X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=renameseqscommand.h;fp=renameseqscommand.h;h=a49240403c6d88ddc23d05691ba6853321c62cf4;hb=ef4c1b4dfeecc17a0ad5c1c114c748a0443a88ac;hp=0000000000000000000000000000000000000000;hpb=f204e1111a6d4da30db9bccfa65f75546f59ba11;p=mothur.git

diff --git a/renameseqscommand.h b/renameseqscommand.h
new file mode 100644
index 0000000..a492404
--- /dev/null
+++ b/renameseqscommand.h
@@ -0,0 +1,46 @@
+//
+//  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