X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=venncommand.h;h=aa1e8562343f899fcaf1e1d60295c47799b533c1;hb=7ae40733a270f73ec8a331540cc7f28fd60b24fc;hp=d91aaef1c7e47185862cf1a681976a31c47ebb75;hpb=f20505bcd9f07e0b5f967be0e8d414076d9a5678;p=mothur.git

diff --git a/venncommand.h b/venncommand.h
index d91aaef..aa1e856 100644
--- a/venncommand.h
+++ b/venncommand.h
@@ -11,7 +11,7 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "sharedlistvector.h"
 #include "venn.h"
 #include "validcalculator.h"
@@ -23,27 +23,31 @@ class GlobalData;
 class VennCommand : public Command {
 
 public:
-	VennCommand();
+	VennCommand(string);
 	~VennCommand();
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
-	ReadMatrix* read;
+	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;
 	
-	void setGroups();
+	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