X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=venncommand.h;h=4762902c51d4f1195e8f3fc604b1781ddb1df39f;hp=fe0e2a6c1a9a063e9eb08527c64b23703153fed0;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/venncommand.h b/venncommand.h
index fe0e2a6..4762902 100644
--- a/venncommand.h
+++ b/venncommand.h
@@ -25,8 +25,12 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "venn";					}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getHelpString();	
 	
+	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()); }	
 	
@@ -36,11 +40,11 @@ private:
 	Venn* venn;
 	vector<Calculator*> vennCalculators;	
 	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, sharedfile, listfile, inputfile;
 	vector<string> Estimators, Groups, outputNames;