X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;h=0626b86cd96792dfce2b4c523760749f44d74858;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=a727c973c5954052f577479eed1046142e2cc49a;hpb=a8ff535f332ee97582f735a35ef8f3dfb04f8de1;p=mothur.git

diff --git a/mgclustercommand.h b/mgclustercommand.h
index a727c97..0626b86 100644
--- 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*);
 
 };