org.biojavax.ontology.SimpleComparableTerm Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojavax.ontology;
import java.util.Arrays;
import java.util.Set;
import java.util.TreeSet;
import org.biojava.bio.Annotation;
import org.biojava.ontology.Ontology;
import org.biojava.ontology.Term;
import org.biojava.utils.AbstractChangeable;
import org.biojava.utils.ChangeEvent;
import org.biojava.utils.ChangeSupport;
import org.biojava.utils.ChangeVetoException;
import org.biojavax.RankedCrossRef;
import org.biojavax.RichAnnotation;
/**
* A Term object that can be compared and thus sorted.
* @author Richard Holland
* @since 1.5
*/
public class SimpleComparableTerm extends AbstractChangeable implements ComparableTerm {
private String name;
private String description;
private ComparableOntology ontology;
private String identifier;
private Boolean obsolete;
private Set synonyms = new TreeSet();
private Set rankedcrossrefs = new TreeSet();
/**
* Creates a new instance of SimpleComparableTerm with synonyms.
* @param ontology The ontology to put the term in. Must not be null.
* @param name the name of the term. Must not be null.
* @param synonyms a set of synonyms for the term. Can be null.
*/
SimpleComparableTerm(ComparableOntology ontology, String name, Object[] synonyms) {
if (name == null || name.equals("")) throw new IllegalArgumentException("Name must not be null or empty");
if (ontology == null) throw new IllegalArgumentException("Ontology must not be null");
this.name = name;
this.description = null;
this.ontology = ontology;
this.identifier = null;
this.obsolete = Boolean.FALSE;
if (synonyms!=null
&& synonyms.length != 0) this.synonyms.addAll(Arrays.asList(synonyms));
}
// Hibernate requirement - not for public use.
protected SimpleComparableTerm() {}
/**
* {@inheritDoc}
*/
public int hashCode() {
int value = 17;
// Hibernate comparison - we haven't been populated yet
if (this.ontology==null) return value;
// Normal comparison
value = 37*value + this.name.hashCode();
value = 37*value + this.ontology.hashCode();
return value;
}
/**
* {@inheritDoc}
* Two terms are equal if they are in the same ontology and
* share the same name.
*/
public boolean equals(Object obj) {
if (obj == this) return true;
if (!(obj instanceof Term)) return false;
// Hibernate comparison - we haven't been populated yet
if (this.ontology==null) return false;
// Normal comparison
Term that = (Term) obj;
return this.ontology.equals(that.getOntology()) &&
this.name.equals(that.getName());
}
/**
* {@inheritDoc}
* Terms are sorted by ontology first, then name.
*/
public int compareTo(Object o) {
if (o==this) return 0;
// Hibernate comparison - we haven't been populated yet
if (this.ontology==null) return -1;
// Normal comparison
Term them = (Term)o;
if (!this.ontology.equals(them.getOntology())) return this.ontology.compareTo(them.getOntology());
return this.name.compareTo(them.getName());
}
/**
* {@inheritDoc}
* Synonyms are stored in the database as the results of a toString() operation
* on each synonym object. This doesn't happen until it reaches the database
* though, so if you are not using a database, don't worry about it.
*/
public void addSynonym(Object synonym) { this.synonyms.add(synonym); }
/**
* {@inheritDoc}
*/
public void removeSynonym(Object synonym) { this.synonyms.remove(synonym); }
/**
* {@inheritDoc}
*/
public Object[] getSynonyms() { return this.synonyms.toArray(); }
// Hibernate requirement - not for public use.
Set getSynonymSet() { return this.synonyms; }
// Hibernate requirement - not for public use.
void setSynonymSet(Set synonyms) { this.synonyms = synonyms; }
/**
* {@inheritDoc}
* Warning this method gives access to the original
* Collection not a copy. This is required by Hibernate. If you
* modify the object directly the behaviour may be unpredictable.
*/
public Set getRankedCrossRefs() { return this.rankedcrossrefs; } // original for Hibernate
/**
* {@inheritDoc}
* Warning this method gives access to the original
* Collection not a copy. This is required by Hibernate. If you
* modify the object directly the behaviour may be unpredictable.
*/
public void setRankedCrossRefs(Set rankedcrossrefs) throws ChangeVetoException {
this.rankedcrossrefs = rankedcrossrefs; // original for Hibernate
}
/**
* {@inheritDoc}
*/
public void addRankedCrossRef(RankedCrossRef crossref) throws ChangeVetoException {
if (crossref==null) throw new IllegalArgumentException("Crossref cannot be null");
if(!this.hasListeners(ComparableTerm.RANKEDCROSSREF)) {
this.rankedcrossrefs.add(crossref);
} else {
ChangeEvent ce = new ChangeEvent(
this,
ComparableTerm.RANKEDCROSSREF,
crossref,
null
);
ChangeSupport cs = this.getChangeSupport(ComparableTerm.RANKEDCROSSREF);
synchronized(cs) {
cs.firePreChangeEvent(ce);
this.rankedcrossrefs.add(crossref);
cs.firePostChangeEvent(ce);
}
}
}
/**
* {@inheritDoc}
*/
public void removeRankedCrossRef(RankedCrossRef crossref) throws ChangeVetoException {
if (crossref==null) throw new IllegalArgumentException("Crossref cannot be null");
if(!this.hasListeners(ComparableTerm.RANKEDCROSSREF)) {
this.rankedcrossrefs.remove(crossref);
} else {
ChangeEvent ce = new ChangeEvent(
this,
ComparableTerm.RANKEDCROSSREF,
null,
crossref
);
ChangeSupport cs = this.getChangeSupport(ComparableTerm.RANKEDCROSSREF);
synchronized(cs) {
cs.firePreChangeEvent(ce);
this.rankedcrossrefs.remove(crossref);
cs.firePostChangeEvent(ce);
}
}
}
/**
* {@inheritDoc}
*/
public String getName() { return this.name; }
// Hibernate requirement - not for public use.
void setName(String name) { this.name = name; }
/**
* {@inheritDoc}
*/
public String getDescription() { return this.description; }
/**
* {@inheritDoc}
*/
public void setDescription(String description) throws ChangeVetoException {
if(!this.hasListeners(ComparableTerm.DESCRIPTION)) {
this.description = description;
} else {
ChangeEvent ce = new ChangeEvent(
this,
ComparableTerm.DESCRIPTION,
description,
this.description
);
ChangeSupport cs = this.getChangeSupport(ComparableTerm.DESCRIPTION);
synchronized(cs) {
cs.firePreChangeEvent(ce);
this.description = description;
cs.firePostChangeEvent(ce);
}
}
}
/**
* {@inheritDoc}
*/
public Ontology getOntology() { return this.ontology; }
// Hibernate requirement - not for public use.
void setOntology(ComparableOntology ontology) { this.ontology = ontology; }
/**
* {@inheritDoc}
* Form: "ontology:name [obsolete]" where [obsolete] is optional
*/
public String toString() {
boolean isobs = (this.obsolete!=null && this.obsolete.booleanValue());
return this.ontology+":"+this.name+(isobs?" [obsolete]":"");
}
/**
* {@inheritDoc}
* ALWAYS RETURNS AN EMPTY ANNOTATION OBJECT
*/
public Annotation getAnnotation() { return RichAnnotation.EMPTY_ANNOTATION; }
/**
* {@inheritDoc}
*/
public String getIdentifier() { return this.identifier; }
/**
* {@inheritDoc}
*/
public void setIdentifier(String identifier) throws ChangeVetoException {
if(!this.hasListeners(ComparableTerm.IDENTIFIER)) {
this.identifier = identifier;
} else {
ChangeEvent ce = new ChangeEvent(
this,
ComparableTerm.IDENTIFIER,
identifier,
this.identifier
);
ChangeSupport cs = this.getChangeSupport(ComparableTerm.IDENTIFIER);
synchronized(cs) {
cs.firePreChangeEvent(ce);
this.identifier = identifier;
cs.firePostChangeEvent(ce);
}
}
}
// Hibernate requirement - not for public use.
String getObsoleteChar() {
return (this.getObsolete()!=null && this.getObsolete().equals(Boolean.TRUE))?"X":null;
}
// Hibernate requirement - not for public use.
void setObsoleteChar(String obsolete) throws ChangeVetoException {
this.setObsolete(Boolean.valueOf(obsolete!=null && obsolete.equals("X")));
}
/**
* {@inheritDoc}
*/
public Boolean getObsolete() { return this.obsolete; }
/**
* {@inheritDoc}
*/
public void setObsolete(Boolean obsolete) throws ChangeVetoException {
if(!this.hasListeners(ComparableTerm.OBSOLETE)) {
this.obsolete = obsolete;
} else {
ChangeEvent ce = new ChangeEvent(
this,
ComparableTerm.OBSOLETE,
obsolete,
this.obsolete
);
ChangeSupport cs = this.getChangeSupport(ComparableTerm.OBSOLETE);
synchronized(cs) {
cs.firePreChangeEvent(ce);
this.obsolete = obsolete;
cs.firePostChangeEvent(ce);
}
}
}
// Hibernate requirement - not for public use.
private Integer id;
/**
* Gets the Hibernate ID. Should be used with caution.
* @return the Hibernate ID, if using Hibernate.
*/
public Integer getId() { return this.id; }
/**
* Sets the Hibernate ID. Should be used with caution.
* @param id the Hibernate ID, if using Hibernate.
*/
public void setId(Integer id) { this.id = id;}
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