changes while testing

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index b5b295f1edb4495d321a7e614db1e8309d8bc481..3865bb20811a0ac29e29e0fec02392268ea0a657 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -31,8 +31,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "mgcluster";   }
        string getCommandCategory()             { return "Clustering";  }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
        string getDescription()         { return "cluster your sequences into OTUs using a blast file"; }
 
@@ -55,9 +56,9 @@ private:
        string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
        ofstream sabundFile, rabundFile, listFile;
        double cutoff;
-       float penalty;
+       float penalty, adjust;
        int precision, length, precisionLength;
-       bool abort, minWanted, hclusterWanted, merge, hard;
+       bool abort, minWanted, hclusterWanted, merge, hard, cutoffSet;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);