// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import java.util.ArrayList;
import java.util.List;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.species.Species;
+
public class AdjactantDirectedCombinableDomains extends BasicCombinableDomains {
- public AdjactantDirectedCombinableDomains( final DomainId n_terminal_key_domain, final Species species ) {
+ public AdjactantDirectedCombinableDomains( final String n_terminal_key_domain, final Species species ) {
super( n_terminal_key_domain, species );
}
@Override
public List<BinaryDomainCombination> toBinaryDomainCombinations() {
final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
- for( final DomainId domain : getCombiningDomains().keySet() ) {
+ for( final String domain : getCombiningDomains().keySet() ) {
// Precondition (!): key domain is most upstream domain.
//TODO ensure this is true.
- binary_combinations.add( new AdjactantDirectedBinaryDomainCombination( getKeyDomain(), domain ) );
+ binary_combinations.add( AdjactantDirectedBinaryDomainCombination.obtainInstance( getKeyDomain(), domain ) );
}
return binary_combinations;
}