aligncommand.h

   1 #ifndef ALIGNCOMMAND_H
   2 #define ALIGNCOMMAND_H
   3
   4 /*
   5  *  aligncommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 5/15/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "database.hpp"
  16 #include "alignment.hpp"
  17 #include "alignmentdb.h"
  18
  19 class AlignCommand : public Command {
  20
  21 public:
  22         AlignCommand(string);
  23         AlignCommand();
  24         ~AlignCommand();
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "align.seqs";                  }
  28         string getCommandCategory()             { return "Sequence Processing"; }
  29         string getHelpString();
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34 private:
  35         struct linePair {
  36                 unsigned long int start;
  37                 unsigned long int end;
  38                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  39         };
  40         vector<int> processIDS;   //processid
  41         vector<linePair*> lines;
  42         bool MPIWroteAccnos;
  43
  44         AlignmentDB* templateDB;
  45         Alignment* alignment;
  46
  47         int driver(linePair*, string, string, string, string);
  48         int createProcesses(string, string, string, string);
  49         void appendAlignFiles(string, string);
  50         void appendReportFiles(string, string);
  51
  52         #ifdef USE_MPI
  53         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  54         #endif
  55
  56         string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
  57         float match, misMatch, gapOpen, gapExtend, threshold;
  58         int processors, kmerSize;
  59         vector<string> candidateFileNames;
  60         vector<string> outputNames;
  61
  62         bool abort, flip, calledHelp;
  63
  64 };
  65
  66 #endif