package org.forester.surfacing;
import java.util.ArrayList;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
+import java.util.Set;
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;
+import org.forester.util.ForesterUtil;
public class BasicCombinableDomains implements CombinableDomains {
- final private DomainId _key_domain;
- private int _key_domain_count;
- private int _key_domain_proteins_count;
- final private Species _species;
- final private TreeMap<DomainId, Integer> _combining_domains;
- private DescriptiveStatistics _key_domain_confidence_statistics;
+ final private TreeMap<String, Integer> _combining_domains;
+ final private String _key_domain;
+ private int _key_domain_count;
+ final private Set<String> _proteins_with_key_domain;
+ final private Species _species;
- public BasicCombinableDomains( final DomainId key_domain, final Species species ) {
+ public BasicCombinableDomains( final String key_domain, final Species species ) {
_key_domain = key_domain;
_species = species;
- _combining_domains = new TreeMap<DomainId, Integer>();
- init();
+ _combining_domains = new TreeMap<String, Integer>();
+ _proteins_with_key_domain = new HashSet<String>();
+ _key_domain_count = 0;
}
@Override
- public void addCombinableDomain( final DomainId protein_domain ) {
+ public void addCombinableDomain( final String 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();
+ public void addKeyDomainProtein( final String protein ) {
+ if ( ForesterUtil.isEmpty( protein ) ) {
+ throw new IllegalArgumentException( "attempt to add null or empty protein" );
+ }
+ getKeyDomainProteins().add( protein );
+ }
+
+ @Override
+ public List<String> getAllDomains() {
+ final List<String> domains = getCombinableDomains();
if ( !domains.contains( getKeyDomain() ) ) {
domains.add( getKeyDomain() );
}
}
@Override
- public List<DomainId> getCombinableDomains() {
- final List<DomainId> domains = new ArrayList<DomainId>( getNumberOfCombinableDomains() );
- for( final DomainId domain : getCombiningDomains().keySet() ) {
+ public List<String> getCombinableDomains() {
+ final List<String> domains = new ArrayList<String>( getNumberOfCombinableDomains() );
+ for( final String domain : getCombiningDomains().keySet() ) {
domains.add( domain );
}
return domains;
}
@Override
- public SortedMap<DomainId, Integer> getCombinableDomainsIds() {
- final SortedMap<DomainId, Integer> ids = new TreeMap<DomainId, Integer>();
- for( final DomainId domain : getCombiningDomains().keySet() ) {
- final DomainId pd = domain;
+ public SortedMap<String, Integer> getCombinableDomainsIds() {
+ final SortedMap<String, Integer> ids = new TreeMap<String, Integer>();
+ for( final String domain : getCombiningDomains().keySet() ) {
+ final String pd = domain;
ids.put( pd, getCombiningDomains().get( pd ) );
}
return ids;
@Override
public StringBuilder getCombiningDomainIdsAsStringBuilder() {
final StringBuilder sb = new StringBuilder();
- for( final Iterator<DomainId> iter = getCombiningDomains().keySet().iterator(); iter.hasNext(); ) {
- final DomainId key = iter.next();
+ for( final Iterator<String> iter = getCombiningDomains().keySet().iterator(); iter.hasNext(); ) {
+ final String key = iter.next();
sb.append( key.toString() );
sb.append( " [" );
final int count = getCombiningDomains().get( key );
return sb;
}
- protected TreeMap<DomainId, Integer> getCombiningDomains() {
- return _combining_domains;
- }
-
@Override
- public DomainId getKeyDomain() {
+ public String getKeyDomain() {
return _key_domain;
}
@Override
- public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics() {
- return _key_domain_confidence_statistics;
+ public int getKeyDomainCount() {
+ return _key_domain_count;
}
@Override
- public int getKeyDomainCount() {
- return _key_domain_count;
+ public Set<String> getKeyDomainProteins() {
+ return _proteins_with_key_domain;
}
@Override
public int getKeyDomainProteinsCount() {
- return _key_domain_proteins_count;
+ return getKeyDomainProteins().size();
}
@Override
}
@Override
- public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain ) {
+ public int getNumberOfProteinsExhibitingCombination( final String protein_domain ) {
if ( getCombiningDomains().containsKey( protein_domain ) ) {
return getCombiningDomains().get( protein_domain );
}
return _species;
}
- private void init() {
- _key_domain_count = 0;
- _key_domain_proteins_count = 0;
- _key_domain_confidence_statistics = null;
- }
-
@Override
- public boolean isCombinable( final DomainId protein_domain ) {
+ public boolean isCombinable( final String 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;
- }
-
- @Override
public List<BinaryDomainCombination> toBinaryDomainCombinations() {
final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
- for( final DomainId domain : getCombiningDomains().keySet() ) {
- binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+ for( final String domain : getCombiningDomains().keySet() ) {
+ // binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+ binary_combinations.add( BasicBinaryDomainCombination.obtainInstance( getKeyDomain(), domain ) );
}
return binary_combinations;
}
sb.append( getCombiningDomainIdsAsStringBuilder() );
return sb.toString();
}
+
+ protected TreeMap<String, Integer> getCombiningDomains() {
+ return _combining_domains;
+ }
}