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Overlap_AMOS.hh

Go to the documentation of this file.

#ifndef __Overlap_AMOS_HH
#define __Overlap_AMOS_HH 1

#include "Universal_AMOS.hh"
#include <utility>




namespace AMOS {

typedef char OverlapAdjacency_t;

//================================================ Overlap_t ===================
//==============================================================================
class Overlap_t : public Universal_t
{

public:

  static const OverlapAdjacency_t NULL_ADJACENCY = 0;
  static const OverlapAdjacency_t NORMAL     = 'N';     
  static const OverlapAdjacency_t ANTINORMAL = 'A';     
  static const OverlapAdjacency_t INNIE      = 'I';     
  static const OverlapAdjacency_t OUTIE      = 'O';     


private:

  Size_t aHang_m;          
  Size_t bHang_m;          
  std::pair<ID_t, ID_t> reads_m;   


protected:

  static const uint8_t FIRST_BIT  = 0x1;  
  static const uint8_t SECOND_BIT = 0x2;  


  //--------------------------------------------------- readRecord -------------
  virtual void readRecord (std::istream & fix,
                           std::istream & var);


  //--------------------------------------------------- sizeVar ----------------
  virtual Size_t sizeVar ( ) const;


  //--------------------------------------------------- writeRecord ------------
  virtual void writeRecord (std::ostream & fix,
                            std::ostream & var) const;


public:

  //--------------------------------------------------- NCode ------------------
  static NCode_t NCode ( )
  {
    return Bank_k::OVERLAP;
  }


  //--------------------------------------------------- Overlap_t --------------
  Overlap_t ( )
  {
    aHang_m = bHang_m = 0;
    reads_m . first = reads_m . second = NULL_ID;
  }


  //--------------------------------------------------- Overlap_t --------------
  Overlap_t (const Overlap_t & source)
  {
    *this = source;
  }


  //--------------------------------------------------- ~Overlap_t -------------
  ~Overlap_t ( )
  {

  }


  //--------------------------------------------------- clear ------------------
  virtual void clear ( )
  {
    Universal_t::clear( );
    aHang_m = bHang_m = 0;
    reads_m . first = reads_m . second = NULL_ID;
  }


  //--------------------------------------------------- flip -------------------
  void flip ( )
  {
    OverlapAdjacency_t oa = getAdjacency( );
    if ( oa == NORMAL ) setAdjacency (ANTINORMAL);
    else if ( oa == ANTINORMAL ) setAdjacency (NORMAL);

    Size_t tHang = aHang_m; aHang_m = bHang_m; bHang_m = tHang;

    reads_m = make_pair (reads_m . second, reads_m . first);
  }


  //--------------------------------------------------- getAdjacency -----------
  OverlapAdjacency_t getAdjacency ( ) const;


  //--------------------------------------------------- getAhang ---------------
  Size_t getAhang ( ) const
  {
    return aHang_m;
  }


  //--------------------------------------------------- getBhang ---------------
  Size_t getBhang ( ) const
  {
    return bHang_m;
  }


  //--------------------------------------------------- getNCode ---------------
  virtual NCode_t getNCode ( ) const
  {
    return Overlap_t::NCode( );
  }


  //--------------------------------------------------- getReads ---------------
  std::pair<ID_t, ID_t> getReads ( ) const
  {
    return reads_m;
  }


  //--------------------------------------------------- readMessage ------------
  virtual void readMessage (const Message_t & msg);


  //--------------------------------------------------- setAdjacency -----------
  void setAdjacency (OverlapAdjacency_t adj);


  //--------------------------------------------------- setAhang ---------------
  void setAhang (Size_t aHang)
  {
    aHang_m = aHang;
  }


  //--------------------------------------------------- setBhang ---------------
  void setBhang (Size_t bHang)
  {
    bHang_m = bHang;
  }


  //--------------------------------------------------- setReads ---------------
  void setReads (std::pair<ID_t, ID_t> reads)
  {
    reads_m = reads;
  }


  //--------------------------------------------------- writeMessage -----------
  virtual void writeMessage (Message_t & msg) const;

};

} // namespace AMOS

#endif // #ifndef __Overlap_AMOS_HH

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