fixed pointers in mgcluster

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 889586ae305ac47bdb0f2d15880507aa68655dff..0626b86cd96792dfce2b4c523760749f44d74858 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -18,6 +18,7 @@
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
+#include "counttable.h"
 
 /**********************************************************************/
 
@@ -46,22 +47,24 @@ 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;
+       bool abort, minWanted, hclusterWanted, merge, hard, large;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);
        void sortHclusterFiles(string, string);
        vector<seqDist> getSeqs(ifstream&);
-    RAbundVector createRabund(ListVector, map<string, int>);
+    void createRabund(CountTable*, ListVector*);
 
 };