X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=2eee7c44e674073420c217f1b4d49aa4dc769497;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=fa87d8fa2a705287045489f9cdfef7f3bf51901c;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index fa87d8f..2eee7c4 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -60,8 +60,8 @@ class UnifracWeightedCommand : public Command {
 		vector< map<float, float> > rCumul;  //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c								
 		map<float, float>  validScores;  //map contains scores from random
 		
-		bool abort, phylip, random;
-		string groups, itersString;
+		bool abort, phylip, random, includeRoot;
+		string groups, itersString, outputForm;
 		vector<string> Groups, outputNames; //holds groups to be used
 		map<string, vector<string> > outputTypes;
 		int processors;
@@ -75,8 +75,8 @@ class UnifracWeightedCommand : public Command {
 		//void removeValidScoresDuplicates();
 		int findIndex(float, int);
 		void calculateFreqsCumuls();
-		int createProcesses(Tree*,  vector< vector<string> >, vector<double>&, vector< vector<double> >&);
-		int driver(Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
+		int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
+		int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
 		
 };