fixed subsample name file name issue. added count parameter to cluster command....

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index e3dd214446d31d187148de2be7dbf2ffbfebe96e..f70bb322c76cd3bf897fd5498333e5da379557fd 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -15,6 +15,7 @@
 #include "listvector.hpp"
 #include "cluster.hpp"
 #include "sparsedistancematrix.h"
+#include "counttable.h"
 
 /* The cluster() command:
        The cluster command outputs a .list , .rabund and .sabund files.  
@@ -52,7 +53,7 @@ private:
 
        bool abort, hard, sim;
 
-       string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile;
+       string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
        double cutoff;
        string showabund, timing;
        int precision, length;
@@ -64,6 +65,8 @@ private:
        
        void printData(string label);
        vector<string> outputNames;
+    
+    int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 };
 
 #endif