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.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() );
- }
- }
- };
+ @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 DomainCombinationType _dc_type;
final private Species _species;
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() ) {
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 ) {