added rename.seqs command.

[mothur.git] / renameseqscommand.h

diff --git a/renameseqscommand.h b/renameseqscommand.h
new file mode 100644 (file)
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