sequence.hpp

   1 #ifndef SEQUENCE_H
   2 #define SEQUENCE_H
   3
   4 /*
   5  *  sequence.h
   6  *
   7  *
   8  *  Created by Pat Schloss on 12/15/08.
   9  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12 using namespace std;
  13
  14 #include "mothur.h"
  15
  16
  17 /**************************************************************************************************/
  18
  19 class Sequence {
  20 public:
  21         Sequence();
  22         Sequence(string, string);
  23
  24         void setName(string);
  25         void setUnaligned(string);
  26         void setPairwise(string);
  27         void setAligned(string);
  28         void setLength();
  29
  30         string convert2ints();
  31         string getName();
  32         string getAligned();
  33         string getPairwise();
  34         string getUnaligned();
  35         int getLength();
  36         void printSequence(ostream&);
  37
  38 private:
  39         string name;
  40         string unaligned;
  41         string aligned;
  42         string pairwise;
  43         int length;
  44         int lengthAligned;
  45 };
  46
  47 /**************************************************************************************************/
  48
  49 #endif