new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims = calc
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list,
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc2 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims2 = calc2
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list2,
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc3 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims3 = calc3
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list3,
if ( !sa3.getDomainId().equals( "A" ) ) {
return false;
}
- final SpeciesSpecificDomainSimilariyData ssdsd = sa3.getSpeciesData().get( new BasicSpecies( "ciona" ) );
+ final SpeciesSpecificDcData ssdsd = sa3.getSpeciesData().get( new BasicSpecies( "ciona" ) );
if ( ssdsd.getCombinableDomainIdToCountsMap().size() != 4 ) {
return false;
}
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc4 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
true,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims4 = calc4
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list4,
if ( !sa4.getDomainId().equals( "A" ) ) {
return false;
}
- final SpeciesSpecificDomainSimilariyData ssdsd4 = sa4.getSpeciesData().get( new BasicSpecies( "ciona" ) );
+ final SpeciesSpecificDcData ssdsd4 = sa4.getSpeciesData().get( new BasicSpecies( "ciona" ) );
if ( ssdsd4.getCombinableDomainIdToCountsMap().size() != 5 ) {
return false;
}
if ( !sa5_d.getSpecies().last().equals( new BasicSpecies( "rabbit" ) ) ) {
return false;
}
- final SpeciesSpecificDomainSimilariyData ssdsd5 = sa5_d.getSpeciesData().get( new BasicSpecies( "ciona" ) );
+ final SpeciesSpecificDcData ssdsd5 = sa5_d.getSpeciesData().get( new BasicSpecies( "ciona" ) );
if ( ssdsd5.getCombinableDomainIdToCountsMap().size() != 4 ) {
return false;
}
if ( !sa6_d.getSpecies().last().equals( new BasicSpecies( "rabbit" ) ) ) {
return false;
}
- final SpeciesSpecificDomainSimilariyData ssdsd6 = sa6_d.getSpeciesData().get( new BasicSpecies( "ciona" ) );
+ final SpeciesSpecificDcData ssdsd6 = sa6_d.getSpeciesData().get( new BasicSpecies( "ciona" ) );
if ( ssdsd6.getCombinableDomainIdToCountsMap().size() != 5 ) {
return false;
}
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims = calc
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list,
new BasicSpecies( "nemve" ) ) );
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
false,
- false );
+ false,
+ true );
final SortedSet<DomainSimilarity> sims = calc
.calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
cdc_list,