public class BasicCombinableDomains implements CombinableDomains {
+ final private TreeMap<String, Integer> _combining_domains;
final private String _key_domain;
private int _key_domain_count;
- final private Species _species;
- final private TreeMap<String, Integer> _combining_domains;
final private Set<String> _proteins_with_key_domain;
+ final private Species _species;
public BasicCombinableDomains( final String key_domain, final Species species ) {
_key_domain = key_domain;
return sb;
}
- protected TreeMap<String, Integer> getCombiningDomains() {
- return _combining_domains;
- }
-
@Override
public String getKeyDomain() {
return _key_domain;
}
@Override
+ public Set<String> getKeyDomainProteins() {
+ return _proteins_with_key_domain;
+ }
+
+ @Override
public int getKeyDomainProteinsCount() {
return getKeyDomainProteins().size();
}
public List<BinaryDomainCombination> toBinaryDomainCombinations() {
final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
for( final String domain : getCombiningDomains().keySet() ) {
- binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+ // binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+ binary_combinations.add( BasicBinaryDomainCombination.obtainInstance( getKeyDomain(), domain ) );
}
return binary_combinations;
}
return sb.toString();
}
- @Override
- public Set<String> getKeyDomainProteins() {
- return _proteins_with_key_domain;
+ protected TreeMap<String, Integer> getCombiningDomains() {
+ return _combining_domains;
}
}