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[mothur.git] / reversecommand.h

diff --git a/reversecommand.h b/reversecommand.h
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+#ifndef REVERSECOMMAND_H
+#define REVERSECOMMAND_H
+
+/*
+ *  reversecommand.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 6/6/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+class ReverseSeqsCommand : public Command {
+public:
+       ReverseSeqsCommand(string);
+       ReverseSeqsCommand();
+       ~ReverseSeqsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "reverse.seqs";                        }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Reverse.seqs"; }
+       string getDescription()         { return "outputs a fasta file containing the reverse-complements"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+
+       bool abort;
+       string fastaFileName, qualFileName, outputDir;
+       vector<string> outputNames;
+       
+};
+
+#endif