org.biopax.paxtools.impl.level3

Class XReferrableImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.XReferrableImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Level3Element, XReferrable

Direct Known Subclasses:

ControlledVocabularyImpl, EvidenceImpl, NamedImpl, ScoreImpl

@Entity
public abstract class XReferrableImpl
extends L3ElementImpl
implements XReferrable

This class helps with managing the bidirectional xref links.

Author:

Emek Demir

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
XReferrableImpl() Default constructor.

Method Summary

Modifier and Type	Method and Description
void	addXref(Xref xref)
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
Set<Xref>	getXref()
void	removeXref(Xref xref)
protected void	setXref(Set<Xref> xref)

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, semanticallyEquivalent, toString

Methods inherited from class java.lang.Object

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

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

addComment, getComment, removeComment

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

getAnnotations, getModelInterface, getRDFId, isEquivalent

Constructor Detail

XReferrableImpl

public XReferrableImpl()

Default constructor.

Method Detail

getXref

@Field(name="xrefid",
       analyze=NO,
       bridge=@FieldBridge(impl=XrefFieldBridge.class),
       boost=@Boost(value=1.5f))
public Set<Xref> getXref()

Specified by:

getXref in interface XReferrable

removeXref

public void removeXref(Xref xref)

Specified by:

removeXref in interface XReferrable

setXref

protected void setXref(Set<Xref> xref)

addXref

public void addXref(Xref xref)

Specified by:

addXref in interface XReferrable

equivalenceCode

public int equivalenceCode()

Description copied from interface: BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

Specified by:

equivalenceCode in interface BioPAXElement

Overrides:

equivalenceCode in class BioPAXElementImpl

Returns:

an integer that is same across all equivalent entities.