started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index ea2c41814ac1940a61bd8c48995ecebcff30f324..751343b3f641d29799c8704d71f6684c04d504ac 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -14,6 +14,8 @@
 #include "weighted.h"
 #include "treemap.h"
 #include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
 using namespace std;
 
@@ -23,11 +25,13 @@ class UnifracWeightedCommand : public Command {
        
        public:
                UnifracWeightedCommand();       
-               ~UnifracWeightedCommand() { delete weighted; }
+               ~UnifracWeightedCommand() { delete weighted; delete util; }
                int execute();  
        
        private:
                GlobalData* globaldata;
+               SharedUtil* util;
+               FileOutput* output;
                vector<Tree*> T;           //user trees
                vector<double> utreeScores;  //user tree unweighted scores
                vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
@@ -54,11 +58,10 @@ class UnifracWeightedCommand : public Command {
                void printWeightedFile();  
                //void removeValidScoresDuplicates();
                int findIndex(float, int);
-               void setGroups(); 
                void calculateFreqsCumuls();
-               void initFile(string);
-               void output(vector<double>);
-               void resetFile();
+               //void initFile(string);
+               //void output(vector<double>);
+               //void resetFile();
 
 };