--- /dev/null
+#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