Link_AMOS.hh

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#ifndef __Link_AMOS_HH
#define __Link_AMOS_HH 1

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




namespace AMOS {

typedef char LinkType_t;
typedef char LinkAdjacency_t;

//====================================================== Link_t ================
//==============================================================================
class Link_t : public Universal_t
{

private:

  std::pair<ID_t, ID_t> nods_m;           
  std::pair<ID_t, NCode_t> source_m;      
  NCode_t nodtype_m;                      
  SD_t sd_m;                              
  Size_t size_m;                          
  LinkType_t type_m;                      


protected:

  static const uint8_t ADJACENCY_BIT   = 0x4;  
  static const uint8_t ADJACENCY_BITS  = 0x3;  
  static const uint8_t NORMAL_BITS     = 0x1;
  static const uint8_t ANTINORMAL_BITS = 0x2;
  static const uint8_t INNIE_BITS      = 0x3;
  static const uint8_t OUTIE_BITS      = 0x0;


  //--------------------------------------------------- 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 LinkType_t NULL_LINK = 0;
  static const LinkType_t OTHER     = 'X';
  static const LinkType_t MATEPAIR  = 'M';
  static const LinkType_t OVERLAP   = 'O';
  static const LinkType_t PHYSICAL  = 'P';
  static const LinkType_t ALIGNMENT = 'A';
  static const LinkType_t SYNTENY   = 'S';

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


  //--------------------------------------------------------- Link_t -----------
  Link_t ( )
  {
    nods_m . first = nods_m . second = source_m . first = NULL_ID;
    source_m . second = NULL_NCODE;
    nodtype_m = NULL_NCODE;
    sd_m = size_m = 0;
    type_m = NULL_LINK;
  }


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


  //--------------------------------------------------------- ~Link_t ----------
  ~Link_t ( )
  {

  }


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


  //--------------------------------------------------- flip -------------------
  void flip ( );


  //--------------------------------------------------- getAdjacency -----------
  LinkAdjacency_t getAdjacency ( ) const;


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


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


  //--------------------------------------------------- getSD ------------------
  SD_t getSD ( ) const
  {
    return sd_m;
  }


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


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


  //----------------------------------------------------- getNodeType ----------
  NCode_t getNodeType( ) const
  {
    return nodtype_m;
  }


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


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


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


  //----------------------------------------------------- setNodes -------------
  void setNodes (std::pair<ID_t, ID_t> nods)
  {
    nods_m = nods;
  }


  //----------------------------------------------------- setNodeType ----------
  void setNodeType (NCode_t nodtype)
  {
    nodtype_m = nodtype;
  }


  //--------------------------------------------------- setSD ------------------
  void setSD (SD_t sd)
  {
    sd_m = sd;
  }


  //--------------------------------------------------- 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 (LinkType_t type);


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

};

} // namespace AMOS

#endif // #ifndef __Link_AMOS_HH

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