Merge remote-tracking branch 'origin/master'

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 96410bfc39f1a28140357cdf2ee9233fe5e51bc2..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"
 
 /**********************************************************************/
 
@@ -46,12 +47,13 @@ private:
        Cluster* cluster;
        HCluster* hcluster;
        ListVector* list;
+    CountTable* ct;
        ListVector oldList;
-        RAbundVector rav;
+    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;
@@ -62,7 +64,7 @@ private:
        ListVector* mergeOPFs(map<string, int>, float);
        void sortHclusterFiles(string, string);
        vector<seqDist> getSeqs(ifstream&);
-        void createRabund(map<string, int>);
+    void createRabund(CountTable*, ListVector*);
 
 };