Merge remote-tracking branch 'origin/master'

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index d5c784e27a28bb27e6b7cbdadbb8b94e25b199b5..ce3ffec189fa50d025a0fa0a1f39ef8faaa6da93 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -31,9 +31,11 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "mgcluster";   }
        string getCommandCategory()             { return "Clustering";  }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Mgcluster"; }
-       
+       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()); }  
        
@@ -45,6 +47,7 @@ private:
        HCluster* hcluster;
        ListVector* list;
        ListVector oldList;
+    RAbundVector rav;
        vector<seqDist> overlapMatrix;
        vector<string> outputNames;
        
@@ -53,12 +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>);
 
 };