org.biopax.paxtools.impl.level3

Class NucleicAcidRegionReferenceImpl

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

org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, EntityReference, Level3Element, Named, NucleicAcidReference, NucleicAcidRegionReference, Observable, SequenceEntityReference, UtilityClass, XReferrable

Direct Known Subclasses:

DnaRegionReferenceImpl, RnaRegionReferenceImpl

@Entity
public abstract class NucleicAcidRegionReferenceImpl
extends NucleicAcidReferenceImpl
implements NucleicAcidRegionReference

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
NucleicAcidRegionReferenceImpl()

Method Summary

Modifier and Type	Method and Description
void	addRegionType(SequenceRegionVocabulary regionType)
SequenceLocation	getAbsoluteRegion()
Set<SequenceRegionVocabulary>	getRegionType()
Set<NucleicAcidReference>	getSubRegionOf()
void	removeRegionType(SequenceRegionVocabulary regionType)
void	setAbsoluteRegion(SequenceLocation absoluteRegion)
protected void	setRegionType(Set<SequenceRegionVocabulary> regionType)
protected void	setSubRegionOf(Set<NucleicAcidReference> subRegionOf)

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

addSubRegion, getSubRegion, removeSubRegion, setSubRegion

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

equivalenceCode, 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, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setStandardName, setStandardNameX

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

addXref, 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, 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.NucleicAcidReference

addSubRegion, getSubRegion, removeSubRegion

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, setName, 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

NucleicAcidRegionReferenceImpl

public NucleicAcidRegionReferenceImpl()

Method Detail

getSubRegionOf

public Set<NucleicAcidReference> getSubRegionOf()

Specified by:

getSubRegionOf in interface NucleicAcidRegionReference

setSubRegionOf

protected void setSubRegionOf(Set<NucleicAcidReference> subRegionOf)

getAbsoluteRegion

public SequenceLocation getAbsoluteRegion()

Specified by:

getAbsoluteRegion in interface NucleicAcidRegionReference

setAbsoluteRegion

public void setAbsoluteRegion(SequenceLocation absoluteRegion)

Specified by:

setAbsoluteRegion in interface NucleicAcidRegionReference

getRegionType

public Set<SequenceRegionVocabulary> getRegionType()

Specified by:

getRegionType in interface NucleicAcidRegionReference

addRegionType

public void addRegionType(SequenceRegionVocabulary regionType)

Specified by:

addRegionType in interface NucleicAcidRegionReference

removeRegionType

public void removeRegionType(SequenceRegionVocabulary regionType)

Specified by:

removeRegionType in interface NucleicAcidRegionReference

setRegionType

protected void setRegionType(Set<SequenceRegionVocabulary> regionType)