X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.h;h=ef8b8f17e37051be4951d6dd662d0db1beb1dbaa;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=30a578221f09042817534b51f91d8e33f3125c6c;hpb=0e051b4cfda410b0d441da6ff2f96d4bbe1d9e5a;p=mothur.git

diff --git a/phylotypecommand.h b/phylotypecommand.h
index 30a5782..ef8b8f1 100644
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -26,19 +26,22 @@ 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()); }
 	
 private:
 	bool abort, allLines;
-	string taxonomyFileName, label, outputDir, namefile;
+	string taxonomyFileName, label, outputDir, namefile, countfile;
 	set<string> labels; //holds labels to be used
 	int cutoff;
 	map<string, string> namemap;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	map<int, int> currentNodes;
 	map<int, int> parentNodes;