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:

java.io.Serializable, java.lang.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

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

XReferrableImpl()
Default constructor.

Method Summary

void	addXref(Xref xref)
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
java.util.Set<Xref>	getXref()
protected boolean	hasCommonUnificationXref(XReferrable xReferrable) Answers whether two BioPAX objects that implement
void	removeXref(Xref xref)
protected boolean	semanticallyEquivalent(BioPAXElement element)
protected void	setXref(java.util.Set<Xref> xref)

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, toString

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.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

public java.util.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(java.util.Set<Xref> xref)

addXref

public void addXref(Xref xref)

Specified by:

addXref in interface XReferrable

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class BioPAXElementImpl

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.

hasCommonUnificationXref

protected boolean hasCommonUnificationXref(XReferrable xReferrable)

Answers whether two BioPAX objects that implement

Parameters:

xReferrable -

Returns:

true if this and that either share - or neither have a UnificationXref!

See Also:

interface have at least one UnificationXref in common or neither have any.