added modify names parameter to set.dir

[mothur.git] / clusterdoturcommand.h

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index 5358488c549ca911f9015a6e3f6caba81b9b4286..ccfe03bb74c42d43921f8a8224c210bc7a3a7ab0 100644 (file)
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -25,16 +25,20 @@ public:
        ~ClusterDoturCommand(){}
        
        vector<string> setParameters();
-       string getCommandName()                 { return "cluster.classic";                     }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getCommandName()                 { return "cluster.classic";             }
+       string getCommandCategory()             { return "Clustering";                  }
+    
        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(); 
        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;