public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculator {
- final PrintableDomainSimilarity.DomainSimilaritySortField _sort;
- private final boolean _calc_similarity_score;
- private final boolean _sort_by_species_count_first;
- private final boolean _treat_as_binary_comparison;
+ final DomainSimilarity.DomainSimilaritySortField _sort;
+ private final boolean _calc_similarity_score;
+ private final boolean _sort_by_species_count_first;
+ private final boolean _treat_as_binary_comparison;
+ private final boolean _verbose;
- public BasicDomainSimilarityCalculator( final PrintableDomainSimilarity.DomainSimilaritySortField sort,
+ public BasicDomainSimilarityCalculator( final DomainSimilarity.DomainSimilaritySortField sort,
+ final boolean sort_by_species_count_first,
+ final boolean treat_as_binary_comparison,
+ final boolean calc_similarity_score,
+ final boolean verbose ) {
+ _sort = sort;
+ _sort_by_species_count_first = sort_by_species_count_first;
+ _treat_as_binary_comparison = treat_as_binary_comparison;
+ _calc_similarity_score = calc_similarity_score;
+ _verbose = verbose;
+ }
+
+ public BasicDomainSimilarityCalculator( final DomainSimilarity.DomainSimilaritySortField sort,
final boolean sort_by_species_count_first,
final boolean treat_as_binary_comparison,
final boolean calc_similarity_score ) {
_sort_by_species_count_first = sort_by_species_count_first;
_treat_as_binary_comparison = treat_as_binary_comparison;
_calc_similarity_score = calc_similarity_score;
+ _verbose = false;
}
@Override
- public SortedSet<PrintableDomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
- final List<GenomeWideCombinableDomains> cdc_list,
- final boolean ignore_domains_without_combinations_in_any_genome,
- final boolean ignore_domains_specific_to_one_genome ) {
+ public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
+ final List<GenomeWideCombinableDomains> cdc_list,
+ final boolean ignore_domains_without_combinations_in_any_genome,
+ final boolean ignore_domains_specific_to_one_genome ) {
if ( cdc_list.size() < 2 ) {
throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinale domains collections" );
}
- final SortedSet<PrintableDomainSimilarity> similarities = new TreeSet<PrintableDomainSimilarity>();
+ final SortedSet<DomainSimilarity> similarities = new TreeSet<DomainSimilarity>();
final SortedSet<String> keys = new TreeSet<String>();
for( final GenomeWideCombinableDomains cdc : cdc_list ) {
keys.addAll( ( cdc ).getAllCombinableDomainsIds().keySet() );
}
final DecimalFormat pf = new java.text.DecimalFormat( "000000" );
int counter = 1;
- System.out.println( keys.size() );
+ if ( _verbose ) {
+ System.out.println( keys.size() );
+ }
for( final String key : keys ) {
- ForesterUtil.updateProgress( counter, pf );
+ if ( _verbose ) {
+ ForesterUtil.updateProgress( counter, pf );
+ }
counter++;
final List<CombinableDomains> same_id_cd_list = new ArrayList<CombinableDomains>( cdc_list.size() );
final List<Species> species_with_key_id_domain = new ArrayList<Species>();
}
if ( same_id_cd_list.size() > 0 ) {
if ( !ignore_domains_specific_to_one_genome || ( same_id_cd_list.size() > 1 ) ) {
- final PrintableDomainSimilarity s = calculateSimilarity( pairwise_calculator, same_id_cd_list );
+ final DomainSimilarity s = calculateSimilarity( pairwise_calculator, same_id_cd_list );
if ( s != null ) {
similarities.add( s );
}
throw new RuntimeException( "this should not have happened" );
}
}
- System.out.println();
+ if ( _verbose ) {
+ System.out.println();
+ }
return similarities;
}
return _calc_similarity_score;
}
- private PrintableDomainSimilarity calculateSimilarity( final PairwiseDomainSimilarityCalculator pairwise_calculator,
- final List<CombinableDomains> domains_list ) {
+ private DomainSimilarity calculateSimilarity( final PairwiseDomainSimilarityCalculator pairwise_calculator,
+ final List<CombinableDomains> domains_list ) {
if ( domains_list.size() == 1 ) {
final SortedMap<Species, SpeciesSpecificDcData> species_data = new TreeMap<Species, SpeciesSpecificDcData>();
species_data.put( domains_list.get( 0 ).getSpecies(),
createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
if ( !isCalcSimilarityScore() ) {
- return new PrintableDomainSimilarity( domains_list.get( 0 ),
- 0,
- 0,
- species_data,
- isSortBySpeciesCountFirst(),
- isTreatAsBinaryComparison() );
+ return new DomainSimilarity( domains_list.get( 0 ),
+ 0,
+ 0,
+ species_data,
+ isSortBySpeciesCountFirst(),
+ isTreatAsBinaryComparison() );
}
else {
- return new PrintableDomainSimilarity( domains_list.get( 0 ),
- 1.0,
- 1.0,
- 1.0,
- 1.0,
- 0.0,
- 0,
- 0,
- 0,
- species_data,
- isSortBySpeciesCountFirst(),
- isTreatAsBinaryComparison() );
+ return new DomainSimilarity( domains_list.get( 0 ),
+ 1.0,
+ 1.0,
+ 1.0,
+ 1.0,
+ 0.0,
+ 0,
+ 0,
+ 0,
+ species_data,
+ isSortBySpeciesCountFirst(),
+ isTreatAsBinaryComparison() );
}
}
DescriptiveStatistics stat = null;
max_difference = Math.abs( max_difference );
}
}
- PrintableDomainSimilarity similarity = null;
+ DomainSimilarity similarity = null;
if ( !isCalcSimilarityScore() ) {
- similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
- max_difference_in_counts,
- max_difference,
- species_data,
- isSortBySpeciesCountFirst(),
- isTreatAsBinaryComparison() );
+ similarity = new DomainSimilarity( domains_list.get( 0 ),
+ max_difference_in_counts,
+ max_difference,
+ species_data,
+ isSortBySpeciesCountFirst(),
+ isTreatAsBinaryComparison() );
}
else {
if ( stat.getN() == 1 ) {
- similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
- stat.getMin(),
- stat.getMax(),
- stat.arithmeticMean(),
- stat.median(),
- 0.0,
- stat.getN(),
- max_difference_in_counts,
- max_difference,
- species_data,
- isSortBySpeciesCountFirst(),
- isTreatAsBinaryComparison() );
+ similarity = new DomainSimilarity( domains_list.get( 0 ),
+ stat.getMin(),
+ stat.getMax(),
+ stat.arithmeticMean(),
+ stat.median(),
+ 0.0,
+ stat.getN(),
+ max_difference_in_counts,
+ max_difference,
+ species_data,
+ isSortBySpeciesCountFirst(),
+ isTreatAsBinaryComparison() );
}
else {
- similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
- stat.getMin(),
- stat.getMax(),
- stat.arithmeticMean(),
- stat.median(),
- stat.sampleStandardDeviation(),
- stat.getN(),
- max_difference_in_counts,
- max_difference,
- species_data,
- isSortBySpeciesCountFirst(),
- isTreatAsBinaryComparison() );
+ similarity = new DomainSimilarity( domains_list.get( 0 ),
+ stat.getMin(),
+ stat.getMax(),
+ stat.arithmeticMean(),
+ stat.median(),
+ stat.sampleStandardDeviation(),
+ stat.getN(),
+ max_difference_in_counts,
+ max_difference,
+ species_data,
+ isSortBySpeciesCountFirst(),
+ isTreatAsBinaryComparison() );
}
}
return similarity;
git://source.jalview.org / jalview.git / blobdiff