distancecommand.h

   1 #ifndef DISTANCECOMMAND_H
   2 #define DISTANCECOMMAND_H
   3
   4 /*
   5  *  distancecommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 5/7/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "globaldata.hpp"
  16 #include "validcalculator.h"
  17 #include "dist.h"
  18 #include "sequencedb.h"
  19
  20 class DistanceCommand : public Command {
  21
  22 public:
  23         DistanceCommand();
  24         ~DistanceCommand() {};
  25         int execute();
  26
  27 private:
  28         GlobalData* globaldata;
  29         ValidCalculators* validCalculator;
  30         Dist* distCalculator;
  31         SequenceDB* seqDB;
  32         ofstream out, phylipOut;
  33         ifstream in;
  34         string outputFileName;
  35         string countends;
  36         int processors;
  37         float cutoff;
  38
  39         void appendFiles(string, string);
  40         int driver(Dist*, SequenceDB*, int, int, string, string, float);
  41
  42 };
  43
  44 #endif
  45
  46
  47