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 struct linePair {
  21         int start;
  22         int end;
  23 };
  24
  25 class DistanceCommand : public Command {
  26
  27 public:
  28         DistanceCommand(string);
  29         ~DistanceCommand() {};
  30         int execute();
  31         void help();
  32
  33 private:
  34         GlobalData* globaldata;
  35         ValidCalculators* validCalculator;
  36         Dist* distCalculator;
  37         SequenceDB* seqDB;
  38         ofstream out, outFile;
  39         ifstream in;
  40         string countends, phylip, fastafile, calc;
  41         int processors;
  42         float cutoff;
  43         map<int, int> processIDS;   //end line, processid
  44         map<int, int>::iterator it;
  45         vector<linePair*> lines;
  46
  47         OptionParser* parser;
  48         map<string, string> parameters;
  49         map<string, string>::iterator it2;
  50         bool abort;
  51         vector<string>  Estimators; //holds estimators to be used
  52
  53         void appendFiles(string, string);
  54         void createProcesses(string);
  55         int driver(Dist*, SequenceDB*, int, int, string, float);
  56
  57 };
  58
  59 #endif
  60
  61
  62