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[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
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+#ifndef DECONVOLUTECOMMAND_H
+#define DECONVOLUTECOMMAND_H
+/*
+ *  deconvolute.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 1/21/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "fastamap.h"
+
+/* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
+       containing 2 columns.  The first being the groupname and the second the list of identical sequence names. */ 
+
+
+class DeconvoluteCommand : public Command {
+
+public:
+       DeconvoluteCommand(string);
+       DeconvoluteCommand();
+       ~DeconvoluteCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "unique.seqs";         }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
+       string getDescription()         { return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       string inFastaName, oldNameMapFName, outputDir;
+       vector<string> outputNames;
+
+       bool abort;
+};
+
+#endif