X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=venncommand.h;h=4762902c51d4f1195e8f3fc604b1781ddb1df39f;hp=29beeadc32f422f8b053e1da86f483032e496e8d;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/venncommand.h b/venncommand.h
index 29beead..4762902 100644
--- a/venncommand.h
+++ b/venncommand.h
@@ -11,46 +11,43 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sharedlistvector.h"
 #include "venn.h"
 #include "validcalculator.h"
 
-
-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();
+	~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;
-	ReadOTUFile* read;
 	InputData* input;
 	SharedListVector* SharedList;
 	Venn* venn;
 	vector<Calculator*> vennCalculators;	
-	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
-	set< set<int> > combosOfFour;
+	set< set<int> > combos;
 	SAbundVector* sabund;
-	int abund;
+	int abund, fontsize, perm;
 	
-	bool abort, allLines, nseqs, perm;
+	bool abort, allLines, nseqs, sharedOtus;
 	set<string> labels; //holds labels to be used
-	string format, groups, calc, label, outputDir;
+	string format, groups, calc, label, outputDir, sharedfile, listfile, inputfile;
 	vector<string> Estimators, Groups, outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	set< set<int> > findCombinations(int);
 	int getCombos(set<int>, set< set<int> >&);