X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterdoturcommand.h;h=dd61a35bdcf3e45a72a590ec9b430584cc30376d;hb=d263f4b3a4f96c672317d317061f6adb72656427;hp=5358488c549ca911f9015a6e3f6caba81b9b4286;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index 5358488..dd61a35 100644
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -25,16 +25,19 @@ public:
 	~ClusterDoturCommand(){}
 	
 	vector<string> setParameters();
-	string getCommandName()			{ return "cluster.classic";			}
-	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getHelpString();	
+	string getCommandName()			{ return "cluster.classic";		}
+	string getCommandCategory()		{ return "Clustering";			}
+    string getOutputFileNameTag(string, string);
+	string getHelpString();		
+	string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster.classic\n";}
+	string getDescription()		{ return "cluster your sequences into OTUs using DOTUR’s method"; }
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	bool abort, hard, sim;
-	string method, fileroot, tag, outputDir, phylipfile, namefile;
+	string method, fileroot, tag, outputDir, phylipfile, namefile, countfile;
 	double cutoff;
 	int precision, length;
 	ofstream sabundFile, rabundFile, listFile;