changed unifrac.weighted()

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 5429e77acf8411bd3836e3cc6fa3b1a23db24a5a..ba30d4016886123c1d8b33967899d699619b30b4 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"
@@ -33,10 +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();
                
 };