@Entity public abstract class EntityImpl extends NamedImpl implements Entity
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
UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT
Constructor and Description |
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EntityImpl()
Helper object for managing names
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Modifier and Type | Method and Description |
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void |
addAvailability(String availability_text)
This method adds the given text to the avaialability set.
|
void |
addDataSource(Provenance dataSource)
This method adds the given value to the DATA_SOURCE set.
|
void |
addEvidence(Evidence newEvidence) |
Set<String> |
getAvailability()
The contents of this set can be modified but semantic consistency is not
guaranteed.
|
Set<Provenance> |
getDataSource()
This method returns a set of free text descriptions of the source of this
data, e.g.
|
Set<Evidence> |
getEvidence() |
Set<Interaction> |
getParticipantOf()
This method returns the interaction that this entity/pep takes part in.
|
void |
removeAvailability(String availability_text)
This method removes the given text from the avaialability set.
|
void |
removeDataSource(Provenance dataSource)
This method removes the given value from the DATA_SOURCE set.
|
void |
removeEvidence(Evidence oldEvidence) |
protected boolean |
semanticallyEquivalent(BioPAXElement element) |
void |
setAvailability(Set<String> availability) |
void |
setDataSource(Set<Provenance> dataSource) |
protected void |
setEvidence(Set<Evidence> newEvidence) |
protected void |
setParticipantOf(Set<Interaction> participantOf) |
addName, getDisplayName, getDisplayNameX, getName, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setStandardName, setStandardNameX
addXref, equivalenceCode, getXref, removeXref, setXref
addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment
equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName
addXref, getXref, removeXref
addComment, getComment, removeComment
equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent
public EntityImpl()
@Field(name="availability", analyze=YES) @FieldBridge(impl=SetStringBridge.class) public Set<String> getAvailability()
Entity
Entity.addAvailability(String)
and Entity.removeAvailability(String)
is recommended.getAvailability
in interface Entity
public void setAvailability(Set<String> availability)
public void addAvailability(String availability_text)
Entity
addAvailability
in interface Entity
availability_text
- a string describing the availability of this data
(e.g. a copyright statement).public void removeAvailability(String availability_text)
Entity
removeAvailability
in interface Entity
availability_text
- a string describing the availability of this data
(e.g. a copyright statement).@Field(name="dataSource", store=YES, analyze=NO) @FieldBridge(impl=DataSourceFieldBridge.class) public Set<Provenance> getDataSource()
Entity
Entity.addDataSource(Provenance)
and Entity.removeDataSource(Provenance)
is
recommended.getDataSource
in interface Entity
public void setDataSource(Set<Provenance> dataSource)
public void addDataSource(Provenance dataSource)
Entity
addDataSource
in interface Entity
dataSource
- a free text description of the source of this data,
e.g. a database or person name.public void removeDataSource(Provenance dataSource)
Entity
removeDataSource
in interface Entity
dataSource
- a free text description of the source of this data,
e.g. a database or person name.public Set<Interaction> getParticipantOf()
Entity
Interaction.getParticipant()
getParticipantOf
in interface Entity
protected void setParticipantOf(Set<Interaction> participantOf)
public Set<Evidence> getEvidence()
getEvidence
in interface Observable
public void addEvidence(Evidence newEvidence)
addEvidence
in interface Observable
public void removeEvidence(Evidence oldEvidence)
removeEvidence
in interface Observable
protected void setEvidence(Set<Evidence> newEvidence)
protected boolean semanticallyEquivalent(BioPAXElement element)
semanticallyEquivalent
in class BioPAXElementImpl
Copyright © 2015 BioPAX. All rights reserved.