Merge remote-tracking branch 'origin'

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index a5b792ea7c8a3e35345606765aaa3ede84916a86..5786da220046713d4eb18a26f2aba4529011093c 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -35,8 +35,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "cluster";             }
        string getCommandCategory()             { return "Clustering";  }
-       string getOutputFileNameTag(string, string);
+       
        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"; }
        string getDescription()         { return "cluster your sequences into OTUs using a distance matrix"; }
        
@@ -55,6 +56,7 @@ private:
 
        string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
        double cutoff;
+    float adjust;
        string showabund, timing;
        int precision, length;
        ofstream sabundFile, rabundFile, listFile;