X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;h=c9c23c80f88d0ab0c98ae058748c544a561b76d3;hb=f687723a8357916e86a05116978e6869b039ce36;hp=ce3ffec189fa50d025a0fa0a1f39ef8faaa6da93;hpb=9eb79e6942cf98f3a0296ff9f63b4a47731b49e8;p=mothur.git

diff --git a/mgclustercommand.h b/mgclustercommand.h
index ce3ffec..c9c23c8 100644
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -18,6 +18,7 @@
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
+#include "counttable.h"
 
 /**********************************************************************/
 
@@ -46,23 +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, 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*&);
 
 };