speed up rarefaction.shared

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index e7d2abc239044e7e4e2de376e0503e580e623f5d..1935398ac1c312020e03edc32b30fc7ce10045fb 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -9,18 +9,12 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
-#include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
-#include "groupmap.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
+#include "validcalculator.h"
 
 /* The rarefaction.shared() command:
        The rarefaction command generates a rarefaction curve from a given file representing several groups.  
@@ -45,15 +39,15 @@ public:
        
 private:
        GlobalData* globaldata;
-       GroupMap* groupmap;
-       SharedListVector* SharedList;
-       ReadMatrix* read;
-       SharedOrderVector* order;
+       ReadOTUFile* read;
+       vector<SharedRAbundVector*> lookup;
        InputData* input;
+       ValidCalculators* validCalculator;
        Rarefact* rCurve;
        vector<Display*> rDisplays;
        int freq, nIters;
+       string format;
 
 };
 
-#endif
\ No newline at end of file
+#endif