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