// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
_treat_as_binary_comparison = treat_as_binary_comparison;
}
+ @Override
public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
final List<GenomeWideCombinableDomains> cdc_list,
final boolean ignore_domains_without_combinations_in_any_genome,
}
final DescriptiveStatistics stat = new BasicDescriptiveStatistics();
final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
- species_data.put( domains_list.get( 0 ).getSpecies(), createSpeciesSpecificDomainSimilariyData( domains_list
- .get( 0 ) ) );
+ species_data.put( domains_list.get( 0 ).getSpecies(),
+ createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
int max_difference_in_counts = 0;
int max_difference = 0;
final boolean is_domain_combination_based = pairwise_calculator instanceof CombinationsBasedPairwiseDomainSimilarityCalculator;
}
private static SpeciesSpecificDomainSimilariyData createSpeciesSpecificDomainSimilariyData( final CombinableDomains cd ) {
- final SpeciesSpecificDomainSimilariyData sd = new PrintableSpeciesSpecificDomainSimilariyData( cd
- .getKeyDomainProteinsCount(), cd.getKeyDomainCount(), cd.getNumberOfCombinableDomains(), cd
- .getKeyDomainConfidenceDescriptiveStatistics() );
+ final SpeciesSpecificDomainSimilariyData sd = new PrintableSpeciesSpecificDomainSimilariyData( cd.getKeyDomainProteinsCount(),
+ cd.getKeyDomainCount(),
+ cd.getNumberOfCombinableDomains(),
+ cd.getKeyDomainConfidenceDescriptiveStatistics() );
for( final DomainId domain : cd.getCombinableDomains() ) {
sd.addProteinsExhibitingCombinationCount( domain, cd.getNumberOfProteinsExhibitingCombination( domain ) );
}