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         ~DistanceCommand() {}
  26
  27         vector<string> setParameters();
  28         string getCommandName()                 { return "dist.seqs";                   }
  29         string getCommandCategory()             { return "Sequence Processing"; }
  30         string getHelpString();
  31         string getCitation() { return "http://www.mothur.org/wiki/Dist.seqs"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36
  37 private:
  38         struct distlinePair {
  39                 int start;
  40                 int end;
  41
  42         };
  43
  44         Dist* distCalculator;
  45         SequenceDB alignDB;
  46
  47         string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
  48
  49         int processors, numNewFasta;
  50         float cutoff;
  51         vector<int> processIDS;   //end line, processid
  52         vector<distlinePair> lines;
  53
  54         bool abort;
  55         vector<string>  Estimators, outputNames; //holds estimators to be used
  56
  57         //void m->appendFiles(string, string);
  58         void createProcesses(string);
  59         int driver(/*Dist*, SequenceDB, */int, int, string, float);
  60         int driver(int, int, string, string);
  61
  62         #ifdef USE_MPI
  63         int driverMPI(int, int, MPI_File&, float);
  64         int driverMPI(int, int, string, unsigned long int&);
  65         int driverMPI(int, int, string, unsigned long int&, string);
  66         #endif
  67
  68         //int convertMatrix(string);
  69         bool sanityCheck();
  70         //int convertToLowerTriangle(string);
  71
  72 };
  73
  74 #endif
  75
  76
  77