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         int execute();
  25         void help();
  26
  27 private:
  28         struct linePair {
  29                 int start;
  30                 int numSeqs;
  31                 linePair(long int i, int j) : start(i), numSeqs(j) {}
  32         };
  33         vector<int> processIDS;   //processid
  34         vector<linePair*> lines;
  35
  36         AlignmentDB* templateDB;
  37         Alignment* alignment;
  38
  39         int driver(linePair*, string, string, string, string);
  40         void createProcesses(string, string, string, string);
  41         void appendAlignFiles(string, string);
  42         void appendReportFiles(string, string);
  43
  44         string candidateFileName, templateFileName, distanceFileName, search, align;
  45         float match, misMatch, gapOpen, gapExtend, threshold;
  46         int processors, kmerSize;
  47         vector<string> candidateFileNames;
  48
  49         bool abort, flip;
  50 };
  51
  52 #endif