X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.h;h=77dd10d3490999def3789b91d405ac76e470f360;hb=afed323beddfc099c365104b9071600aea9731bd;hp=5f55deea98379b5813bed720fe9fad3bd76ac23f;hpb=e911fa88572a16ef40e0b51fb132ab6e02370797;p=mothur.git

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 5f55dee..77dd10d 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -23,7 +23,7 @@ class GlobalData;
 class UnifracWeightedCommand : public Command {
 	
 	public:
-		UnifracWeightedCommand(string);	
+		UnifracWeightedCommand(string);
 		~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
 		int execute();	
 		void help();
@@ -39,7 +39,7 @@ class UnifracWeightedCommand : public Command {
 		Tree* randT;  //random tree
 		TreeMap* tmap;
 		Weighted* weighted;
-		string sumFile;
+		string sumFile, outputDir;
 		int iters, numGroups, numComp, counter;
 		EstOutput userData;			//weighted score info for user tree
 		EstOutput randomData;		//weighted score info for random trees
@@ -49,15 +49,16 @@ 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;
+		bool abort, phylip, random;
 		string groups, itersString;
-		vector<string> Groups; //holds groups to be used
+		vector<string> Groups, outputNames; //holds groups to be used
 
 		
 		ofstream outSum;
 		
 		void printWSummaryFile();
 		void printWeightedFile();  
+		void createPhylipFile();
 		//void removeValidScoresDuplicates();
 		int findIndex(float, int);
 		void calculateFreqsCumuls();