added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / chimerabellerophoncommand.h

diff --git a/chimerabellerophoncommand.h b/chimerabellerophoncommand.h
new file mode 100644 (file)
index 0000000..e450b52
--- /dev/null
+++ 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();
+       int execute();
+       void help();
+               
+private:
+
+       bool abort, filter, correction;
+       string fastafile, outputDir;
+       int processors, window, increment, numSeqs;
+       Chimera* chimera;
+};
+
+/***********************************************************/
+
+#endif
+
+