parsimony fix

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index e854294834af55cb0cbe97ec035a0e01f78b66a3..2881dc61e200540588691de3f205420139510561 100644 (file)
--- 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"
@@ -33,6 +28,7 @@ class ParsimonyCommand : public Command {
                GlobalData* globaldata;
                vector<Tree*> T;           //user trees
                Tree* randT;  //random tree
+               Tree* copyUserTree; 
                TreeMap* tmap; 
                TreeMap* savetmap;
                Parsimony* pars;
@@ -56,6 +52,7 @@ class ParsimonyCommand : public Command {
                void printParsimonyFile();  
                void printUSummaryFile();
                void getUserInput();
+               void setGroups();
                
 };