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[mothur.git] / venncommand.h

diff --git a/venncommand.h b/venncommand.h
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+#ifndef VENNCOMMAND_H
+#define VENNCOMMAND_H
+/*
+ *  venncommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/30/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedlistvector.h"
+#include "venn.h"
+#include "validcalculator.h"
+
+class VennCommand : public Command {
+
+public:
+       VennCommand(string);
+       VennCommand();
+       ~VennCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "venn";                                        }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       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:
+       InputData* input;
+       SharedListVector* SharedList;
+       Venn* venn;
+       vector<Calculator*> vennCalculators;    
+       vector<SharedRAbundVector*> lookup;
+       set< set<int> > combosOfFour;
+       SAbundVector* sabund;
+       int abund, fontsize;
+       
+       bool abort, allLines, nseqs, perm;
+       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