X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.h;h=e3dd214446d31d187148de2be7dbf2ffbfebe96e;hb=0cefb55a2616975bd4a144fc345693695ffc9bb6;hp=3dd4410b6a6a7f5aec286adf2f36338c8b198fad;hpb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;p=mothur.git

diff --git a/clustercommand.h b/clustercommand.h
index 3dd4410..e3dd214 100644
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -14,7 +14,7 @@
 #include "sabundvector.hpp"
 #include "listvector.hpp"
 #include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
 
 /* The cluster() command:
 	The cluster command outputs a .list , .rabund and .sabund files.  
@@ -34,15 +34,17 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "cluster";		}
 	string getCommandCategory()		{ return "Clustering";	}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	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. \nhttp://www.mothur.org/wiki/Cluster"; }
+	string getDescription()		{ return "cluster your sequences into OTUs using a distance matrix"; }
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	Cluster* cluster;
-	SparseMatrix* matrix;
+	SparseDistanceMatrix* matrix;
 	ListVector* list;
 	RAbundVector* rabund;
 	RAbundVector oldRAbund;