changed added group output to indicator command. a few changes to work with the guy

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 0626b86cd96792dfce2b4c523760749f44d74858..b5b295f1edb4495d321a7e614db1e8309d8bc481 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "readblast.h"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
 #include "cluster.hpp"
 #include "hcluster.h"
@@ -58,13 +57,13 @@ private:
        double cutoff;
        float penalty;
        int precision, length, precisionLength;
-       bool abort, minWanted, hclusterWanted, merge, hard, large;
+       bool abort, minWanted, hclusterWanted, merge, hard;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);
        void sortHclusterFiles(string, string);
        vector<seqDist> getSeqs(ifstream&);
-    void createRabund(CountTable*, ListVector*);
+    void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 
 };