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 "validcalculator.h"
  16 #include "dist.h"
  17 #include "sequencedb.h"
  18
  19
  20 class DistanceCommand : public Command {
  21
  22 public:
  23         DistanceCommand(string);
  24         ~DistanceCommand();
  25         int execute();
  26         void help();
  27
  28 private:
  29         struct linePair {
  30                 int start;
  31                 int end;
  32         };
  33
  34         Dist* distCalculator;
  35         SequenceDB alignDB;
  36
  37         string countends, output, fastafile, calc, outputDir, oldfastafile, column;
  38         int processors, numNewFasta;
  39         float cutoff;
  40         map<int, int> processIDS;   //end line, processid
  41         vector<linePair*> lines;
  42
  43         bool abort;
  44         vector<string>  Estimators; //holds estimators to be used
  45
  46         //void m->appendFiles(string, string);
  47         void createProcesses(string);
  48         int driver(/*Dist*, SequenceDB, */int, int, string, float);
  49
  50         #ifdef USE_MPI
  51         int driverMPI(int, int, MPI_File&, float);
  52         int driverMPI(int, int, string, long&);
  53         #endif
  54
  55         int convertMatrix(string);
  56         bool sanityCheck();
  57         int convertToLowerTriangle(string);
  58
  59 };
  60
  61 #endif
  62
  63
  64