merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 0da5f0c20548196ed65d6e200620a8b0d9009d39..1bcb0cf490dda8358a6ba55f042e689abc51bf69 100644 (file)
--- 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