fixed multiple bugs for 1.4 release

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 0e3428d35721d19573153f04a4e19cd693cca6f3..e73714a3e294f0af471838d38beb39b49d8c1938 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -14,10 +14,10 @@
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
-#include "sharedlistvector.h"
+#include "readotu.h"
 #include "validcalculator.h"
 
+
 /*The summary.shared() command
        The summary.shared command can only be executed after a successful read.shared command. 
        It outputs a file for each estimator you choose to use.  The summary.shared command parameters are label, 
@@ -43,19 +43,16 @@ public:
        int execute();
        
 private:
-       void getSharedVectors();
-       
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        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;
 
 };