added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / clusterdoturcommand.h

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index 3a3234933e65c885c89490738db9e85e6b95d5e3..0f8657c6236baf9554a136b464118d9104b6dc93 100644 (file)
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -27,16 +27,17 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "cluster.classic";             }
        string getCommandCategory()             { return "Clustering";                  }
-       string getHelpString(); 
+    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 getDescription()         { return "cluster your sequences into OTUs using dotur's method"; }
+       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;