputDir, treefile, groupfile, namefile;
 		vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
 		
+        map<string, int> getRootForGroups(Tree* t);
 		int readNamesFile();
 		void printData(set<int>&, map< string, vector<float> >&, ofstream&, int);
 		void printSumData(map< string, vector<float> >&, ofstream&, int);
-		vector<float> calcBranchLength(Tree*, int, map< string, set<int> >&);
+        vector<float> calcBranchLength(Tree*, int, vector< map<string, bool> >&, map<string, int>);
 		int driver(Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&, bool);
 		int createProcesses(vector<int>&, Tree*, map< string, vector<float> >&, map<string, vector<float> >&, int, int, vector<int>&, set<int>&, ofstream&, ofstream&);