Feature_AMOS.hh

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#ifndef __Feature_AMOS_HH
#define __Feature_AMOS_HH 1

#include "Universal_AMOS.hh"




namespace AMOS {

typedef char FeatureType_t;

//====================================================== Feature_t =============
//==============================================================================
class Feature_t : public Universal_t
{

private:

  std::pair<ID_t, NCode_t> source_m;      
  Range_t range_m;                        
  FeatureType_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 FeatureType_t NULL_FEATURE = 0;
  static const FeatureType_t REPEAT       = 'R';
  static const FeatureType_t UNITIG       = 'U';
  static const FeatureType_t JOIN         = 'J';
  static const FeatureType_t ORF          = 'O';
  static const FeatureType_t FIX          = 'F';

  // forensics features
  static const FeatureType_t COVERAGE     = 'C';
  static const FeatureType_t POLYMORPHISM = 'P';
  static const FeatureType_t BREAKPOINT   = 'B';
  static const FeatureType_t KMER         = 'K';
  static const FeatureType_t MATEPAIR     = 'M';
  static const FeatureType_t MISASSEMBLY  = 'A';


  //--------------------------------------------------------- Feature_t --------
  Feature_t ( )
  {
    source_m . first = NULL_ID;
    source_m . second = NULL_NCODE;
    type_m = NULL_FEATURE;
  }


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


  //--------------------------------------------------------- ~Feature_t -------
  ~Feature_t ( )
  {

  }


  //--------------------------------------------------- clear ------------------
  virtual void clear ( )
  {
    source_m . first = NULL_ID;
    source_m . second = NULL_NCODE;
    range_m . clear( );
    type_m = NULL_FEATURE;
  }


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


  //--------------------------------------------------- getRange ---------------
  Range_t getRange ( ) const
  {
    return range_m;
  }


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


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


  //--------------------------------------------------- setRange ---------------
  void setRange (Range_t range)
  {
    range_m = range;
  }


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


  //--------------------------------------------------- setType ----------------
  void setType (FeatureType_t type)
  {
    type_m = type;
  }


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


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

};

} // namespace AMOS

#endif // #ifndef __Feature_AMOS_HH

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