added ability to put # in front of any line in the batch file you don't want to use

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 9e4a8c87963289644f17a10ce07c3a55f7cfbb7b..ea141d1610c41676cad785690e32b8a16268cbd3 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -14,7 +14,7 @@
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "sharedlistvector.h"
 #include "validcalculator.h"
 #include "sharedutilities.h"
@@ -45,7 +45,7 @@ public:
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        SharedUtil* util;
        vector<Calculator*> sumCalculators;     
        InputData* input;
@@ -53,8 +53,9 @@ private:
        SharedListVector* SharedList;
        SharedOrderVector* order;
        vector<SharedRAbundVector*> lookup;
-       string outputFileName, format;
-       ofstream outputFileHandle;
+       string outputFileName, format, outAllFileName;
+       ofstream outputFileHandle, outAll;
+       bool mult;
 
 };