Index_AMOS.hh

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#ifndef __Index_AMOS_HH
#define __Index_AMOS_HH 1

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




namespace AMOS {

//================================================ Index_t =====================
//==============================================================================
class Index_t : public Universal_t
{

private:

  std::pair<NCode_t, NCode_t> type_m;            
  HASHMAP::hash_multimap<ID_t, ID_t> index_m;    


protected:

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


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

  
public:

  static const NCode_t NCODE;


  typedef HASHMAP::hash_multimap<ID_t, ID_t>::iterator iterator;

  typedef HASHMAP::hash_multimap<ID_t, ID_t>::const_iterator const_iterator;


  //--------------------------------------------------- Index_t ----------------
  Index_t ( )
  {
    type_m . first = type_m . second = NULL_NCODE;
  }


  //--------------------------------------------------- Index_t ----------------
  Index_t (NCode_t a, NCode_t b)
  {
    type_m . first = a;
    type_m . second = b;
  }


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


  //--------------------------------------------------- ~Index_t ---------------
  ~Index_t ( )
  {

  }


  //--------------------------------------------------- begin ------------------
  iterator begin ( )
  {
    return index_m . begin( );
  }


  //--------------------------------------------------- begin ------------------
  const_iterator begin ( ) const
  {
    return index_m . begin( );
  }


  //--------------------------------------------------- buildContigFeature -----
  void buildContigFeature (const std::string bankname);


  //--------------------------------------------------- buildContigScaffold ----
  void buildContigScaffold (const std::string bankname);


  //--------------------------------------------------- buildReadContig --------
  void buildReadContig (const std::string bankname);


  //--------------------------------------------------- buildReadLibrary -------
  void buildReadLibrary (const std::string bankname);


  //--------------------------------------------------- buildReadMate ----------
  void buildReadMate (const std::string bankname);


  //--------------------------------------------------- buildScaffoldFeature ---
  void buildScaffoldFeature (const std::string bankname);


  //--------------------------------------------------- end --------------------
  iterator end ( )
  {
    return index_m . end( );
  }


  //--------------------------------------------------- end --------------------
  const_iterator end ( ) const
  {
    return index_m . end( );
  }


  //--------------------------------------------------- empty ------------------
  bool empty ( ) const
  {
    return index_m . empty( );
  }


  //--------------------------------------------------- clear ------------------
  virtual void clear ( )
  {
    Universal_t::clear( );

    type_m . first = type_m . second = NULL_NCODE;
    index_m . clear( );
  }


  //--------------------------------------------------- count ------------------
  Size_t count (ID_t key) const
  {
    return index_m . count (key);
  }


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


  //--------------------------------------------------- getSize ----------------
  Size_t getSize ( ) const
  {
    return index_m . size( );
  }


  //--------------------------------------------------- getType ----------------
  std::pair<NCode_t, NCode_t> getType( ) const
  {
    return type_m;
  }


  //--------------------------------------------------- insert -----------------
  void insert (ID_t key, ID_t value)
  {
    insert (std::make_pair(key, value));
  }


  //--------------------------------------------------- insert -----------------
  void insert (std::pair<ID_t, ID_t> iids)
  {
    index_m . insert (iids);
  }


  //--------------------------------------------------- isMulti ----------------
  bool isMulti (ID_t key) const
  {
    return (count (key) > 1);
  }


  //--------------------------------------------------- lookup -----------------
  ID_t lookup (ID_t key) const
  {
    return (index_m . find (key)) -> second;
  }


  //--------------------------------------------------- lookupAll --------------
  std::pair<iterator, iterator> lookupAll (ID_t key)
  {
    return index_m . equal_range (key);
  }


  //--------------------------------------------------- lookupAll --------------
  std::pair<const_iterator, const_iterator> lookupAll (ID_t key) const
  {
    return index_m . equal_range (key);
  }


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


  //--------------------------------------------------- remove -----------------
  Size_t remove (ID_t key)
  {
    return index_m . erase (key);
  }


  //--------------------------------------------------- remove -----------------
  void remove (iterator itr)
  {
    index_m . erase (itr);
  }


  //--------------------------------------------------- setType ----------------
  void setType (std::pair<NCode_t, NCode_t> type)
  {
    type_m = type;
  }


  //--------------------------------------------------- setType ----------------
  void setType (NCode_t a, NCode_t b)
  {
    setType (std::make_pair (a, b));
  }


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

};

} // namespace AMOS

#endif // #ifndef __Index_AMOS_HH

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