--- /dev/null
+#ifndef SUMMARYTAXCOMMAND_H
+#define SUMMARYTAXCOMMAND_H
+
+/*
+ * summarytaxcommand.h
+ * Mothur
+ *
+ * Created by westcott on 9/23/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+/**************************************************************************************************/
+
+class SummaryTaxCommand : public Command {
+ public:
+ SummaryTaxCommand(string);
+ SummaryTaxCommand();
+ ~SummaryTaxCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "summary.tax"; }
+ string getCommandCategory() { return "Phylotype Analysis"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
+ string getDescription() { return "summarize the taxonomies of a set of sequences"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+ private:
+ bool abort;
+ string taxfile, outputDir, namefile, groupfile, refTaxonomy;
+ vector<string> outputNames;
+ map<string, int> nameMap;
+};
+
+/**************************************************************************************************/
+
+
+#endif