added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index e093ceb2de8efbbacf2d58e4d46257563b0797c3..26d392e86acd94654ec3a5ec6351770e4efb995f 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -13,6 +13,8 @@
 #include "parsimony.h"
 #include "treemap.h"
 #include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
 using namespace std;
 
@@ -22,11 +24,13 @@ class ParsimonyCommand : public Command {
        
        public:
                ParsimonyCommand();     
-               ~ParsimonyCommand() { delete pars; }
+               ~ParsimonyCommand() { delete pars; delete util; delete output; }
                int execute();  
        
        private:
                GlobalData* globaldata;
+               SharedUtil* util;
+               FileOutput* output;
                vector<Tree*> T;           //user trees
                Tree* randT;  //random tree
                Tree* copyUserTree; 
@@ -34,7 +38,7 @@ class ParsimonyCommand : public Command {
                TreeMap* savetmap;
                Parsimony* pars;
                vector<string> groupComb; // AB. AC, BC...
-               string parsFile, parsFileout, sumFile, randomtree;
+               string 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.
@@ -55,11 +59,6 @@ class ParsimonyCommand : public Command {
                void printParsimonyFile();  
                void printUSummaryFile();
                void getUserInput();
-               void setGroups();
-               void initFile(string);
-               void output(vector<double>);
-               void resetFile();
-
                
 };