fixed multiple bugs for 1.4 release

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 6188b96bea172f9b63a7c45c7a92b9072b6f1e1a..e73714a3e294f0af471838d38beb39b49d8c1938 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -9,15 +9,14 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <vector>
+
 #include "command.hpp"
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
+#include "validcalculator.h"
+
 
 /*The summary.shared() command
        The summary.shared command can only be executed after a successful read.shared command. 
@@ -44,21 +43,17 @@ public:
        int execute();
        
 private:
-       void getGroupComb();
-       void getSharedVectors();
-       
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        vector<Calculator*> sumCalculators;     
        InputData* input;
-       ListVector* list;
-       SharedOrderVector* order;
+       ValidCalculators* validCalculator;
+       SharedListVector* SharedList;
        vector<SharedRAbundVector*> lookup;
-       SharedRAbundVector* shared1, shared2;
-       string outputFileName;
-       ofstream outputFileHandle;
-       vector<string> groupComb;
+       string outputFileName, format, outAllFileName;
+       ofstream outputFileHandle, outAll;
+       bool mult;
 
 };
 
-#endif
\ No newline at end of file
+#endif