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