chimeraseqscommand.h

   1 #ifndef CHIMERACOMMAND_H
   2 #define CHIMERACOMMAND_H
   3
   4 /*
   5  *  chimeraseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 6/29/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "filterseqscommand.h"
  16 #include "sequence.hpp"
  17
  18
  19
  20 /***********************************************************/
  21
  22 class ChimeraSeqsCommand : public Command {
  23 public:
  24         ChimeraSeqsCommand(string);
  25         ~ChimeraSeqsCommand();
  26         int execute();
  27         void help();
  28
  29 private:
  30         //Dist* distCalculator;
  31
  32         struct Preference {
  33                 string leftParent;
  34                 string rightParent;
  35                 float score;
  36
  37         };
  38
  39
  40         bool abort;
  41         string method, fastafile;
  42         bool filter, correction;
  43         int processors, midpoint;
  44         FilterSeqsCommand* filterSeqs;
  45         vector<Sequence> seqs;
  46         vector<Preference> pref;
  47
  48         int findAverageMidPoint();
  49         void readSeqs();
  50
  51
  52 };
  53
  54 /***********************************************************/
  55
  56 #endif
  57