X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.h;h=1bcb0cf490dda8358a6ba55f042e689abc51bf69;hb=cd37904452dc95b183ff313ff05720c562902487;hp=0da5f0c20548196ed65d6e200620a8b0d9009d39;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 0da5f0c..1bcb0cf 100644
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -9,15 +9,13 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
+#include "validcalculator.h"
 
 
 /*The rarefaction() command:
@@ -39,18 +37,27 @@ class GlobalData;
 class RareFactCommand : public Command {
 	
 public:
-	RareFactCommand();	
+	RareFactCommand(string);	
 	~RareFactCommand();
-	int execute();	
+	int execute();
+	void help();	
 	
 private:
 	GlobalData* globaldata;
 	vector<Display*> rDisplays;
-	ReadMatrix* read;
+	ReadOTUFile* read;
 	OrderVector* order;
 	InputData* input;
+	ValidCalculators* validCalculator;
 	Rarefact* rCurve;
-	int freq, nIters;
+	int freq, nIters, abund;
+
+	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