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:

java.io.Serializable, java.lang.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

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

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

SEARCH_FIELD_AVAILABILITY, SEARCH_FIELD_COMMENT, SEARCH_FIELD_EC_NUMBER, SEARCH_FIELD_KEYWORD, SEARCH_FIELD_NAME, SEARCH_FIELD_SEQUENCE, SEARCH_FIELD_TERM, SEARCH_FIELD_XREF_DB, SEARCH_FIELD_XREF_ID, SEARCH_INDEX_NAME

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

ControlledVocabularyImpl()
Constructor.

Method Summary

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

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

addXref, equivalenceCode, getXref, hasCommonUnificationXref, removeXref, setXref

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

addComment, getComment, removeComment, setComment

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

getAnnotations, getProxyId, getRDFId, getVersion, isEquivalent, setProxyId, setRDFId, setVersion

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, 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 java.lang.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",
       index=TOKENIZED)
@FieldBridge(impl=SetStringBridge.class)
public java.util.Set<java.lang.String> getTerm()

Specified by:

getTerm in interface ControlledVocabulary

Returns:

The external controlled vocabulary term.

setTerm

public void setTerm(java.util.Set<java.lang.String> term)

addTerm

public void addTerm(java.lang.String term)

Specified by:

addTerm in interface ControlledVocabulary

Parameters:

term - The external controlled vocabulary term.

removeTerm

public void removeTerm(java.lang.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 XReferrableImpl

toString

public java.lang.String toString()

Overrides:

toString in class BioPAXElementImpl