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  *      A sequence object has three components: i) an accession number / name, ii) the unaligned primary sequence, iii) a
  12  *      pairwise aligned sequence, and iv) a sequence that is aligned to a reference alignment.  This class has methods
  13  *      to set and get these values for the other classes where they are needed.  *
  14  *
  15  */
  16
  17 #include "mothur.h"
  18 #include "mothurout.h"
  19
  20 /**************************************************************************************************/
  21
  22 class Sequence {
  23 public:
  24         Sequence();
  25         Sequence(string, string);
  26         Sequence(ifstream&);
  27         Sequence(istringstream&);
  28         Sequence(const Sequence& se) : name(se.name), unaligned(se.unaligned), aligned(se.aligned), pairwise(se.pairwise), numBases(se.numBases), startPos(se.startPos), endPos(se.endPos),
  29                                                                         alignmentLength(se.alignmentLength), isAligned(se.isAligned), longHomoPolymer(se.longHomoPolymer), ambigBases(se.ambigBases) { m = MothurOut::getInstance(); }
  30
  31         //these constructors just set the unaligned string to save space
  32         Sequence(string, string, string);
  33         Sequence(ifstream&, string);
  34         Sequence(istringstream&, string);
  35
  36         void setName(string);
  37         void setUnaligned(string);
  38         void setPairwise(string);
  39         void setAligned(string);
  40         void setLength();
  41         void reverseComplement();
  42         void trim(int);
  43
  44         string convert2ints();
  45         string getName();
  46         string getAligned();
  47         string getPairwise();
  48         string getUnaligned();
  49         string getInlineSeq();
  50         int getNumBases();
  51         int getStartPos();
  52         int getEndPos();
  53         void padToPos(int);
  54         void padFromPos(int);
  55         int getAlignLength();
  56         int getAmbigBases();
  57         void removeAmbigBases();
  58         int getLongHomoPolymer();
  59         bool getIsAligned();
  60         void printSequence(ostream&);
  61
  62 private:
  63         MothurOut* m;
  64         void initialize();
  65         string getSequenceString(ifstream&);
  66         string getCommentString(ifstream&);
  67         string getSequenceString(istringstream&);
  68         string getCommentString(istringstream&);
  69         string name;
  70         string unaligned;
  71         string aligned;
  72         string pairwise;
  73         int numBases;
  74         int alignmentLength;
  75         bool isAligned;
  76         int longHomoPolymer;
  77         int ambigBases;
  78         int startPos, endPos;
  79 };
  80
  81 /**************************************************************************************************/
  82
  83 #endif