removed comments

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index a51fec5b298991b976095c52b7944c2fbab84cb8..96410bfc39f1a28140357cdf2ee9233fe5e51bc2 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -29,10 +29,13 @@ public:
        ~MGClusterCommand(){}
        
        vector<string> setParameters();
-       string getCommandName()                 { return "mgcluster";                           }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getCommandName()                 { return "mgcluster";   }
+       string getCommandCategory()             { return "Clustering";  }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       
+       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"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -44,6 +47,7 @@ private:
        HCluster* hcluster;
        ListVector* list;
        ListVector oldList;
+        RAbundVector rav;
        vector<seqDist> overlapMatrix;
        vector<string> outputNames;
        
@@ -52,12 +56,13 @@ private:
        double cutoff;
        float penalty;
        int precision, length, precisionLength;
-       bool abort, minWanted, hclusterWanted, merge, hard;
+       bool abort, minWanted, hclusterWanted, merge, hard, large;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);
        void sortHclusterFiles(string, string);
        vector<seqDist> getSeqs(ifstream&);
+        void createRabund(map<string, int>);
 
 };