X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.h;h=ba30d4016886123c1d8b33967899d699619b30b4;hb=3c5c4e255ee8c36feb9e97aebc4e792e6ff8c440;hp=5429e77acf8411bd3836e3cc6fa3b1a23db24a5a;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 5429e77..ba30d40 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -9,11 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "parsimony.h"
 #include "treemap.h"
@@ -33,10 +28,12 @@ class ParsimonyCommand : public Command {
 		GlobalData* globaldata;
 		vector<Tree*> T;	   //user trees
 		Tree* randT;  //random tree
-		TreeMap* tmap;
+		Tree* copyUserTree; 
+		TreeMap* tmap; 
+		TreeMap* savetmap;
 		Parsimony* pars;
-		string parsFile, sumFile, distFile;
-		int iters, randomtree, numGroups;
+		string parsFile, sumFile, randomtree;
+		int iters, numGroups;
 		vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
 		vector<float> userTreeScores; //scores for users trees
 		vector<float> UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
@@ -50,11 +47,12 @@ class ParsimonyCommand : public Command {
 		map<int, float>::iterator it;
 		map<int, float>::iterator it2;
 		
-		ofstream out, outSum, outDist;
+		ofstream out, outSum;
 		
 		void printParsimonyFile();  
 		void printUSummaryFile();
 		void getUserInput();
+		void setGroups();
 		
 };