X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.h;fp=clearcutcommand.h;h=b3ac28e03a293df1acb1f946fcec755294d0ecf5;hb=b1bcc272003b50a8c06dc9120754da1f5b744598;hp=0000000000000000000000000000000000000000;hpb=21805b1c466a341d64a5a451f156a56d12c75dca;p=mothur.git

diff --git a/clearcutcommand.h b/clearcutcommand.h
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+#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
+