added concensus command and updated calcs

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 0e3428d35721d19573153f04a4e19cd693cca6f3..ea141d1610c41676cad785690e32b8a16268cbd3 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -14,9 +14,10 @@
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "sharedlistvector.h"
 #include "validcalculator.h"
+#include "sharedutilities.h"
 
 /*The summary.shared() command
        The summary.shared command can only be executed after a successful read.shared command. 
@@ -43,19 +44,18 @@ public:
        int execute();
        
 private:
-       void getSharedVectors();
-       
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
+       SharedUtil* util;
        vector<Calculator*> sumCalculators;     
        InputData* input;
        ValidCalculators* validCalculator;
        SharedListVector* SharedList;
        SharedOrderVector* order;
        vector<SharedRAbundVector*> lookup;
-       SharedRAbundVector* shared1, shared2;
-       string outputFileName, format;
-       ofstream outputFileHandle;
+       string outputFileName, format, outAllFileName;
+       ofstream outputFileHandle, outAll;
+       bool mult;
 
 };