X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.h;h=3e6d8354af5eda2c21f85c632a09b886962afb37;hb=ca0785e447ca7aa7e2f0ab8bb1155db126b551ea;hp=2fca41a8388e7d3a6f20bbe79536cae9246eb2fb;hpb=163b300cfd7d4ca4e70c454be20f07b1d8346650;p=mothur.git

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 2fca41a..3e6d835 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -23,7 +23,7 @@ class UnifracUnweightedCommand : public Command {
 	
 	public:
 		UnifracUnweightedCommand(string);	
-		~UnifracUnweightedCommand() { delete unweighted; delete util; }
+		~UnifracUnweightedCommand() { globaldata->Groups.clear();  if (abort == false) { delete unweighted; delete util; } }
 		int execute();
 		void help();	
 	
@@ -36,7 +36,7 @@ class UnifracUnweightedCommand : public Command {
 		Unweighted* unweighted;
 		string sumFile, allGroups;
 		vector<string> groupComb; // AB. AC, BC...
-		int iters, numGroups, numComp, counter;
+		int iters, numGroups, numComp, counter, processors;
 		EstOutput userData;			//unweighted score info for user tree
 		EstOutput randomData;		//unweighted score info for random trees
 		vector< vector<float> > utreeScores; //scores for users trees for each comb.
@@ -45,15 +45,16 @@ class UnifracUnweightedCommand : public Command {
 		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.
 		
-		bool abort;
-		string groups, itersString;
-		vector<string> Groups; //holds groups to be used
+		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);
 		 
 		
 };