public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDomains {
- private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_COUNT_ORDER = new Comparator<CombinableDomains>() {
+ private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER = new Comparator<CombinableDomains>() {
@Override
public int compare( final CombinableDomains d1,
final CombinableDomains d2 ) {
- if ( d1.getKeyDomainCount() < d2
- .getKeyDomainCount() ) {
+ if ( d1.getNumberOfCombinableDomains() < d2
+ .getNumberOfCombinableDomains() ) {
return 1;
}
else if ( d1
- .getKeyDomainCount() > d2
- .getKeyDomainCount() ) {
+ .getNumberOfCombinableDomains() > d2
+ .getNumberOfCombinableDomains() ) {
return -1;
}
else {
}
}
};
- private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER = new Comparator<CombinableDomains>() {
+ private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_COUNT_ORDER = new Comparator<CombinableDomains>() {
@Override
public int compare( final CombinableDomains d1,
final CombinableDomains d2 ) {
- if ( d1.getKeyDomainProteinsCount() < d2
- .getKeyDomainProteinsCount() ) {
+ if ( d1.getKeyDomainCount() < d2
+ .getKeyDomainCount() ) {
return 1;
}
else if ( d1
- .getKeyDomainProteinsCount() > d2
- .getKeyDomainProteinsCount() ) {
+ .getKeyDomainCount() > d2
+ .getKeyDomainCount() ) {
return -1;
}
else {
}
}
};
- private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER = new Comparator<CombinableDomains>() {
+ private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER = new Comparator<CombinableDomains>() {
@Override
public int compare( final CombinableDomains d1,
final CombinableDomains d2 ) {
- if ( d1.getNumberOfCombinableDomains() < d2
- .getNumberOfCombinableDomains() ) {
+ if ( d1.getKeyDomainProteinsCount() < d2
+ .getKeyDomainProteinsCount() ) {
return 1;
}
else if ( d1
- .getNumberOfCombinableDomains() > d2
- .getNumberOfCombinableDomains() ) {
+ .getKeyDomainProteinsCount() > d2
+ .getKeyDomainProteinsCount() ) {
return -1;
}
else {
}
};
final private SortedMap<String, CombinableDomains> _combinable_domains_map;
- final private Species _species;
final private DomainCombinationType _dc_type;
+ final private Species _species;
private BasicGenomeWideCombinableDomains( final Species species, final DomainCombinationType dc_type ) {
_combinable_domains_map = new TreeMap<String, CombinableDomains>();
_dc_type = dc_type;
}
- private void add( final String key, final CombinableDomains cdc ) {
- _combinable_domains_map.put( key, cdc );
- }
-
@Override
public boolean contains( final String key_id ) {
return _combinable_domains_map.containsKey( key_id );
return sb;
}
- private static void countDomains( final Map<String, Integer> domain_counts,
- final Set<String> saw_c,
- final String id_i ) {
- if ( domain_counts.containsKey( id_i ) ) {
- domain_counts.put( id_i, 1 + domain_counts.get( ( id_i ) ) );
- }
- else {
- domain_counts.put( id_i, 1 );
- }
- saw_c.add( id_i );
+ private void add( final String key, final CombinableDomains cdc ) {
+ _combinable_domains_map.put( key, cdc );
}
public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
}
return instance;
}
+
+ private static void countDomains( final Map<String, Integer> domain_counts,
+ final Set<String> saw_c,
+ final String id_i ) {
+ if ( domain_counts.containsKey( id_i ) ) {
+ domain_counts.put( id_i, 1 + domain_counts.get( ( id_i ) ) );
+ }
+ else {
+ domain_counts.put( id_i, 1 );
+ }
+ saw_c.add( id_i );
+ }
}