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         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32 private:
  33         struct linePair {
  34                 unsigned long int start;
  35                 unsigned long int end;
  36                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  37         };
  38         vector<int> processIDS;   //processid
  39         vector<linePair*> lines;
  40         bool MPIWroteAccnos;
  41         map<string, vector<string> > outputTypes;
  42
  43         AlignmentDB* templateDB;
  44         Alignment* alignment;
  45
  46         int driver(linePair*, string, string, string, string);
  47         int createProcesses(string, string, string, string);
  48         void appendAlignFiles(string, string);
  49         void appendReportFiles(string, string);
  50
  51         #ifdef USE_MPI
  52         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  53         #endif
  54
  55         string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
  56         float match, misMatch, gapOpen, gapExtend, threshold;
  57         int processors, kmerSize;
  58         vector<string> candidateFileNames;
  59         vector<string> outputNames;
  60
  61         bool abort, flip, calledHelp;
  62
  63 };
  64
  65 #endif