org.biopax.paxtools.impl.level3
Class EntityFeatureImpl

java.lang.Object
  org.biopax.paxtools.impl.BioPAXElementImpl
      org.biopax.paxtools.impl.level3.L3ElementImpl
          org.biopax.paxtools.impl.level3.EntityFeatureImpl

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, BioPAXElement, EntityFeature, Level3Element, Observable, UtilityClass

Direct Known Subclasses:

BindingFeatureImpl, FragmentFeatureImpl, ModificationFeatureImpl

@Entity
@Indexed
public class EntityFeatureImpl
extends L3ElementImpl
implements EntityFeature

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

EntityFeatureImpl()

Method Summary

void	addEvidence(Evidence evidence)
void	addMemberFeature(EntityFeature feature) An entity feature that belongs to this homology grouping.
boolean	atEquivalentLocation(EntityFeature that)
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
EntityReference	getEntityFeatureOf() Inverse of EntityReference.getEntityFeature()
protected EntityReference	getEntityFeatureXOf()
java.util.Set<Evidence>	getEvidence()
SequenceLocation	getFeatureLocation() Location of the feature on the sequence of the interactor.
SequenceRegionVocabulary	getFeatureLocationType() A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain.
java.util.Set<PhysicalEntity>	getFeatureOf() Inverse of PhysicalEntity.getFeature() Contents of this set is generated automatically and should not be modified.
java.util.Set<EntityFeature>	getMemberFeature() An entity feature that belongs to this homology grouping.
java.util.Set<EntityFeature>	getMemberFeatureOf() Reverse of EntityFeature.getMemberFeature()
java.lang.Class<? extends EntityFeature>	getModelInterface() This method returns the actual model interface that a class implements.
java.util.Set<PhysicalEntity>	getNotFeatureOf() Inverse of PhysicalEntity.getNotFeature() Contents of this set is generated automatically and should not be modified.
protected int	locationCode()
void	removeEvidence(Evidence evidence)
void	removeMemberFeature(EntityFeature feature) An entity feature that belongs to this homology grouping.
protected boolean	semanticallyEquivalent(BioPAXElement element)
protected void	setEntityFeatureOf(EntityReference newEntityReference) This method sets the EntityReference for this feature.
protected void	setEntityFeatureXOf(EntityReference entityReference)
protected void	setEvidence(java.util.Set<Evidence> evidence)
void	setFeatureLocation(SequenceLocation featureLocation) Location of the feature on the sequence of the interactor.
void	setFeatureLocationType(SequenceRegionVocabulary regionVocabulary) A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain.
protected void	setFeatureOf(java.util.Set<PhysicalEntity> featureOf)
protected void	setMemberFeature(java.util.Set<EntityFeature> memberFeature)
protected void	setMemberFeatureOf(java.util.Set<EntityFeature> memberFeatureOf)
protected void	setNotFeatureOf(java.util.Set<PhysicalEntity> notFeatureOf)

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, getRDFId, isEquivalent

Constructor Detail

EntityFeatureImpl

public EntityFeatureImpl()

Method Detail

getModelInterface

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

getEntityFeatureOf

public EntityReference getEntityFeatureOf()

Description copied from interface: EntityFeature

Inverse of EntityReference.getEntityFeature()

Specified by:

getEntityFeatureOf in interface EntityFeature

Returns:

Reference entity that this feature belongs to.

setEntityFeatureOf

protected void setEntityFeatureOf(EntityReference newEntityReference)

This method sets the EntityReference for this feature. This method should only be used by the new EntityReference for updating the bidirectional link.

Parameters:

newEntityReference - New owner of this feature. TODO make it Set of EntityReference (consider, e.g., cloned ERs or what could happen during model merge, etc..)?

getEntityFeatureXOf

protected EntityReference getEntityFeatureXOf()

setEntityFeatureXOf

protected void setEntityFeatureXOf(EntityReference entityReference)

getFeatureOf

public java.util.Set<PhysicalEntity> getFeatureOf()

Description copied from interface: EntityFeature

Inverse of PhysicalEntity.getFeature() Contents of this set is generated automatically and should not be modified.

Specified by:

getFeatureOf in interface EntityFeature

Returns:

The list of PhysicalEntities that were observed to have this feature.

getNotFeatureOf

public java.util.Set<PhysicalEntity> getNotFeatureOf()

Description copied from interface: EntityFeature

Inverse of PhysicalEntity.getNotFeature() Contents of this set is generated automatically and should not be modified.

Specified by:

getNotFeatureOf in interface EntityFeature

Returns:

The list of PhysicalEntities that were observed to NOT have this feature.

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

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

getFeatureLocation

public SequenceLocation getFeatureLocation()

Description copied from interface: EntityFeature

Location of the feature on the sequence of the interactor.

For modification features this is the modified base or residue. For binding features this is the binding site and for fragment features this is the location of the fragment on the "base" sequence.

One feature may have more than one location, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence.

Small Molecules can have binding features but currently it is not possible to define the binding site on the small molecules. In those cases this property should not be specified.

Specified by:

getFeatureLocation in interface EntityFeature

Returns:

Location of the feature on the sequence of the interactor.

setFeatureLocation

public void setFeatureLocation(SequenceLocation featureLocation)

Description copied from interface: EntityFeature

Location of the feature on the sequence of the interactor.

For modification features this is the modified base or residue. For binding features this is the binding site and for fragment features this is the location of the fragment on the "base" sequence.

One feature may have more than one location, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence.

Small Molecules can have binding features but currently it is not possible to define the binding site on the small molecules. In those cases this property should not be specified.

Specified by:

setFeatureLocation in interface EntityFeature

Parameters:

featureLocation - of the feature

getFeatureLocationType

public SequenceRegionVocabulary getFeatureLocationType()

Description copied from interface: EntityFeature

A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain. Using Sequence Ontology (http://www.sequenceontology.org) is recommended.

Specified by:

getFeatureLocationType in interface EntityFeature

Returns:

A CV term describing the location of the feature

setFeatureLocationType

public void setFeatureLocationType(SequenceRegionVocabulary regionVocabulary)

Description copied from interface: EntityFeature

A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain. Using Sequence Ontology (http://www.sequenceontology.org) is recommended.

Specified by:

setFeatureLocationType in interface EntityFeature

Parameters:

regionVocabulary - A CV term describing the location of the feature

getMemberFeature

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

Description copied from interface: EntityFeature

An entity feature that belongs to this homology grouping.

Members of this set should be of the same class of this EntityFeature.

Members of this set should be an EntityFeature of an EntityReference which is a memberEntityReference of the EntityReference of this feature.

If this set is not empty than the sequenceLocation of this feature should be null.

Example: a homologous phosphorylation site across a protein family.

Specified by:

getMemberFeature in interface EntityFeature

Returns:

An entity feature that belongs to this homology grouping.

setMemberFeature

protected void setMemberFeature(java.util.Set<EntityFeature> memberFeature)

addMemberFeature

public void addMemberFeature(EntityFeature feature)

Description copied from interface: EntityFeature

An entity feature that belongs to this homology grouping.

Members of this set should be of the same class of this EntityFeature.

Members of this set should be an EntityFeature of an EntityReference which is a memberEntityReference of the EntityReference of this feature.

If this set is not empty than the sequenceLocation of this feature should be null.

Example: a homologous phosphorylation site across a protein family.

Specified by:

addMemberFeature in interface EntityFeature

Parameters:

feature - An entity feature that belongs to this homology grouping.

removeMemberFeature

public void removeMemberFeature(EntityFeature feature)

Description copied from interface: EntityFeature

An entity feature that belongs to this homology grouping.

Members of this set should be of the same class of this EntityFeature.

Members of this set should be an EntityFeature of an EntityReference which is a memberEntityReference of the EntityReference of this feature.

If this set is not empty than the sequenceLocation of this feature should be null.

Example: a homologous phosphorylation site across a protein family.

Specified by:

removeMemberFeature in interface EntityFeature

Parameters:

feature - An entity feature that belongs to this homology grouping.

getMemberFeatureOf

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

Description copied from interface: EntityFeature

Reverse of EntityFeature.getMemberFeature()

Specified by:

getMemberFeatureOf in interface EntityFeature

Returns:

the generic feature(s) that this feature belong to

setMemberFeatureOf

protected void setMemberFeatureOf(java.util.Set<EntityFeature> memberFeatureOf)

atEquivalentLocation

public boolean atEquivalentLocation(EntityFeature that)

Specified by:

atEquivalentLocation in interface EntityFeature

Parameters:

that - EntityFeature to be compared

Returns:

returns true iff the given feature is at the equivalent sequence location with this feature

locationCode

protected int locationCode()

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.

setFeatureOf

protected void setFeatureOf(java.util.Set<PhysicalEntity> featureOf)

setNotFeatureOf

protected void setNotFeatureOf(java.util.Set<PhysicalEntity> notFeatureOf)