X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=countgroupscommand.h;fp=countgroupscommand.h;h=2532a80eca171fefd776e3722474084e42a1f396;hb=d3aed959ca3b68890eeb7b815e24210bcfeb256c;hp=0000000000000000000000000000000000000000;hpb=fc1ed1ae1b022719176910ab71993bd6535810ad;p=mothur.git

diff --git a/countgroupscommand.h b/countgroupscommand.h
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+#ifndef COUNTGROUPSCOMMAND_H
+#define COUNTGROUPSCOMMAND_H
+
+/*
+ *  countgroupscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 8/9/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+class CountGroupsCommand : public Command {
+	
+public:
+	
+	CountGroupsCommand(string);
+	CountGroupsCommand();	
+	~CountGroupsCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "count.groups";			}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Count.groups"; }
+	string getDescription()		{ return "counts the number of sequences in each group"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+	
+private:
+	string sharedfile, groupfile, outputDir, groups, accnosfile;
+	bool abort;
+	vector<string> Groups;
+	
+	void readAccnos();
+};
+
+#endif