org.biopax.paxtools.impl.level3
Class EntityImpl

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.EntityImpl

All Implemented Interfaces:

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

Direct Known Subclasses:

GeneImpl, PhysicalEntityImpl, ProcessImpl

@Entity
public abstract class EntityImpl
extends NamedImpl
implements Entity

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

EntityImpl()
Helper object for managing names

Method Summary

void	addAvailability(java.lang.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)
java.util.Set<java.lang.String>	getAvailability() The contents of this set can be modified but semantic consistency is not guaranteed.
java.util.Set<Provenance>	getDataSource() This method returns a set of free text descriptions of the source of this data, e.g.
java.util.Set<Evidence>	getEvidence()
java.util.Set<Interaction>	getParticipantOf() This method returns the interaction that this entity/pep takes part in.
void	removeAvailability(java.lang.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(java.util.Set<java.lang.String> availability)
void	setDataSource(java.util.Set<Provenance> dataSource)
protected void	setEvidence(java.util.Set<Evidence> newEvidence)
protected void	setParticipantOf(java.util.Set<Interaction> participantOf)

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, getModelInterface, getRDFId, isEquivalent

Constructor Detail

EntityImpl

public EntityImpl()

Helper object for managing names

Method Detail

getAvailability

@Field(name="availability",
       index=TOKENIZED)
@FieldBridge(impl=SetStringBridge.class)
public java.util.Set<java.lang.String> getAvailability()

Description copied from interface: Entity

The contents of this set can be modified but semantic consistency is not guaranteed. Using Entity.addAvailability(String) and Entity.removeAvailability(String) is recommended.

Specified by:

getAvailability in interface Entity

Returns:

a set of strings describing the availability of this data (e.g. a copyright statement).

setAvailability

public void setAvailability(java.util.Set<java.lang.String> availability)

addAvailability

public void addAvailability(java.lang.String availability_text)

Description copied from interface: Entity

This method adds the given text to the avaialability set.

Specified by:

addAvailability in interface Entity

Parameters:

availability_text - a string describing the availability of this data (e.g. a copyright statement).

removeAvailability

public void removeAvailability(java.lang.String availability_text)

Description copied from interface: Entity

This method removes the given text from the avaialability set.

Specified by:

removeAvailability in interface Entity

Parameters:

availability_text - a string describing the availability of this data (e.g. a copyright statement).

getDataSource

public java.util.Set<Provenance> getDataSource()

Description copied from interface: Entity

This method returns a set of free text descriptions of the source of this data, e.g. a database or person name. This property should be used to describe the source of the data. This is meant to be used by databases that export their data to the BioPAX format or by systems that are integrating data from multiple sources. The granularity of use (specifying the data source in many or few instances) is up to the user. It is intended that this property report the last data source, not all data sources that the data has passed through from creation.

The contents of this set can be modified but semantic consistency is not guaranteed. Using Entity.addDataSource(Provenance) and Entity.removeDataSource(Provenance) is recommended.

Specified by:

getDataSource in interface Entity

Returns:

a set of free text descriptions of the source of this data, e.g. a database or person name.

setDataSource

public void setDataSource(java.util.Set<Provenance> dataSource)

addDataSource

public void addDataSource(Provenance dataSource)

Description copied from interface: Entity

This method adds the given value to the DATA_SOURCE set.

Specified by:

addDataSource in interface Entity

Parameters:

dataSource - a free text description of the source of this data, e.g. a database or person name.

removeDataSource

public void removeDataSource(Provenance dataSource)

Description copied from interface: Entity

This method removes the given value from the DATA_SOURCE set.

Specified by:

removeDataSource in interface Entity

Parameters:

dataSource - a free text description of the source of this data, e.g. a database or person name.

getParticipantOf

public java.util.Set<Interaction> getParticipantOf()

Description copied from interface: Entity

This method returns the interaction that this entity/pep takes part in. Contents of this set should not be modified. Reverse of Interaction.getParticipant()

Specified by:

getParticipantOf in interface Entity

Returns:

a set of interactions that

setParticipantOf

protected void setParticipantOf(java.util.Set<Interaction> participantOf)

getEvidence

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

Specified by:

getEvidence in interface Observable

addEvidence

public void addEvidence(Evidence newEvidence)

Specified by:

addEvidence in interface Observable

removeEvidence

public void removeEvidence(Evidence oldEvidence)

Specified by:

removeEvidence in interface Observable

setEvidence

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

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class XReferrableImpl