org.biopax.paxtools.impl.level3
Class EntityReferenceImpl

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

All Implemented Interfaces:

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

Direct Known Subclasses:

SequenceEntityReferenceImpl, SmallMoleculeReferenceImpl

@Entity
public abstract class EntityReferenceImpl
extends NamedImpl
implements EntityReference

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

EntityReferenceImpl()
Constructor.

Method Summary

void	addEntityFeature(EntityFeature entityFeature) Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.
void	addEntityReferenceType(EntityReferenceTypeVocabulary entityReferenceType) Adds the given cv to the list of types
void	addEvidence(Evidence evidence)
void	addMemberEntityReference(EntityReference memberEntity) Adds the given entityReference to the member list
java.util.Set<EntityFeature>	getEntityFeature() The contents of this set should NOT be modified.
java.util.Set<SimplePhysicalEntity>	getEntityReferenceOf() Inverse of SimplePhysicalEntity.getEntityReference()
java.util.Set<EntityReferenceTypeVocabulary>	getEntityReferenceType()
java.util.Set<Evidence>	getEvidence()
java.util.Set<EntityReference>	getMemberEntityReference()
java.util.Set<EntityReference>	getMemberEntityReferenceOf() Reverse of EntityReference.getMemberEntityReference()
java.lang.Class<? extends EntityReference>	getModelInterface() This method returns the actual model interface that a class implements.
void	removeEntityFeature(EntityFeature entityFeature) Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.
void	removeEntityReferenceType(EntityReferenceTypeVocabulary entityReferenceType) Removes the given cv from the list of types
void	removeEvidence(Evidence evidence)
void	removeMemberEntityReference(EntityReference memberEntity) Removes the given entityReference from the member list
protected boolean	semanticallyEquivalent(BioPAXElement element)
protected void	setEntityFeature(java.util.Set<EntityFeature> entityFeature)
protected void	setEntityReferenceOf(java.util.Set<SimplePhysicalEntity> entityReferenceOf)
protected void	setEntityReferenceType(java.util.Set<EntityReferenceTypeVocabulary> entityReferenceType)
void	setEvidence(java.util.Set<Evidence> evidence)
protected void	setMemberEntity(java.util.Set<EntityReference> memberEntity)
void	setMemberEntityReference(java.util.Set<EntityReference> memberEntity)
protected void	setMemberEntityReferenceOf(java.util.Set<EntityReference> newOwnerEntityReferenceSet)

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.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, getRDFId, isEquivalent

Constructor Detail

EntityReferenceImpl

public EntityReferenceImpl()

Constructor.

Method Detail

getModelInterface

public java.lang.Class<? extends EntityReference> 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.

getEntityFeature

public java.util.Set<EntityFeature> getEntityFeature()

The contents of this set should NOT be modified. For manipulating the contents use addNew and remove instead.

Specified by:

getEntityFeature in interface EntityReference

Returns:

A set of entity features for the reference entity.

addEntityFeature

public void addEntityFeature(EntityFeature entityFeature)

Description copied from interface: EntityReference

Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds. Note that this is an aggregate list of all known features and it does not represent a state itself.

Specified by:

addEntityFeature in interface EntityReference

Parameters:

entityFeature - to be added.

removeEntityFeature

public void removeEntityFeature(EntityFeature entityFeature)

Description copied from interface: EntityReference

Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds. Note that this is an aggregate list of all known features and it does not represent a state itself.

Specified by:

removeEntityFeature in interface EntityReference

Parameters:

entityFeature - to be removed.

setEntityFeature

protected void setEntityFeature(java.util.Set<EntityFeature> entityFeature)

getEntityReferenceOf

public java.util.Set<SimplePhysicalEntity> getEntityReferenceOf()

Description copied from interface: EntityReference

Inverse of SimplePhysicalEntity.getEntityReference()

Specified by:

getEntityReferenceOf in interface EntityReference

Returns:

a set of SimplePhysicalEntity that has this EntityReference

getEntityReferenceType

public java.util.Set<EntityReferenceTypeVocabulary> getEntityReferenceType()

Specified by:

getEntityReferenceType in interface EntityReference

Returns:

Controlled vocabulary terms that is used to describe the type of grouping such as homology or functional group.

addEntityReferenceType

public void addEntityReferenceType(EntityReferenceTypeVocabulary entityReferenceType)

Description copied from interface: EntityReference

Adds the given cv to the list of types

Specified by:

addEntityReferenceType in interface EntityReference

Parameters:

entityReferenceType - A controlled vocabulary term that is used to describe the type of grouping such as homology or functional group.

removeEntityReferenceType

public void removeEntityReferenceType(EntityReferenceTypeVocabulary entityReferenceType)

Description copied from interface: EntityReference

Removes the given cv from the list of types

Specified by:

removeEntityReferenceType in interface EntityReference

Parameters:

entityReferenceType - A controlled vocabulary term that is used to describe the type of grouping such as homology or functional group.

setEntityReferenceType

protected void setEntityReferenceType(java.util.Set<EntityReferenceTypeVocabulary> entityReferenceType)

getMemberEntityReference

public java.util.Set<EntityReference> getMemberEntityReference()

Specified by:

getMemberEntityReference in interface EntityReference

Returns:

Entity references that qualifies for the definition of this group. For example a member of a PFAM protein family.

addMemberEntityReference

public void addMemberEntityReference(EntityReference memberEntity)

Description copied from interface: EntityReference

Adds the given entityReference to the member list

Specified by:

addMemberEntityReference in interface EntityReference

Parameters:

memberEntity - An entity reference that qualifies for the definition of this group. For example a member of a PFAM protein family.

removeMemberEntityReference

public void removeMemberEntityReference(EntityReference memberEntity)

Description copied from interface: EntityReference

Removes the given entityReference from the member list

Specified by:

removeMemberEntityReference in interface EntityReference

Parameters:

memberEntity - An entity reference that qualifies for the definition of this group. For example a member of a PFAM protein family.

setMemberEntityReference

public void setMemberEntityReference(java.util.Set<EntityReference> memberEntity)

getMemberEntityReferenceOf

public java.util.Set<EntityReference> getMemberEntityReferenceOf()

Description copied from interface: EntityReference

Reverse of EntityReference.getMemberEntityReference()

Specified by:

getMemberEntityReferenceOf in interface EntityReference

Returns:

EntityReferences that this EntityReference is a member of.

setMemberEntityReferenceOf

protected void setMemberEntityReferenceOf(java.util.Set<EntityReference> newOwnerEntityReferenceSet)

getEvidence

public java.util.Set<Evidence> getEvidence()

Specified by:

getEvidence in interface Observable

addEvidence

public void addEvidence(Evidence evidence)

Specified by:

addEvidence in interface Observable

removeEvidence

public void removeEvidence(Evidence evidence)

Specified by:

removeEvidence in interface Observable

setEvidence

public void setEvidence(java.util.Set<Evidence> evidence)

setEntityReferenceOf

protected void setEntityReferenceOf(java.util.Set<SimplePhysicalEntity> entityReferenceOf)

setMemberEntity

protected void setMemberEntity(java.util.Set<EntityReference> memberEntity)

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class XReferrableImpl