changes while testing 1.27

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index 7349961e252104c93cf26942d79b44f11ba7c0f5..f70bb322c76cd3bf897fd5498333e5da379557fd 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -14,7 +14,8 @@
 #include "sabundvector.hpp"
 #include "listvector.hpp"
 #include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
+#include "counttable.h"
 
 /* The cluster() command:
        The cluster command outputs a .list , .rabund and .sabund files.  
@@ -44,7 +45,7 @@ public:
        
 private:
        Cluster* cluster;
-       SparseMatrix* matrix;
+       SparseDistanceMatrix* matrix;
        ListVector* list;
        RAbundVector* rabund;
        RAbundVector oldRAbund;
@@ -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