changed defaults in allign.seqs command

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 3c250db030b04740e59df7ce24ba6b2752dc2023..e900af4f8b0cc434bf16fae2f15535779032f901 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -13,6 +13,8 @@
 #include "command.hpp"
 #include "unweighted.h"
 #include "treemap.h"
+#include "sharedutilities.h"
+#include "fileoutput.h"
 
 
 using namespace std;
@@ -23,15 +25,17 @@ class UnifracUnweightedCommand : public Command {
        
        public:
                UnifracUnweightedCommand();     
-               ~UnifracUnweightedCommand() { delete unweighted; }
+               ~UnifracUnweightedCommand() { delete unweighted; delete util; }
                int execute();  
        
        private:
                GlobalData* globaldata;
+               SharedUtil* util;
+               FileOutput* output;
                vector<Tree*> T;           //user trees
                TreeMap* tmap;
                Unweighted* unweighted;
-               string sumFile, unweightedFile, unweightedFileout;
+               string sumFile, allGroups;
                vector<string> groupComb; // AB. AC, BC...
                int iters, numGroups, numComp, counter;
                EstOutput userData;                     //unweighted score info for user tree
@@ -47,13 +51,9 @@ class UnifracUnweightedCommand : public Command {
                ofstream outSum, out;
                ifstream inFile;
                
-               void printUWSummaryFile();
+               void printUWSummaryFile(int);
                void printUnweightedFile();
-               void setGroups();  
-               void initFile(string);
-               void output(vector<double>);
-               void resetFile();
- 
+                
                
 };