added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / venncommand.h

diff --git a/venncommand.h b/venncommand.h
index 30ff74eb0433240b784ef221e2e0bdc22d1f4066..aa1e8562343f899fcaf1e1d60295c47799b533c1 100644 (file)
--- a/venncommand.h
+++ b/venncommand.h
@@ -11,11 +11,10 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "sharedlistvector.h"
 #include "venn.h"
 #include "validcalculator.h"
-#include "sharedutilities.h"
 
 
 class GlobalData;
@@ -24,26 +23,31 @@ class GlobalData;
 class VennCommand : public Command {
 
 public:
-       VennCommand();
+       VennCommand(string);
        ~VennCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
-       SharedUtil* util;
+       ReadOTUFile* read;
        InputData* input;
        SharedListVector* SharedList;
-       SharedOrderVector* order;
-       OrderVector* ordersingle;
        Venn* venn;
-       string format;
        vector<Calculator*> vennCalculators;    
        ValidCalculators* validCalculator;
+       vector<SharedRAbundVector*> lookup;
+       SAbundVector* sabund;
        int abund;
+       
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string format, groups, calc, label, outputDir;
+       vector<string> Estimators, Groups;
+
 
 };
 
 
 
-#endif
\ No newline at end of file
+#endif