// 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
import java.util.SortedMap;
import java.util.TreeMap;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.protein.DomainId;
+import org.forester.species.Species;
import org.forester.util.DescriptiveStatistics;
public class BasicCombinableDomains implements CombinableDomains {
init();
}
+ @Override
public void addCombinableDomain( final DomainId protein_domain ) {
if ( getCombiningDomains().containsKey( protein_domain ) ) {
getCombiningDomains().put( protein_domain, getCombiningDomains().get( protein_domain ) + 1 );
}
}
+ @Override
public List<DomainId> getAllDomains() {
final List<DomainId> domains = getCombinableDomains();
if ( !domains.contains( getKeyDomain() ) ) {
return domains;
}
+ @Override
public List<DomainId> getCombinableDomains() {
final List<DomainId> domains = new ArrayList<DomainId>( getNumberOfCombinableDomains() );
for( final DomainId domain : getCombiningDomains().keySet() ) {
return domains;
}
+ @Override
public SortedMap<DomainId, Integer> getCombinableDomainsIds() {
final SortedMap<DomainId, Integer> ids = new TreeMap<DomainId, Integer>();
for( final DomainId domain : getCombiningDomains().keySet() ) {
return ids;
}
+ @Override
public StringBuilder getCombiningDomainIdsAsStringBuilder() {
final StringBuilder sb = new StringBuilder();
for( final Iterator<DomainId> iter = getCombiningDomains().keySet().iterator(); iter.hasNext(); ) {
return _combining_domains;
}
+ @Override
public DomainId getKeyDomain() {
return _key_domain;
}
+ @Override
public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics() {
return _key_domain_confidence_statistics;
}
+ @Override
public int getKeyDomainCount() {
return _key_domain_count;
}
+ @Override
public int getKeyDomainProteinsCount() {
return _key_domain_proteins_count;
}
+ @Override
public int getNumberOfCombinableDomains() {
return _combining_domains.size();
}
+ @Override
public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain ) {
if ( getCombiningDomains().containsKey( protein_domain ) ) {
return getCombiningDomains().get( protein_domain );
}
}
+ @Override
public Species getSpecies() {
return _species;
}
_key_domain_confidence_statistics = null;
}
+ @Override
public boolean isCombinable( final DomainId protein_domain ) {
return getCombiningDomains().containsKey( protein_domain );
}
+ @Override
public void setKeyDomainConfidenceDescriptiveStatistics( final DescriptiveStatistics key_domain_confidence_statistics ) {
_key_domain_confidence_statistics = key_domain_confidence_statistics;
}
+ @Override
public void setKeyDomainCount( final int key_domain_count ) {
_key_domain_count = key_domain_count;
}
+ @Override
public void setKeyDomainProteinsCount( final int key_domain_proteins_count ) {
_key_domain_proteins_count = key_domain_proteins_count;
}