clearcutcommand.h

   1 #ifndef CLEARCUTCOMMAND_H
   2 #define CLEARCUTCOMMAND_H
   3
   4 /*
   5  *  clearcutcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 5/11/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15 /*
  16   Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining:
  17   A Fast Distance-Based Phylogenetic Tree Construction Method,
  18   J. Mol. Evol., 62, 785-792
  19  */
  20
  21 /****************************************************************************/
  22
  23 class ClearcutCommand : public Command {
  24
  25 public:
  26         ClearcutCommand(string);
  27         ClearcutCommand();
  28         ~ClearcutCommand() {}
  29
  30         vector<string> setParameters();
  31         string getCommandName()                 { return "clearcut";                    }
  32         string getCommandCategory()             { return "Hypothesis Testing";  }
  33         string getHelpString();
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38 private:
  39         string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
  40         bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
  41         bool abort;
  42         vector<string> outputNames;
  43
  44 };
  45
  46 /****************************************************************************/
  47
  48 #endif
  49