org.biopax.paxtools.impl.level3
Class NucleicAcidReferenceImpl

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.NamedImpl
                  org.biopax.paxtools.impl.level3.EntityReferenceImpl
                      org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl
                          org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, BioPAXElement, EntityReference, Level3Element, Named, NucleicAcidReference, Observable, SequenceEntityReference, UtilityClass, XReferrable

Direct Known Subclasses:

DnaReferenceImpl, NucleicAcidRegionReferenceImpl, RnaReferenceImpl

@Entity
public abstract class NucleicAcidReferenceImpl
extends SequenceEntityReferenceImpl
implements NucleicAcidReference

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

NucleicAcidReferenceImpl()

Method Summary

void	addSubRegion(NucleicAcidRegionReference regionReference)
java.util.Set<NucleicAcidRegionReference>	getSubRegion()
void	removeSubRegion(NucleicAcidRegionReference regionReference)
protected void	setSubRegion(java.util.Set<NucleicAcidRegionReference> subRegion)

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

getOrganism, getSequence, semanticallyEquivalent, setOrganism, setSequence

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

addEntityFeature, addEntityReferenceType, addEvidence, addMemberEntityReference, getEntityFeature, getEntityReferenceOf, getEntityReferenceType, getEvidence, getMemberEntityReference, getMemberEntityReferenceOf, getModelInterface, removeEntityFeature, removeEntityReferenceType, removeEvidence, removeMemberEntityReference, setEntityFeature, setEntityReferenceOf, setEntityReferenceType, setEvidence, setMemberEntity, setMemberEntityReference, setMemberEntityReferenceOf

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

addName, getDisplayName, getDisplayNameX, getName, getNameX, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setNameX, setStandardName, setStandardNameX

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, 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.SequenceEntityReference

getOrganism, getSequence, setOrganism, setSequence

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

addEntityFeature, addEntityReferenceType, addMemberEntityReference, getEntityFeature, getEntityReferenceOf, getEntityReferenceType, getMemberEntityReference, getMemberEntityReferenceOf, removeEntityFeature, removeEntityReferenceType, removeMemberEntityReference

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

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setStandardName

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, getModelInterface, getRDFId, isEquivalent

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

addEvidence, getEvidence, removeEvidence

Constructor Detail

NucleicAcidReferenceImpl

public NucleicAcidReferenceImpl()

Method Detail

getSubRegion

public java.util.Set<NucleicAcidRegionReference> getSubRegion()

Specified by:

getSubRegion in interface NucleicAcidReference

setSubRegion

protected void setSubRegion(java.util.Set<NucleicAcidRegionReference> subRegion)

addSubRegion

public void addSubRegion(NucleicAcidRegionReference regionReference)

Specified by:

addSubRegion in interface NucleicAcidReference

removeSubRegion

public void removeSubRegion(NucleicAcidRegionReference regionReference)

Specified by:

removeSubRegion in interface NucleicAcidReference