added get.rabund and get.sabund command and fixed bug introduced by line by line...

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index e10aa44e8462d4690e095e4ab1ef37ea8542e9cd..5cd93a94c0dcf96547ee409d4ca641092309d2bc 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -13,6 +13,9 @@
 #include "command.hpp"
 #include "weighted.h"
 #include "treemap.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
 using namespace std;
 
@@ -22,11 +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.
@@ -34,7 +39,7 @@ class UnifracWeightedCommand : public Command {
                Tree* randT;  //random tree
                TreeMap* tmap;
                Weighted* weighted;
-               string weightedFile, weightedFileout, sumFile;
+               string sumFile;
                int iters, numGroups, numComp, counter;
                EstOutput userData;                     //weighted score info for user tree
                EstOutput randomData;           //weighted score info for random trees
@@ -53,12 +58,8 @@ 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();
-
+               
 };