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         vector<string> getRequiredParameters();
  31         vector<string> getValidParameters();
  32         vector<string> getRequiredFiles();
  33         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  34         int execute();
  35         void help();
  36
  37 private:
  38         string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
  39         bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
  40         bool abort;
  41         vector<string> outputNames;
  42         map<string, vector<string> > outputTypes;
  43 };
  44
  45 /****************************************************************************/
  46
  47 #endif
  48