universals_AMOS.cc

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#include "universals_AMOS.hh"
#include <cassert>
using namespace AMOS;
using namespace std;
using namespace HASHMAP;




//================================================ UniversalSet_t ==============
//----------------------------------------------------- UniversalSet_t ---------
UniversalSet_t::UniversalSet_t ( )
{
  //-- Order must maintain definition-before-reference rule!
  objs_m . push_back (new Universal_t( ));
  objs_m . push_back (new Sequence_t( ));
  objs_m . push_back (new Library_t( ));
  objs_m . push_back (new Fragment_t( ));
  objs_m . push_back (new Read_t( ));
  objs_m . push_back (new Overlap_t( ));
  objs_m . push_back (new Kmer_t( ));
  objs_m . push_back (new Layout_t( ));
  objs_m . push_back (new Contig_t( ));
  objs_m . push_back (new Scaffold_t( ));
  objs_m . push_back (new Link_t( ));
  objs_m . push_back (new ContigLink_t( ));
  objs_m . push_back (new ScaffoldLink_t( ));
  objs_m . push_back (new Edge_t( ));
  objs_m . push_back (new ContigEdge_t( ));
  objs_m . push_back (new ScaffoldEdge_t( ));
  objs_m . push_back (new Feature_t( ));
  objs_m . push_back (new Group_t( ));
  objs_m . push_back (new Index_t( ));

  //-- Set up the hash
  for ( iterator i = begin( ); i != end( ); ++ i )
    hash_m [i -> getNCode( )] = &(*i);

  //-- Make sure everything went OK, e.g. all the NCodes were unique
  assert ( objs_m . size( ) == hash_m . size( ) );
}



//----------------------------------------------------- ~UniversalSet_t --------
UniversalSet_t::~UniversalSet_t ( )
{
  for ( iterator i = begin( ); i != end( ); ++ i )
    delete &(*i);
}


//----------------------------------------------------- clearAll ---------------
void UniversalSet_t::clearAll ( )
{
  for ( iterator i = begin( ); i != end( ); ++ i )
    i -> clear( );
}



//================================================ BankSet_t ===================
//----------------------------------------------------- BankSet_t --------------
BankSet_t::BankSet_t ( )
{
  UniversalSet_t objs;
  UniversalSet_t::iterator ui;
  iterator bi;

  //-- Set up the banks
  for ( ui = objs . begin( ); ui != objs . end( ); ++ ui )
    bnks_m . push_back (new Bank_t (ui -> getNCode( )));

  //-- Set up the hash
  for ( bi = begin( ); bi != end( ); ++ bi )
    hash_m [bi -> getType( )] = &(*bi);

  //-- Make sure everything went OK, e.g. all the NCodes were unique
  assert ( bnks_m . size( ) == hash_m . size( ) );
}


//----------------------------------------------------- ~BankSet_t -------------
BankSet_t::~BankSet_t ( )
{
  for ( iterator i = begin( ); i != end( ); ++ i )
    {
      i -> close( );
      delete &(*i);
    }
}


//----------------------------------------------------- clearAll ---------------
void BankSet_t::clearAll ( )
{
  for ( iterator i = begin( ); i != end( ); ++ i )
    i -> clear( );
}


//----------------------------------------------------- closeAll ---------------
void BankSet_t::closeAll ( )
{
  for ( iterator i = begin( ); i != end( ); ++ i )
    i -> close( );
}



//================================================ BankStreamSet_t =============
//----------------------------------------------------- BankStreamSet_t --------
BankStreamSet_t::BankStreamSet_t ( )
{
  UniversalSet_t objs;
  UniversalSet_t::iterator ui;
  iterator bi;

  //-- Set up the banks
  for ( ui = objs . begin( ); ui != objs . end( ); ++ ui )
    bnks_m . push_back (new BankStream_t (ui -> getNCode( )));

  //-- Set up the hash
  for ( bi = begin( ); bi != end( ); ++ bi )
    hash_m [bi -> getType( )] = &(*bi);

  //-- Make sure everything went OK, e.g. all the NCodes were unique
  assert ( bnks_m . size( ) == hash_m . size( ) );
}


//----------------------------------------------------- ~BankStreamSet_t -------
BankStreamSet_t::~BankStreamSet_t ( )
{
  for ( iterator i = begin( ); i != end( ); ++ i )
    {
      i -> close( );
      delete &(*i);
    }
}


//----------------------------------------------------- clearAll ---------------
void BankStreamSet_t::clearAll ( )
{
  for ( iterator i = begin( ); i != end( ); ++ i )
    i -> clear( );
}


//----------------------------------------------------- closeAll ---------------
void BankStreamSet_t::closeAll ( )
{
  for ( iterator i = begin( ); i != end( ); ++ i )
    i -> close( );
}

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