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 #include "readfasta.h"
  20 #include "readnexus.h"
  21 #include "readclustal.h"
  22 #include "readseqsphylip.h"
  23
  24
  25 using namespace std;
  26
  27 class DistanceCommand : public Command {
  28
  29 public:
  30         DistanceCommand();
  31         ~DistanceCommand() {};
  32         int execute();
  33
  34 private:
  35         GlobalData* globaldata;
  36         ValidCalculators* validCalculator;
  37         Dist* distCalculator;
  38         SequenceDB* seqDB;
  39         ReadSeqs* readSeqs;
  40         ofstream out;
  41         string outputFileName;
  42         string ends;
  43         int processors;
  44         float cutoff;
  45
  46         void appendFiles(string, string);
  47         int driver(Dist*, SequenceDB*, int, int, string, float);
  48
  49 };
  50
  51 #endif
  52
  53
  54