Fragment_AMOS.hh

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#ifndef __Fragment_AMOS_HH
#define __Fragment_AMOS_HH 1

#include "Universal_AMOS.hh"




namespace AMOS {

typedef char FragmentType_t;

//================================================ Fragment_t ==================
//==============================================================================
class Fragment_t : public Universal_t
{

private:

  ID_t library_m;                     
  Size_t size_m;                      
  std::pair<ID_t, NCode_t> source_m;  
  std::pair<ID_t, ID_t> reads_m;      
  FragmentType_t type_m;              


protected:

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



  //--------------------------------------------------- readRecordFix ----------
  virtual void readRecordFix (std::istream & fix);


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


public:

  static const NCode_t NCODE;

  static const FragmentType_t NULL_FRAGMENT = 0;
  static const FragmentType_t OTHER         = 'X';
  static const FragmentType_t BAC           = 'B';
  static const FragmentType_t INSERT        = 'I';
  static const FragmentType_t TRANSPOSON    = 'T';
  static const FragmentType_t WALK          = 'W';


  //--------------------------------------------------- Fragment_t -------------
  Fragment_t ( )
  {
    size_m = 0;
    library_m = source_m . first = reads_m . first = reads_m . second = NULL_ID;
    source_m . second = NULL_NCODE;
    type_m = NULL_FRAGMENT;
  }


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


  //--------------------------------------------------- ~Fragment_t ------------
  ~Fragment_t ( )
  {

  }


  //--------------------------------------------------- clear ------------------
  virtual void clear ( );


  //--------------------------------------------------- getNCode ---------------
  virtual NCode_t getNCode ( ) const
  {
    return Fragment_t::NCODE;
  }


  //--------------------------------------------------- getLibrary -------------
  ID_t getLibrary ( ) const
  {
    return library_m;
  }


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


  //--------------------------------------------------- getSize ----------------
  Size_t getSize ( ) const
  {
    return size_m;
  }


  //--------------------------------------------------- getSource --------------
  std::pair<ID_t, NCode_t> getSource ( ) const
  {
    return source_m;
  }


  //--------------------------------------------------- getType ----------------
  FragmentType_t getType ( ) const
  {
    return type_m;
  }


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


  //--------------------------------------------------- setLibrary -------------
  void setLibrary (ID_t library)
  {
    library_m = library;
  }


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


  //--------------------------------------------------- setSize ----------------
  void setSize (Size_t size)
  {
    size_m = size;
  }


  //--------------------------------------------------- setSource --------------
  void setSource (std::pair<ID_t, NCode_t> source)
  {
    source_m = source;
  }


  //--------------------------------------------------- setType ----------------
  void setType (FragmentType_t type);


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

};

} // namespace AMOS

#endif // #ifndef __Fragment_AMOS_HH

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