X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clusterfragmentscommand.h;h=ee25fb30da91c4ab338b0b173bcf05a6f1689c81;hp=c322529f3bedf95600a8b30e0ac013be2870d290;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index c322529..ee25fb3 100644
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "sequence.hpp"
+#include "counttable.h"
 
 /************************************************************/
 struct seqRNode {
@@ -37,8 +38,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "cluster.fragments";		}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
 	string getDescription()		{ return "creates a namesfile with sequences that are a fragment of a larger sequence"; }
 	
@@ -46,8 +48,9 @@ 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