X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clusterdoturcommand.h;h=ccfe03bb74c42d43921f8a8224c210bc7a3a7ab0;hp=ec2f083e987e47f3125f381bd0c1199307dbdaf8;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=f687723a8357916e86a05116978e6869b039ce36

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index ec2f083..ccfe03b 100644
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -27,9 +27,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "cluster.classic";		}
 	string getCommandCategory()		{ return "Clustering";			}
-    string getOutputFileNameTag(string, string);
-	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 getHelpString();	
+    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(); 
@@ -37,7 +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;