X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterfragmentscommand.h;h=e3d861a8a1477c0edf71ae7208c86560ceb56860;hb=16f9c4ab6f39769856b13e048eae2c8eaa413c02;hp=c322529f3bedf95600a8b30e0ac013be2870d290;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index c322529..e3d861a 100644
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "sequence.hpp"
+#include "counttable.h"
 
 /************************************************************/
 struct seqRNode {
@@ -46,8 +47,9 @@ public:
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
+    CountTable ct;
 	bool abort;
-	string fastafile, namefile, outputDir;
+	string fastafile, namefile, countfile, outputDir;
 	int diffs, percent;
 	vector<seqRNode> alignSeqs; 
 	map<string, string> names; //represents the names file first column maps to second column