chimerabellerophoncommand.h

   1 #ifndef CHIMERABELLEROPHONCOMMAND_H
   2 #define CHIMERABELLEROPHONCOMMAND_H
   3
   4 /*
   5  *  chimerabellerophoncommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 4/1/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "chimera.h"
  16
  17
  18 /***********************************************************/
  19
  20 class ChimeraBellerophonCommand : public Command {
  21 public:
  22         ChimeraBellerophonCommand(string);
  23         ChimeraBellerophonCommand();
  24         ~ChimeraBellerophonCommand(){}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "chimera.bellerophon"; }
  28         string getCommandCategory()             { return "Sequence Processing"; }
  29         string getHelpString();
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34
  35 private:
  36
  37         bool abort, filter, correction;
  38         string fastafile, outputDir;
  39         int processors, window, increment, numSeqs;
  40         Chimera* chimera;
  41         vector<string> outputNames;
  42         vector<string> fastaFileNames;
  43 };
  44
  45 /***********************************************************/
  46
  47 #endif
  48
  49