X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;fp=mgclustercommand.h;h=6f4453316a33d41cb18774d6c9b435bc563980e2;hb=7a2c74cd89b3c21e9ec2207e529304db68f1391a;hp=ce3ffec189fa50d025a0fa0a1f39ef8faaa6da93;hpb=0469e54185b42ce6e22245718e5e35f35bd4bbb6;p=mothur.git

diff --git a/mgclustercommand.h b/mgclustercommand.h
index ce3ffec..6f44533 100644
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -18,6 +18,7 @@
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
+#include "counttable.h"
 
 /**********************************************************************/
 
@@ -51,7 +52,7 @@ private:
 	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 +63,7 @@ private:
 	ListVector* mergeOPFs(map<string, int>, float);
 	void sortHclusterFiles(string, string);
 	vector<seqDist> getSeqs(ifstream&);
-    void createRabund(map<string, int>);
+    void createRabund(CountTable);
 
 };