--- /dev/null
+//
+// renameseqscommand.h
+// Mothur
+//
+// Created by SarahsWork on 5/28/13.
+// Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_renameseqscommand_h
+#define Mothur_renameseqscommand_h
+
+#include "command.hpp"
+
+class RenameSeqsCommand : public Command {
+
+public:
+ RenameSeqsCommand(string);
+ RenameSeqsCommand();
+ ~RenameSeqsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "rename.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Rename.seqs"; }
+ string getDescription() { return "rename sequences"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+
+private:
+
+ string fastaFile, nameFile, groupfile, outputDir;
+ vector<string> outputNames;
+ bool abort;
+
+ map<string, string> nameMap;
+};
+
+
+
+#endif