Scaffold_AMOS.hh

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#ifndef __Scaffold_AMOS_HH
#define __Scaffold_AMOS_HH 1

#include "Universal_AMOS.hh"
#include "Layout_AMOS.hh"
#include <vector>




namespace AMOS {

//================================================ Scaffold_t ==================
//==============================================================================
class Scaffold_t : public Universal_t
{

private:

  std::vector<Tile_t> contigs_m;   
  std::vector<ID_t> edges_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;


  //--------------------------------------------------- Scaffold_t -------------
  Scaffold_t ( )
  {

  }


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


  //--------------------------------------------------- ~Scaffold_t ------------
  ~Scaffold_t ( )
  {

  }


  //--------------------------------------------------- clear ------------------
  virtual void clear ( )
  {
    Universal_t::clear( );
    contigs_m . clear( );
    edges_m . clear( );
  }


  //--------------------------------------------------- getContigTiling --------
  const std::vector<Tile_t> & getContigTiling ( ) const
  {
    return contigs_m;
  }


  //--------------------------------------------------- getContigTiling --------
  std::vector<Tile_t> & getContigTiling ( )
  {
    return contigs_m;
  }


  //--------------------------------------------------- getContigEdges ---------
  const std::vector<ID_t> & getContigEdges ( ) const
  {
    return edges_m;
  }


  //--------------------------------------------------- getContigEdges ---------
  std::vector<ID_t> & getContigEdges ( )
  {
    return edges_m;
  }


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


  //--------------------------------------------------- getSpan ----------------
  Size_t getSpan ( ) const;


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


  //--------------------------------------------------- setContigTiling --------
  void setContigTiling (const std::vector<Tile_t> & contigs)
  {
    contigs_m = contigs;
  }


  //--------------------------------------------------- setContigTiling --------
  void setContigTiling (const Layout_t & layout)
  {
    contigs_m = layout . getTiling( );
  }


  //--------------------------------------------------- setContigEdges ---------
  void setContigEdges (const std::vector<ID_t> & edges)
  {
    edges_m = edges;
  }


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

};

} // namespace AMOS

#endif // #ifndef __Scaffold_AMOS_HH

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