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