version working on mac with .tellg changed to unget for windows

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index 4b7e1616e18a99785505a6cbe1c196ce76e2cc99..b12f76f4e9812b7d26de87769d746167fe3552c1 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -13,7 +13,7 @@
 #include "sabundvector.hpp"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 
 /* The summary() command:
@@ -33,19 +33,27 @@ class GlobalData;
 class SummaryCommand : public Command {
 
 public:
-       SummaryCommand();
+       SummaryCommand(string);
        ~SummaryCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        vector<Calculator*> sumCalculators;     
        InputData* input;
        ValidCalculators* validCalculator;
        SAbundVector* sabund;
        string outputFileName;
        ofstream outputFileHandle;
-       int abund;
+       int abund, size;
+
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string line, label, calc;
+       vector<string>  Estimators;
+
 };
 #endif