X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;h=ce3ffec189fa50d025a0fa0a1f39ef8faaa6da93;hb=2ecee16fec29d4c525f740ec19b27962ca09c050;hp=a51fec5b298991b976095c52b7944c2fbab84cb8;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/mgclustercommand.h b/mgclustercommand.h
index a51fec5..ce3ffec 100644
--- 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>);
 
 };