org.biopax.paxtools.impl.level3

Class ControlledVocabularyImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.XReferrableImpl

org.biopax.paxtools.impl.level3.ControlledVocabularyImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, ControlledVocabulary, Level3Element, UtilityClass, XReferrable

Direct Known Subclasses:

CellularLocationVocabularyImpl, CellVocabularyImpl, EntityReferenceTypeVocabularyImpl, EvidenceCodeVocabularyImpl, ExperimentalFormVocabularyImpl, InteractionVocabularyImpl, PhenotypeVocabularyImpl, RelationshipTypeVocabularyImpl, SequenceModificationVocabularyImpl, SequenceRegionVocabularyImpl, TissueVocabularyImpl

@Entity
 @Indexed
public class ControlledVocabularyImpl
extends XReferrableImpl
implements ControlledVocabulary

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_AVAILABILITY, FIELD_COMMENT, FIELD_DATASOURCE, FIELD_ECNUMBER, FIELD_KEYWORD, FIELD_NAME, FIELD_ORGANISM, FIELD_PATHWAY, FIELD_SEQUENCE, FIELD_TERM, FIELD_XREFDB, FIELD_XREFID, FILTER_BY_DATASOURCE, FILTER_BY_ORGANISM

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
ControlledVocabularyImpl() Constructor.

Method Summary

Modifier and Type	Method and Description
void	addTerm(String term)
Class<? extends ControlledVocabulary>	getModelInterface() This method returns the actual model interface that a class implements.
Set<String>	getTerm()
void	removeTerm(String term)
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setTerm(Set<String> term)
String	toString()

Methods inherited from class org.biopax.paxtools.impl.level3.XReferrableImpl

addXref, equivalenceCode, getXref, removeXref, setXref

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getRDFId, isEquivalent

Constructor Detail

ControlledVocabularyImpl

public ControlledVocabularyImpl()

Constructor.

Method Detail

getModelInterface

public Class<? extends ControlledVocabulary> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getTerm

@Field(name="term",
       analyze=YES)
 @FieldBridge(impl=SetStringBridge.class)
public Set<String> getTerm()

Specified by:

getTerm in interface ControlledVocabulary

Returns:

The external controlled vocabulary term.

setTerm

public void setTerm(Set<String> term)

addTerm

public void addTerm(String term)

Specified by:

addTerm in interface ControlledVocabulary

Parameters:

term - The external controlled vocabulary term.

removeTerm

public void removeTerm(String term)

Specified by:

removeTerm in interface ControlledVocabulary

Parameters:

term - The external controlled vocabulary term.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class BioPAXElementImpl

toString

public String toString()

Overrides:

toString in class BioPAXElementImpl