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[mothur.git] / clearcutcommand.h

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
+