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
  28         vector<string> setParameters();
  29         string getCommandName()                 { return "pairwise.seqs";               }
  30         string getCommandCategory()             { return "Sequence Processing"; }
  31         string getHelpString();
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         struct distlinePair {
  38                 int start;
  39                 int end;
  40         };
  41
  42         vector<int> processIDS;   //end line, processid
  43         vector<distlinePair> lines;
  44
  45         Alignment* alignment;
  46         Dist* distCalculator;
  47         SequenceDB alignDB;
  48
  49         void createProcesses(string);
  50         int driver(int, int, string, float);
  51         int driver(int, int, string, string);
  52
  53         #ifdef USE_MPI
  54         int driverMPI(int, int, MPI_File&, float);
  55         int driverMPI(int, int, string, unsigned long int&);
  56         int driverMPI(int, int, string, unsigned long int&, string);
  57         #endif
  58
  59         string fastaFileName, align, calc, outputDir, output;
  60         float match, misMatch, gapOpen, gapExtend, cutoff;
  61         int processors;
  62         vector<string> fastaFileNames, Estimators;
  63         vector<string> outputNames;
  64
  65         bool abort, countends, compress;
  66 };
  67
  68 #endif
  69