added clearcut command

[mothur.git] / clearcutcommand.h

diff --git a/clearcutcommand.h b/clearcutcommand.h
new file mode 100644 (file)
index 0000000..b3ac28e
--- /dev/null
+++ b/clearcutcommand.h
@@ -0,0 +1,41 @@
+#ifndef CLEARCUTCOMMAND_H
+#define CLEARCUTCOMMAND_H
+
+/*
+ *  clearcutcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 5/11/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+
+/* 
+  Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining: 
+  A Fast Distance-Based Phylogenetic Tree Construction Method, 
+  J. Mol. Evol., 62, 785-792
+ */ 
+
+/****************************************************************************/
+
+class ClearcutCommand : public Command {
+
+public:
+       ClearcutCommand(string);
+       ~ClearcutCommand() {};
+       int execute();
+       void help();    
+       
+private:
+       string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
+       bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdout, kimura, jukes, protein, DNA, stdin;
+       bool abort;
+};
+
+/****************************************************************************/
+
+#endif
+