changes while testing 1.27

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index ce3ffec189fa50d025a0fa0a1f39ef8faaa6da93..b5b295f1edb4495d321a7e614db1e8309d8bc481 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -12,12 +12,12 @@
 
 #include "command.hpp"
 #include "readblast.h"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
 #include "cluster.hpp"
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
+#include "counttable.h"
 
 /**********************************************************************/
 
@@ -46,23 +46,24 @@ private:
        Cluster* cluster;
        HCluster* hcluster;
        ListVector* list;
+    CountTable* ct;
        ListVector oldList;
     RAbundVector rav;
        vector<seqDist> overlapMatrix;
        vector<string> outputNames;
        
-       string blastfile, method, namefile, overlapFile, distFile, outputDir;
+       string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
        ofstream sabundFile, rabundFile, listFile;
        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(map<string, int>);
+    void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 
 };