added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index 23f728755aadb4c4f878e299790ed8669790034a..e3dd214446d31d187148de2be7dbf2ffbfebe96e 100644 (file)
--- 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 "http://www.mothur.org/wiki/Cluster"; }
+       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;