X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.h;h=534dc8eefcc643bda6f71d23291462b01c4d3940;hb=67ea6ccd74dbd64828d31b952808255f206364ff;hp=30a578221f09042817534b51f91d8e33f3125c6c;hpb=0e051b4cfda410b0d441da6ff2f96d4bbe1d9e5a;p=mothur.git

diff --git a/phylotypecommand.h b/phylotypecommand.h
index 30a5782..534dc8e 100644
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -26,8 +26,12 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "phylotype";		}
 	string getCommandCategory()		{ return "Clustering";		}
-	string getHelpString();	
 	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
+	string getDescription()		{ return "cluster your sequences into OTUs based on their classifications"; }
+
 	int execute();
 	void help() { m->mothurOut(getHelpString()); }
 	
@@ -38,7 +42,6 @@ private:
 	int cutoff;
 	map<string, string> namemap;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	map<int, int> currentNodes;
 	map<int, int> parentNodes;