X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clusterdoturcommand.h;h=ccfe03bb74c42d43921f8a8224c210bc7a3a7ab0;hp=643551a35c0289efe46a9bd5f2e280566faea31e;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=b72799e7908e2a3a0cf4f03e796b077a97ace6ac

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index 643551a..ccfe03b 100644
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -27,8 +27,10 @@ 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 getOutputPattern(string);		
+	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 +38,7 @@ 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;