X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.h;h=dd4e2377e93a0708d7722d13c19068e3db578bf8;hb=c5c7502f435e1413c19e373dab1dfebcaa67588d;hp=e093ceb2de8efbbacf2d58e4d46257563b0797c3;hpb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949;p=mothur.git

diff --git a/parsimonycommand.h b/parsimonycommand.h
index e093ceb..dd4e237 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -13,6 +13,7 @@
 #include "parsimony.h"
 #include "treemap.h"
 #include "progress.hpp"
+#include "sharedutilities.h"
 
 using namespace std;
 
@@ -22,11 +23,12 @@ class ParsimonyCommand : public Command {
 	
 	public:
 		ParsimonyCommand();	
-		~ParsimonyCommand() { delete pars; }
+		~ParsimonyCommand() { delete pars; delete util; }
 		int execute();	
 	
 	private:
 		GlobalData* globaldata;
+		SharedUtil* util;
 		vector<Tree*> T;	   //user trees
 		Tree* randT;  //random tree
 		Tree* copyUserTree; 
@@ -34,7 +36,7 @@ class ParsimonyCommand : public Command {
 		TreeMap* savetmap;
 		Parsimony* pars;
 		vector<string> groupComb; // AB. AC, BC...
-		string parsFile, parsFileout, sumFile, randomtree;
+		string parsFile, parsFileout, sumFile, randomtree, allGroups;
 		int iters, numGroups, numComp, counter;
 		vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
 		vector< vector<float> > userTreeScores; //scores for users trees for each comb.
@@ -55,7 +57,6 @@ class ParsimonyCommand : public Command {
 		void printParsimonyFile();  
 		void printUSummaryFile();
 		void getUserInput();
-		void setGroups();
 		void initFile(string);
 		void output(vector<double>);
 		void resetFile();