moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / clearcutcommand.h

diff --git a/clearcutcommand.h b/clearcutcommand.h
deleted file mode 100644 (file)
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
-