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 #include "mothurfiles.h"
  19
  20 class AlignCommand : public Command {
  21
  22 public:
  23         AlignCommand(string);
  24         AlignCommand();
  25         ~AlignCommand();
  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                 unsigned long int start;
  36                 unsigned long int end;
  37                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  38         };
  39         vector<int> processIDS;   //processid
  40         vector<linePair*> lines;
  41         bool MPIWroteAccnos;
  42         map<string, vector<string> > outputTypes;
  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         CurrentFile* currentFiles;
  64
  65 };
  66
  67 #endif