X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.h;h=b12f76f4e9812b7d26de87769d746167fe3552c1;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=8e2d74b0b52252250cd5cede8a1bf9b10a689449;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git

diff --git a/summarycommand.h b/summarycommand.h
index 8e2d74b..b12f76f 100644
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -9,14 +9,11 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "sabundvector.hpp"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 
 /* The summary() command:
@@ -36,18 +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, 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