X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clusterdoturcommand.h;h=ccfe03bb74c42d43921f8a8224c210bc7a3a7ab0;hp=3a3234933e65c885c89490738db9e85e6b95d5e3;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index 3a32349..ccfe03b 100644
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -27,16 +27,18 @@ 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 getDescription()		{ return "cluster your sequences into OTUs using dotur's method"; }
+    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(); 
 	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;