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 #include "globaldata.hpp"
  15
  16 /*
  17   Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining:
  18   A Fast Distance-Based Phylogenetic Tree Construction Method,
  19   J. Mol. Evol., 62, 785-792
  20  */
  21
  22 /****************************************************************************/
  23
  24 class ClearcutCommand : public Command {
  25
  26 public:
  27         ClearcutCommand(string);
  28         ClearcutCommand();
  29         ~ClearcutCommand() {}
  30
  31         vector<string> setParameters();
  32         string getCommandName()                 { return "clearcut";                    }
  33         string getCommandCategory()             { return "Hypothesis Testing";  }
  34         string getHelpString();
  35
  36         int execute();
  37         void help() { m->mothurOut(getHelpString()); }
  38
  39 private:
  40         string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
  41         bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
  42         bool abort;
  43         vector<string> outputNames;
  44
  45 };
  46
  47 /****************************************************************************/
  48
  49 #endif
  50