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         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map< string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32 private:
  33
  34         bool abort, filter, correction;
  35         string fastafile, outputDir;
  36         int processors, window, increment, numSeqs;
  37         Chimera* chimera;
  38         vector<string> outputNames;
  39         map<string, vector<string> > outputTypes;
  40         vector<string> fastaFileNames;
  41 };
  42
  43 /***********************************************************/
  44
  45 #endif
  46
  47