public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDomains {
+ private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER = new Comparator<CombinableDomains>() {
+
+ @Override
+ public int compare( final CombinableDomains d1,
+ final CombinableDomains d2 ) {
+ if ( d1.getNumberOfCombinableDomains() < d2
+ .getNumberOfCombinableDomains() ) {
+ return 1;
+ }
+ else if ( d1
+ .getNumberOfCombinableDomains() > d2
+ .getNumberOfCombinableDomains() ) {
+ return -1;
+ }
+ else {
+ return d1
+ .getKeyDomain()
+ .compareTo( d2
+ .getKeyDomain() );
+ }
+ }
+ };
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.getKeyDomainCount() < d2
- .getKeyDomainCount() ) {
- return 1;
- }
- else if ( d1
- .getKeyDomainCount() > d2
- .getKeyDomainCount() ) {
- return -1;
- }
- else {
- return d1
- .getKeyDomain()
- .compareTo( d2
- .getKeyDomain() );
- }
- }
- };
+ @Override
+ public int compare( final CombinableDomains d1,
+ final CombinableDomains d2 ) {
+ if ( d1.getKeyDomainCount() < d2
+ .getKeyDomainCount() ) {
+ return 1;
+ }
+ else if ( d1
+ .getKeyDomainCount() > d2
+ .getKeyDomainCount() ) {
+ return -1;
+ }
+ else {
+ return d1
+ .getKeyDomain()
+ .compareTo( d2
+ .getKeyDomain() );
+ }
+ }
+ };
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.getKeyDomainProteinsCount() < d2
- .getKeyDomainProteinsCount() ) {
- return 1;
- }
- else if ( d1
- .getKeyDomainProteinsCount() > d2
- .getKeyDomainProteinsCount() ) {
- return -1;
- }
- else {
- return d1
- .getKeyDomain()
- .compareTo( d2
- .getKeyDomain() );
- }
- }
- };
- private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER = new Comparator<CombinableDomains>() {
-
- @Override
- public int compare( final CombinableDomains d1,
- final CombinableDomains d2 ) {
- if ( d1.getNumberOfCombinableDomains() < d2
- .getNumberOfCombinableDomains() ) {
- return 1;
- }
- else if ( d1
- .getNumberOfCombinableDomains() > d2
- .getNumberOfCombinableDomains() ) {
- return -1;
- }
- else {
- return d1
- .getKeyDomain()
- .compareTo( d2
- .getKeyDomain() );
- }
- }
- };
+ @Override
+ public int compare( final CombinableDomains d1,
+ final CombinableDomains d2 ) {
+ if ( d1.getKeyDomainProteinsCount() < d2
+ .getKeyDomainProteinsCount() ) {
+ return 1;
+ }
+ else if ( d1
+ .getKeyDomainProteinsCount() > d2
+ .getKeyDomainProteinsCount() ) {
+ return -1;
+ }
+ else {
+ return d1
+ .getKeyDomain()
+ .compareTo( d2
+ .getKeyDomain() );
+ }
+ }
+ };
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 toStringBuilder( GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID ).toString();
}
- // Produces something like:
- // 2-oxoacid_dh 5 5 2 Biotin_lipoyl [4], E3_binding [3]
- @Override
- public StringBuilder toStringBuilder( final GenomeWideCombinableDomainsSortOrder sort_order ) {
+ // Produces something like:
+ // 2-oxoacid_dh 5 5 2 Biotin_lipoyl [4], E3_binding [3]
+ @Override
+ public StringBuilder toStringBuilder( final GenomeWideCombinableDomainsSortOrder sort_order ) {
final StringBuilder sb = new StringBuilder();
final List<CombinableDomains> combinable_domains = new ArrayList<CombinableDomains>();
for( final String key : getAllCombinableDomainsIds().keySet() ) {
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,
for( final Protein protein : protein_list ) {
if ( !protein.getSpecies().equals( species ) ) {
throw new IllegalArgumentException( "species (" + protein.getSpecies()
- + ") does not match species of combinable domains collection (" + species + ")" );
+ + ") does not match species of combinable domains collection (" + species + ")" );
}
final Set<String> saw_i = new HashSet<String>();
final Set<String> saw_c = new HashSet<String>();
saw_j.add( id );
if ( dc_type != DomainCombinationType.DIRECTED_ADJACTANT ) {
domain_combination
- .addCombinableDomain( protein.getProteinDomain( j ).getDomainId() );
+ .addCombinableDomain( protein.getProteinDomain( j ).getDomainId() );
}
else {
if ( closest == null ) {
}
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 );
+ }
}