added root parameter to the unifrac commands so you can choose to include the entire...

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index fa87d8fa2a705287045489f9cdfef7f3bf51901c..2eee7c44e674073420c217f1b4d49aa4dc769497 100644 (file)
--- 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> >&);
                
 };