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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
surfacing
/
BasicCombinableDomains.java
diff --git
a/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
b/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
index
84408dc
..
02a8278
100644
(file)
--- a/
forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
+++ b/
forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
@@
-27,29
+27,31
@@
package org.forester.surfacing;
import java.util.ArrayList;
package org.forester.surfacing;
import java.util.ArrayList;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
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.species.Species;
import java.util.SortedMap;
import java.util.TreeMap;
import org.forester.protein.BinaryDomainCombination;
import org.forester.species.Species;
-import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterUtil;
public class BasicCombinableDomains implements CombinableDomains {
public class BasicCombinableDomains implements CombinableDomains {
+ final private TreeMap<String, Integer> _combining_domains;
final private String _key_domain;
private int _key_domain_count;
final private String _key_domain;
private int _key_domain_count;
- private int _key_domain_proteins_count;
+ final private Set<String> _proteins_with_key_domain;
final private Species _species;
final private Species _species;
- final private TreeMap<String, Integer> _combining_domains;
- private DescriptiveStatistics _key_domain_confidence_statistics;
public BasicCombinableDomains( final String key_domain, final Species species ) {
_key_domain = key_domain;
_species = species;
_combining_domains = new TreeMap<String, Integer>();
public BasicCombinableDomains( final String key_domain, final Species species ) {
_key_domain = key_domain;
_species = species;
_combining_domains = new TreeMap<String, Integer>();
- init();
+ _proteins_with_key_domain = new HashSet<String>();
+ _key_domain_count = 0;
}
@Override
}
@Override
@@
-63,6
+65,14
@@
public class BasicCombinableDomains implements CombinableDomains {
}
@Override
}
@Override
+ 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() ) ) {
public List<String> getAllDomains() {
final List<String> domains = getCombinableDomains();
if ( !domains.contains( getKeyDomain() ) ) {
@@
-107,28
+117,24
@@
public class BasicCombinableDomains implements CombinableDomains {
return sb;
}
return sb;
}
- protected TreeMap<String, Integer> getCombiningDomains() {
- return _combining_domains;
- }
-
@Override
public String getKeyDomain() {
return _key_domain;
}
@Override
@Override
public String getKeyDomain() {
return _key_domain;
}
@Override
- public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics() {
- return _key_domain_confidence_statistics;
+ public int getKeyDomainCount() {
+ return _key_domain_count;
}
@Override
}
@Override
- public int getKeyDomainCount() {
- return _key_domain_count;
+ public Set<String> getKeyDomainProteins() {
+ return _proteins_with_key_domain;
}
@Override
public int getKeyDomainProteinsCount() {
}
@Override
public int getKeyDomainProteinsCount() {
- return _key_domain_proteins_count;
+ return getKeyDomainProteins().size();
}
@Override
}
@Override
@@
-151,37
+157,22
@@
public class BasicCombinableDomains implements CombinableDomains {
return _species;
}
return _species;
}
- private void init() {
- _key_domain_count = 0;
- _key_domain_proteins_count = 0;
- _key_domain_confidence_statistics = null;
- }
-
@Override
public boolean isCombinable( final String protein_domain ) {
return getCombiningDomains().containsKey( protein_domain );
}
@Override
@Override
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 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 String domain : getCombiningDomains().keySet() ) {
public List<BinaryDomainCombination> toBinaryDomainCombinations() {
final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
for( final String domain : getCombiningDomains().keySet() ) {
- binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+ // binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+ binary_combinations.add( BasicBinaryDomainCombination.obtainInstance( getKeyDomain(), domain ) );
}
return binary_combinations;
}
}
return binary_combinations;
}
@@
-200,4
+191,8
@@
public class BasicCombinableDomains implements CombinableDomains {
sb.append( getCombiningDomainIdsAsStringBuilder() );
return sb.toString();
}
sb.append( getCombiningDomainIdsAsStringBuilder() );
return sb.toString();
}
+
+ protected TreeMap<String, Integer> getCombiningDomains() {
+ return _combining_domains;
+ }
}
}