pairwiseseqscommand.h

   1 #ifndef PAIRWISESEQSCOMMAND_H
   2 #define PAIRWISESEQSCOMMAND_H
   3
   4 /*
   5  *  pairwiseseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 10/20/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "database.hpp"
  16 #include "alignment.hpp"
  17 #include "validcalculator.h"
  18 #include "dist.h"
  19 #include "sequencedb.h"
  20
  21 class PairwiseSeqsCommand : public Command {
  22
  23 public:
  24         PairwiseSeqsCommand(string);
  25         PairwiseSeqsCommand();
  26         ~PairwiseSeqsCommand();
  27         vector<string> getRequiredParameters();
  28         vector<string> getValidParameters();
  29         vector<string> getRequiredFiles();
  30         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  31         int execute();
  32         void help();
  33
  34 private:
  35         struct linePair {
  36                 int start;
  37                 int end;
  38         };
  39         map<int, int> processIDS;   //end line, processid
  40         vector<linePair*> lines;
  41         map<string, vector<string> > outputTypes;
  42
  43         Alignment* alignment;
  44         Dist* distCalculator;
  45         SequenceDB alignDB;
  46
  47         void createProcesses(string);
  48         int driver(int, int, string, float);
  49         int driver(int, int, string, string);
  50
  51         #ifdef USE_MPI
  52         int driverMPI(int, int, MPI_File&, float);
  53         int driverMPI(int, int, string, unsigned long int&);
  54         int driverMPI(int, int, string, unsigned long int&, string);
  55         #endif
  56
  57         string fastaFileName, align, calc, outputDir, output;
  58         float match, misMatch, gapOpen, gapExtend, cutoff;
  59         int processors;
  60         vector<string> fastaFileNames, Estimators;
  61         vector<string> outputNames;
  62
  63         bool abort, countends, compress;
  64 };
  65
  66 #endif
  67