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[mothur.git] / chimerabellerophoncommand.h

diff --git a/chimerabellerophoncommand.h b/chimerabellerophoncommand.h
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+#ifndef CHIMERABELLEROPHONCOMMAND_H
+#define CHIMERABELLEROPHONCOMMAND_H
+
+/*
+ *  chimerabellerophoncommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 4/1/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "command.hpp"
+#include "chimera.h"
+
+
+/***********************************************************/
+
+class ChimeraBellerophonCommand : public Command {
+public:
+       ChimeraBellerophonCommand(string);
+       ChimeraBellerophonCommand();
+       ~ChimeraBellerophonCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.bellerophon"; }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       string getCitation() { return "Huber T, Faulkner G, Hugenholtz P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-9. \nhttp://www.mothur.org/wiki/Chimera.bellerophon"; }
+       string getDescription()         { return "detect chimeric sequences"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+               
+private:
+
+       bool abort, filter, correction;
+       string fastafile, outputDir;
+       int processors, window, increment, numSeqs;
+       Chimera* chimera;
+       vector<string> outputNames;
+       vector<string> fastaFileNames;
+};
+
+/***********************************************************/
+
+#endif
+
+