line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 9e4a8c87963289644f17a10ce07c3a55f7cfbb7b..0f2f75386b23382699fbb2b524268fee373dfc25 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -14,10 +14,9 @@
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
-#include "sharedlistvector.h"
+#include "readotu.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. 
@@ -45,16 +44,16 @@ public:
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
-       SharedUtil* util;
+       ReadOTUFile* read;
        vector<Calculator*> sumCalculators;     
        InputData* input;
        ValidCalculators* validCalculator;
        SharedListVector* SharedList;
-       SharedOrderVector* order;
        vector<SharedRAbundVector*> lookup;
-       string outputFileName, format;
-       ofstream outputFileHandle;
+       string outputFileName, format, outAllFileName;
+       ofstream outputFileHandle, outAll;
+       bool mult;
+       void process(vector<SharedRAbundVector*>);
 
 };