org.sbolstandard.core2

Class Interaction

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.Measured

org.sbolstandard.core2.Interaction

public class Interaction
extends Measured

Represents an Interaction object in the SOBL data model.

Version:

2.1

Author:

Zhen Zhang, Nicholas Roehner, Chris Myers

Method Summary

Modifier and Type	Method and Description
boolean	addType(URI typeURI) Adds the given type URI to this interaction's set of type URIs.
void	clearParticipations() Removes all entries of this interaction list of participations.
boolean	containsType(URI typeURI) Checks if the given type URI is included in this interaction's set of type URIs.
Participation	createParticipation(String displayId, String participantId, Set<URI> roles) Creates a child participation for this interaction with the given arguments, and then adds to this interaction's list of participations.
Participation	createParticipation(String displayId, String participantId, URI role) Creates a child participation for this interaction with the given arguments, and then adds to this interaction's list of participations.
Participation	createParticipation(String displayId, URI participant, Set<URI> roles) Creates a child participation for this interaction with the given arguments, and then adds to this interaction's list of participations.
Participation	createParticipation(String displayId, URI participant, URI role) Creates a child participation for this interaction with the given arguments, and then adds to its list of participations.
boolean	equals(Object obj)
Participation	getParticipation(String displayId) Returns the participation matching the given display ID from this interaction's list of participations.
Participation	getParticipation(URI participationURI) Returns the participation matching the given participation URI from this interaction's list of participations.
Set<Participation>	getParticipations() Returns the set of participations owned by this interaction.
Set<URI>	getTypes() Returns the set of type URIs owned by this Interaction object.
int	hashCode()
boolean	removeParticipation(Participation participation) Removes the given participation from this interaction's list of participations.
boolean	removeType(URI typeURI) Removes the given type URI from this interation's the set of type URIs.
void	setTypes(Set<URI> types) Clears the existing set of type URIs first, then adds the given set of the type URIs to this interaction.
String	toString()

Methods inherited from class org.sbolstandard.core2.Measured

clearMeasures, createMeasure, getMeasure, getMeasure, getMeasures, removeMeasure

Methods inherited from class org.sbolstandard.core2.Identified

addWasDerivedFrom, addWasGeneratedBy, clearAnnotations, clearWasDerivedFroms, clearWasGeneratedBys, containsWasDerivedFrom, containsWasGeneratedBy, createAnnotation, createAnnotation, createAnnotation, createAnnotation, createAnnotation, createAnnotation, getAnnotation, getAnnotations, getDescription, getDisplayId, getIdentity, getName, getPersistentIdentity, getVersion, getWasDerivedFrom, getWasDerivedFroms, getWasGeneratedBys, hasAnnotations, isSetDescription, isSetDisplayId, isSetName, isSetPersistentIdentity, isSetVersion, isSetWasDerivedFrom, removeAnnotation, removeWasDerivedFrom, removeWasGeneratedBy, setDescription, setName, setWasDerivedFrom, setWasDerivedFroms, setWasGeneratedBys, unsetDescription, unsetName, unsetWasDerivedFrom

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Method Detail

addType

public boolean addType(URI typeURI)

Adds the given type URI to this interaction's set of type URIs.

Parameters:

typeURI - the given type URI to be added

Returns:

true if this set did not contain the given type, false otherwise

removeType

public boolean removeType(URI typeURI)
                   throws SBOLValidationException

Removes the given type URI from this interation's the set of type URIs.

Parameters:

typeURI - the type URI to be removed

Returns:

true if the matching type URI was removed successfully, false otherwise

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 11902.

setTypes

public void setTypes(Set<URI> types)
              throws SBOLValidationException

Clears the existing set of type URIs first, then adds the given set of the type URIs to this interaction.

Parameters:

types - the given set of type URIs to set to

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 11902.

getTypes

public Set<URI> getTypes()

Returns the set of type URIs owned by this Interaction object.

Returns:

the set of type URIs owned by this Interaction object.

containsType

public boolean containsType(URI typeURI)

Checks if the given type URI is included in this interaction's set of type URIs.

Parameters:

typeURI - the given type URI to be checked for existence

Returns:

true if this set contains the given URI, false otherwise

createParticipation

public Participation createParticipation(String displayId,
                                         String participantId,
                                         URI role)
                                  throws SBOLValidationException

Creates a child participation for this interaction with the given arguments, and then adds to this interaction's list of participations.

This method creates a new set of roles, and adds to it the given role. It then calls createParticipation(String, String, Set) with the given display IDs for the participation and its reference participant, and the set of roles created in this method.

Parameters:

displayId - the display ID of the participation to be created

participantId - the display ID of the participant functional component referenced by the participation to be created

role - the role of the participation to be created

Returns:

the created participation

Throws:

SBOLValidationException - if an SBOL validation rule was violated in createParticipation(String, String, Set).

createParticipation

public Participation createParticipation(String displayId,
                                         String participantId,
                                         Set<URI> roles)
                                  throws SBOLValidationException

Creates a child participation for this interaction with the given arguments, and then adds to this interaction's list of participations.

This first method creates a compliant URI for the reference functional component of the participation, i.e., the participant property of the participation. This participant URI starts with the persistent identity of the module definition that hosts this interaction, followed by the particpant's display ID, and ends with the hosting module definition's version.

If no functional component exists with the provided participantId and isCreateDefaults is true, it creates a new functionalComponent instantiation for the componentDefinition with the displayId that matches the participantId.

This method then calls createParticipation(String, URI, Set) with the given display ID, the created compliant URI for the participant, and the set of roles.

Parameters:

displayId - the display ID of the participation to be created

participantId - the display ID of the participant functional component

roles - the roles of the participation to be created

Returns:

the created participation

Throws:

SBOLValidationException - if either of the following condition is satisfied:

• if either of the following SBOL validation rules was violated: 10204, 10206;
• an SBOL validation rule violation occurred in ModuleDefinition.createFunctionalComponent(String, AccessType, String, String, DirectionType)
• an SBOL validation rule violation occurred in createParticipation(String, URI, Set).

createParticipation

public Participation createParticipation(String displayId,
                                         URI participant,
                                         URI role)
                                  throws SBOLValidationException

Creates a child participation for this interaction with the given arguments, and then adds to its list of participations.

This method creates a new set of roles, and adds to it the given role. It then calls createParticipation(String, URI, Set) with the given display ID for the participation, the URI identity of its reference participant, and the set of roles created in this method.

Parameters:

displayId - the display ID of the participation to be created

participant - the participant functional component for the participation to be created

role - the role of the participation to be created

Returns:

the created participation

Throws:

SBOLValidationException - if an SBOL validation rule violation occurred in createParticipation(String, URI, Set).

createParticipation

public Participation createParticipation(String displayId,
                                         URI participant,
                                         Set<URI> roles)
                                  throws SBOLValidationException

Creates a child participation for this interaction with the given arguments, and then adds to this interaction's list of participations.

This method first creates a compliant URI for the participation to be created. It starts with this Interaction object's persistent identity URI, followed by the given display ID, and ends with this interaction's version.

Parameters:

displayId - The displayId identifier for this

participant - specify precisely one FunctionalComponent object that plays the designated 3 role in its parent Interaction object

roles - describes the behavior of a Participation

Returns:

the created participation

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 12002, 12003, 12004,

removeParticipation

public boolean removeParticipation(Participation participation)

Removes the given participation from this interaction's list of participations.

Parameters:

participation - the given participation to be removed

Returns:

true if the matching participation was removed successfully, false otherwise

getParticipation

public Participation getParticipation(String displayId)

Returns the participation matching the given display ID from this interaction's list of participations.

This method first creates a compliant URI for the participation to be retrieved. It starts with this interaction's persistent identity, followed by the given display ID, and ends with this interation's version.

Parameters:

displayId - the display ID of the participation to be retrieved

Returns:

the matching participation if present, or null otherwise

getParticipation

public Participation getParticipation(URI participationURI)

Returns the participation matching the given participation URI from this interaction's list of participations.

Parameters:

participationURI - the identity URI for the participation to be retrieved

Returns:

the matching participation if present, or null otherwise

getParticipations

public Set<Participation> getParticipations()

Returns the set of participations owned by this interaction.

Returns:

the set of the set of participations owned by this interaction

clearParticipations

public void clearParticipations()

Removes all entries of this interaction list of participations. The list will be empty after this call returns.

This method calls removeParticipation(Participation) to iteratively remove each participation owned by this object.

hashCode

public int hashCode()

Overrides:

hashCode in class Measured

equals

public boolean equals(Object obj)

Overrides:

equals in class Measured

toString

public String toString()

Overrides:

toString in class Measured