org.sbolstandard.core2

Class Activity

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.TopLevel

org.sbolstandard.core2.Activity

public class Activity
extends TopLevel

Represents a Activity object in the SBOL data model.

Version:

2.2

Author:

Chris Myers

Field Summary

Fields inherited from class org.sbolstandard.core2.TopLevel

ACTIVITY, AGENT, ANNOTATION, ATTACHMENT, COLLECTION, COMBINATORIAL_DERIVATION, COMPONENT_DEFINITION, EXPERIMENT, EXPERIMENTAL_DATA, GENERIC_TOP_LEVEL, IMPLEMENTATION, MODEL, MODULE_DEFINITION, PLAN, SEQUENCE

Method Summary

Modifier and Type	Method and Description
boolean	addType(URI typeURI) Adds the given type URI to this activity's set of type URIs.
boolean	addWasInformedBy(Activity activity) Adds the URI of the given Activity instance to this Activity's set of wasInformdBy URIs.
boolean	addWasInformedBy(String displayId) Constructs a compliant activity URI using the given activity display ID, and then adds this URI to this activity's set of wasInformedBy URIs.
boolean	addWasInformedBy(String displayId, String version) Constructs a compliant activity URI with the given display ID and version, and then adds this URI to this activity's set of wasInformedBy URIs.
boolean	addWasInformedBy(URI activityURI) Adds the given activity URI to this Activity's set of wasInformedBy URIs.
void	clearAssociations() Removes all entries of this activity's list of associations.
void	clearUsages() Removes all entries of this activity's list of usages.
void	clearWasInformedBys() Removes all entries of this activity's set of reference wasInformedBy URIs.
boolean	containsType(URI typeURI) Checks if the given type URI is included in this activity's set of type URIs.
Association	createAssociation(String displayId, URI agent) Creates a child association for this activity with the given arguments, and then adds to this activity's list of associations.
Usage	createUsage(String displayId, URI entity) Creates a child usage for this activity with the given arguments, and then adds to this activity's list of usages.
boolean	equals(Object obj)
Association	getAssociation(String displayId) Returns the association matching the given association's display ID.
Association	getAssociation(URI associationURI) Returns the instance matching the given association's identity URI.
Set<Association>	getAssociations() Returns the set of associations owned by this activity.
org.joda.time.DateTime	getEndedAtTime()
org.joda.time.DateTime	getStartedAtTime()
Set<URI>	getTypes() Returns the set of type URIs owned by this activity.
Usage	getUsage(String displayId) Returns the usage matching the given usage's display ID.
Usage	getUsage(URI usageURI) Returns the instance matching the given usage's identity URI.
Set<Usage>	getUsages() Returns the set of usages owned by this activity.
Set<URI>	getWasInformedByIdentities() Returns the set of wasInformedBys identities referenced by this activity.
Set<Activity>	getWasInformedBys() Returns the set of wasInformedBys referenced by this activity.
Set<URI>	getWasInformedByURIs() Returns the set of wasInformedBy URIs referenced by this activity.
int	hashCode()
boolean	isSetEndedAtTime() Test if the endedAtTime is set.
boolean	isSetStartedAtTime() Test if the startedAtTime is set.
boolean	removeAssociation(Association association) Removes the given association from the list of associations.
boolean	removeType(URI typeURI) Removes the given type URI from the set of types.
boolean	removeUsages(Usage usage) Removes the given usage from the list of usages.
void	setEndedAtTime(org.joda.time.DateTime endedAtTime)
void	setStartedAtTime(org.joda.time.DateTime startedAtTime)
void	setTypes(Set<URI> types) Clears the existing set of types first, then adds the given set of the types to this activity.
void	setWasInformedBys(Set<URI> wasInformedBys)
String	toString()

Methods inherited from class org.sbolstandard.core2.TopLevel

addAttachment, addAttachment, addAttachment, clearAttachments, containsAttachment, getAttachments, getAttachmentURIs, removeAttachment, setAttachments

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 activity's set of type URIs.

Parameters:

typeURI - the given type URI

Returns:

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

removeType

public boolean removeType(URI typeURI)

Removes the given type URI from the set of types.

Parameters:

typeURI - the specified type URI

Returns:

true if the matching type reference was removed successfully, false otherwise.

setTypes

public void setTypes(Set<URI> types)

Clears the existing set of types first, then adds the given set of the types to this activity.

Parameters:

types - the set of types to set to

getTypes

public Set<URI> getTypes()

Returns the set of type URIs owned by this activity.

Returns:

the set of type URIs owned by this actviity

containsType

public boolean containsType(URI typeURI)

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

Parameters:

typeURI - the type URI to be checked

Returns:

true if this set contains the given type URI, false otherwise.

createAssociation

public Association createAssociation(String displayId,
                                     URI agent)
                              throws SBOLValidationException

Creates a child association for this activity with the given arguments, and then adds to this activity's list of associations.

This method first creates a compliant URI for the child association to be created. This URI starts with this activity's persistent identity, followed by the given display ID and ends with this activity's version.

Parameters:

displayId - the display ID for the association to be created

agent - URI for the agent associated with this activity

Returns:

the created association

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12602, 12604, 12605, 12606

createUsage

public Usage createUsage(String displayId,
                         URI entity)
                  throws SBOLValidationException

Creates a child usage for this activity with the given arguments, and then adds to this activity's list of usages.

This method first creates a compliant URI for the child usage to be created. This URI starts with this activity's persistent identity, followed by the given display ID and ends with this activity's version.

Parameters:

displayId - the display ID for the usage to be created

entity - URI reference to the entity used

Returns:

the created usage

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12502, 12503

hashCode

public int hashCode()

Overrides:

hashCode in class TopLevel

equals

public boolean equals(Object obj)

Overrides:

equals in class TopLevel

toString

public String toString()

Overrides:

toString in class Identified

isSetStartedAtTime

public boolean isSetStartedAtTime()

Test if the startedAtTime is set.

Returns:

true if it is not null, or false otherwise

getStartedAtTime

public org.joda.time.DateTime getStartedAtTime()

Returns:

the startedAtTime

setStartedAtTime

public void setStartedAtTime(org.joda.time.DateTime startedAtTime)

Parameters:

startedAtTime - the startedAtTime to set

isSetEndedAtTime

public boolean isSetEndedAtTime()

Test if the endedAtTime is set.

Returns:

true if it is not null, or false otherwise

getEndedAtTime

public org.joda.time.DateTime getEndedAtTime()

Returns:

the endedAtTime

setEndedAtTime

public void setEndedAtTime(org.joda.time.DateTime endedAtTime)

Parameters:

endedAtTime - the endedAtTime to set

addWasInformedBy

public boolean addWasInformedBy(Activity activity)
                         throws SBOLValidationException

Adds the URI of the given Activity instance to this Activity's set of wasInformdBy URIs. This method calls addWasInformedBy(URI) with this Activity URI.

Parameters:

activity - the Activity instance whose identity URI to be added

Returns:

true if this set did not already contain the identity URI of the given Activity, false otherwise.

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 12407.

addWasInformedBy

public boolean addWasInformedBy(URI activityURI)
                         throws SBOLValidationException

Adds the given activity URI to this Activity's set of wasInformedBy URIs.

Parameters:

activityURI - the identity URI of the Activity to be added

Returns:

true if this set did not already contain the given activity's URI, false otherwise.

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 12407.

addWasInformedBy

public boolean addWasInformedBy(String displayId,
                                String version)
                         throws SBOLValidationException

Constructs a compliant activity URI with the given display ID and version, and then adds this URI to this activity's set of wasInformedBy URIs.

This method creates a compliant activity URI with the default URI prefix, which was set in the SBOLDocument instance hosting this activity, the given display ID and version. It then calls addWasInformedBy(URI) with this Activity URI.

Parameters:

displayId - the display ID of the activity whose identity URI is to be added

version - version of the activity whose identity URI is to be added

Returns:

true if this set did not already contain the given activity's URI, false otherwise.

Throws:

SBOLValidationException - see addWasInformedBy(URI)

addWasInformedBy

public boolean addWasInformedBy(String displayId)
                         throws SBOLValidationException

Constructs a compliant activity URI using the given activity display ID, and then adds this URI to this activity's set of wasInformedBy URIs. This method calls addWasInformedBy(String, String) with the given sequence display ID and an empty string as its version.

Parameters:

displayId - the display ID of the activity whose identity URI is to be added

Returns:

true if this set did not already contain the given activity's URI, false otherwise.

Throws:

SBOLValidationException - see addWasInformedBy(String, String)

getWasInformedByURIs

public Set<URI> getWasInformedByURIs()

Returns the set of wasInformedBy URIs referenced by this activity.

Returns:

the set of wasInformedBy URIs referenced by this activity

getWasInformedByIdentities

public Set<URI> getWasInformedByIdentities()

Returns the set of wasInformedBys identities referenced by this activity.

Returns:

the set of wasInformedBys identities referenced by this activity

getWasInformedBys

public Set<Activity> getWasInformedBys()

Returns the set of wasInformedBys referenced by this activity.

Returns:

the set of wasInformedBys referenced by this activity

clearWasInformedBys

public void clearWasInformedBys()

Removes all entries of this activity's set of reference wasInformedBy URIs. The set will be empty after this call returns.

setWasInformedBys

public void setWasInformedBys(Set<URI> wasInformedBys)
                       throws SBOLValidationException

Parameters:

wasInformedBys - the wasInformedBys to set

Throws:

SBOLValidationException - if an SBOL validation rule violation occurred in addWasInformedBy(URI)

getAssociation

public Association getAssociation(String displayId)

Returns the association matching the given association's display ID.

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

Parameters:

displayId - the display ID of the association to be retrieved

Returns:

the matching association if present, or null otherwise.

getAssociation

public Association getAssociation(URI associationURI)

Returns the instance matching the given association's identity URI.

Parameters:

associationURI - the identity URI of the association to be retrieved

Returns:

the matching association if present, or null otherwise.

getAssociations

public Set<Association> getAssociations()

Returns the set of associations owned by this activity.

Returns:

the set of associations owned by this activity.

removeAssociation

public boolean removeAssociation(Association association)

Removes the given association from the list of associations.

Parameters:

association - the given association

Returns:

true if the matching association was removed successfully, false otherwise.

clearAssociations

public void clearAssociations()

Removes all entries of this activity's list of associations. The list will be empty after this call returns.

This method calls removeAssociation(Association association) to iteratively remove each association.

getUsage

public Usage getUsage(String displayId)

Returns the usage matching the given usage's display ID.

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

Parameters:

displayId - the display ID of the usage to be retrieved

Returns:

the matching usage if present, or null otherwise.

getUsage

public Usage getUsage(URI usageURI)

Returns the instance matching the given usage's identity URI.

Parameters:

usageURI - the identity URI of the usage to be retrieved

Returns:

the matching usage if present, or null otherwise.

getUsages

public Set<Usage> getUsages()

Returns the set of usages owned by this activity.

Returns:

the set of usages owned by this activity.

removeUsages

public boolean removeUsages(Usage usage)

Removes the given usage from the list of usages.

Parameters:

usage - the given usage

Returns:

true if the matching usage was removed successfully, false otherwise.

clearUsages

public void clearUsages()

Removes all entries of this activity's list of usages. The list will be empty after this call returns.

This method calls removeUsages(Usage usage) to iteratively remove each usage.