X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.h;fp=clearcutcommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=942953f71bef907980d93355c5a1070599383f61;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/clearcutcommand.h b/clearcutcommand.h
deleted file mode 100644
index 942953f..0000000
--- a/clearcutcommand.h
+++ /dev/null
@@ -1,51 +0,0 @@
-#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
-