X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.h;fp=clearcutcommand.h;h=942953f71bef907980d93355c5a1070599383f61;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;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();
+	~ClearcutCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "clearcut";			}
+	string getCommandCategory()		{ return "Hypothesis Testing";	}
+	string getHelpString();	
+	string getCitation() { return "Sheneman L, Evans J, Foster JA (2006). Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-4. \nhttp://www.mothur.org/wiki/Clearcut"; }
+	string getDescription()		{ return "create a tree from a fasta or phylip file"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+	string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
+	bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
+	bool abort;
+	vector<string> outputNames;
+	
+};
+
+/****************************************************************************/
+
+#endif
+