X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=venncommand.h;h=29beeadc32f422f8b053e1da86f483032e496e8d;hb=b663591fb57c9508f017fd0891911fd959530125;hp=063b8afdfbf4f733c6e537b6c245dc6f17aca516;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git

diff --git a/venncommand.h b/venncommand.h
index 063b8af..29beead 100644
--- a/venncommand.h
+++ b/venncommand.h
@@ -15,7 +15,6 @@
 #include "sharedlistvector.h"
 #include "venn.h"
 #include "validcalculator.h"
-#include "sharedutilities.h"
 
 
 class GlobalData;
@@ -24,26 +23,41 @@ class GlobalData;
 class VennCommand : public Command {
 
 public:
+	VennCommand(string);
 	VennCommand();
 	~VennCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
 	ReadOTUFile* read;
-	SharedUtil* util;
 	InputData* input;
 	SharedListVector* SharedList;
-	SharedOrderVector* order;
-	OrderVector* ordersingle;
 	Venn* venn;
-	string format;
 	vector<Calculator*> vennCalculators;	
 	ValidCalculators* validCalculator;
+	vector<SharedRAbundVector*> lookup;
+	set< set<int> > combosOfFour;
+	SAbundVector* sabund;
 	int abund;
+	
+	bool abort, allLines, nseqs, perm;
+	set<string> labels; //holds labels to be used
+	string format, groups, calc, label, outputDir;
+	vector<string> Estimators, Groups, outputNames;
+	map<string, vector<string> > outputTypes;
+	
+	set< set<int> > findCombinations(int);
+	int getCombos(set<int>, set< set<int> >&);
+
 
 };
 
 
 
-#endif
\ No newline at end of file
+#endif