X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerabellerophoncommand.h;fp=chimerabellerophoncommand.h;h=b759d5a99dd8f1864506e3dd81eac46bedab235e;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/chimerabellerophoncommand.h b/chimerabellerophoncommand.h
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+++ 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
+
+