X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterdoturcommand.h;h=dd61a35bdcf3e45a72a590ec9b430584cc30376d;hb=006601d68abe8d0061f77e8d28323b160750e343;hp=643551a35c0289efe46a9bd5f2e280566faea31e;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index 643551a..dd61a35 100644
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -27,8 +27,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "cluster.classic";		}
 	string getCommandCategory()		{ return "Clustering";			}
-	string getHelpString();	
-	string getCitation() { return "Schloss 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"; }
+    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(); 
@@ -36,7 +37,7 @@ public:
 	
 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;