--- /dev/null
+#ifndef GETOTUSCOMMAND_H
+#define GETOTUSCOMMAND_H
+
+/*
+ * getotuscommand.h
+ * Mothur
+ *
+ * Created by westcott on 11/10/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "command.hpp"
+#include "groupmap.h"
+#include "listvector.hpp"
+
+class GetOtusCommand : public Command {
+
+public:
+
+ GetOtusCommand(string);
+ GetOtusCommand();
+ ~GetOtusCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.otus"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
+ string getDescription() { return "outputs a new list file containing the otus containing sequences from the groups specified"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+
+private:
+ string accnosfile, groupfile, listfile, outputDir, groups, label;
+ bool abort;
+ vector<string> outputNames, Groups;
+ GroupMap* groupMap;
+
+ void readAccnos();
+ int readListGroup();
+ int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
+
+};
+
+#endif
+
+
+