X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=venncommand.h;h=98a59d404099dcb32052e07e93644be9f01e2869;hp=f8151c1bdf0e3a547638639dfbf2aa5ac9f437ed;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=62f1ae1378c4c36175ec11fec8f70a3d2d26112e

diff --git a/venncommand.h b/venncommand.h
index f8151c1..98a59d4 100644
--- a/venncommand.h
+++ b/venncommand.h
@@ -11,35 +11,50 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
 #include "sharedlistvector.h"
 #include "venn.h"
-
-
-class GlobalData;
-
+#include "validcalculator.h"
 
 class VennCommand : public Command {
 
 public:
+	VennCommand(string);
 	VennCommand();
-	~VennCommand();
-	int execute();
+	~VennCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "venn";					}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Venn"; }
+	string getDescription()		{ return "generates a Venn diagram from data provided in a shared file"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
-	ReadMatrix* read;
 	InputData* input;
 	SharedListVector* SharedList;
-	SharedOrderVector* order;
-	OrderVector* ordersingle;
 	Venn* venn;
-	string format;
+	vector<Calculator*> vennCalculators;	
+	vector<SharedRAbundVector*> lookup;
+	set< set<int> > combosOfFour;
+	SAbundVector* sabund;
+	int abund, fontsize;
 	
-	void setGroups();
+	bool abort, allLines, nseqs, perm, sharedOtus;
+	set<string> labels; //holds labels to be used
+	string format, groups, calc, label, outputDir, sharedfile, listfile, inputfile;
+	vector<string> Estimators, Groups, outputNames;
+	
+	set< set<int> > findCombinations(int);
+	int getCombos(set<int>, set< set<int> >&);
+
 
 };
 
 
 
-#endif
\ No newline at end of file
+#endif