X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;h=f6f867877620e7e6e69e4e446bdbe8da3815861a;hb=c7f1abdd8b8d24f186320880515a848039ce051a;hp=e900af4f8b0cc434bf16fae2f15535779032f901;hpb=9653c9f8c1b63ecb1a63b45e781c303713d5b5df;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index e900af4..f6f8678 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -17,16 +17,15 @@
 #include "fileoutput.h"
 
 
-using namespace std;
-
 class GlobalData;
 
 class UnifracUnweightedCommand : public Command {
 	
 	public:
-		UnifracUnweightedCommand();	
-		~UnifracUnweightedCommand() { delete unweighted; delete util; }
-		int execute();	
+		UnifracUnweightedCommand(string);	
+		~UnifracUnweightedCommand() { globaldata->Groups.clear();  if (abort == false) { delete unweighted; delete util; } }
+		int execute();
+		void help();	
 	
 	private:
 		GlobalData* globaldata;
@@ -45,18 +44,19 @@ class UnifracUnweightedCommand : public Command {
 		map<float, float>  validScores;  //map contains scores from random
 		vector< map<float, float> > rscoreFreq;  //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
 		vector< map<float, float> > rCumul;  //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
-		map<float, float>::iterator it2;
-		map<float, float>::iterator it;
 		
+		bool abort, phylip, random;
+		string groups, itersString, outputDir;
+		vector<string> Groups, outputNames; //holds groups to be used
+
 		ofstream outSum, out;
 		ifstream inFile;
 		
 		void printUWSummaryFile(int);
 		void printUnweightedFile();
+		void createPhylipFile(int);
 		 
 		
 };
 
-
-
-#endif
\ No newline at end of file
+#endif