org.sbolstandard.core2

Class TopLevel

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.TopLevel

Direct Known Subclasses:

Activity, Agent, Attachment, Collection, CombinatorialDerivation, ComponentDefinition, Experiment, ExperimentalData, GenericTopLevel, Implementation, Model, ModuleDefinition, Plan, Sequence

public abstract class TopLevel
extends Identified

Represents a TopLevel object in the SBOL data model.

Version:

2.1

Author:

Zhen Zhang, Nicholas Roehner, Chris Myers

Field Summary

Fields

Modifier and Type	Field and Description
static String	ACTIVITY The abbreviation for the Activity type in URI
static String	AGENT The abbreviation for the Agent type in URI
static String	ANNOTATION The abbreviation for the Annotation type in URI
static String	ATTACHMENT The abbreviation for the Attachment type in URI
static String	COLLECTION The abbreviation for the Collection type in URI
static String	COMBINATORIAL_DERIVATION The abbreviation for the CombinatorialDerivation type in URI
static String	COMPONENT_DEFINITION The abbreviation for the ComponentDefinition type in URI
static String	EXPERIMENT The abbreviation for the Experiment type in URI
static String	EXPERIMENTAL_DATA The abbreviation for the Experimental_DATA type in URI
static String	GENERIC_TOP_LEVEL The abbreviation for the GenericTopLevel type in URI
static String	IMPLEMENTATION The abbreviation for the Implementation type in URI
static String	MODEL The abbreviation for the Model type in URI
static String	MODULE_DEFINITION The abbreviation for the ModuleDefinition type in URI
static String	PLAN The abbreviation for the Plan type in URI
static String	SEQUENCE The abbreviation for the Sequence type in URI

Method Summary

Modifier and Type	Method and Description
boolean	addAttachment(Attachment attachment) Adds the URI of the given Attachment instance to this top level's set of attachment URIs.
boolean	addAttachment(String displayId) Constructs a compliant sequence URI using the given attachment display ID, and then adds this URI to this top level's set of attachment URIs.
boolean	addAttachment(String displayId, String version) Constructs a compliant attachment URI with the given display ID and version, and then adds this URI to this top level's set of attachment URIs.
void	clearAttachments() Removes all entries of this top level's list of attachments.
boolean	containsAttachment(URI attachmentURI) Checks if the given attachment URI is included in this top level's set of attachment URIs.
boolean	equals(Object obj)
Set<Attachment>	getAttachments() Returns the set of attachments referenced by this top level.
Set<URI>	getAttachmentURIs() Returns the set of attachment URIs referenced by this top level.
int	hashCode()
boolean	removeAttachment(URI attachment) Removes the given attachment from the list of attachments.
void	setAttachments(Set<URI> attachments) Clears the existing set of attachments first, and then adds the given set of the attachments to this top level.

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, toString, unsetDescription, unsetName, unsetWasDerivedFrom

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Detail

COLLECTION

public static final String COLLECTION

The abbreviation for the Collection type in URI

See Also:

Constant Field Values

MODULE_DEFINITION

public static final String MODULE_DEFINITION

The abbreviation for the ModuleDefinition type in URI

See Also:

Constant Field Values

MODEL

public static final String MODEL

The abbreviation for the Model type in URI

See Also:

Constant Field Values

COMPONENT_DEFINITION

public static final String COMPONENT_DEFINITION

The abbreviation for the ComponentDefinition type in URI

See Also:

Constant Field Values

SEQUENCE

public static final String SEQUENCE

The abbreviation for the Sequence type in URI

See Also:

Constant Field Values

GENERIC_TOP_LEVEL

public static final String GENERIC_TOP_LEVEL

The abbreviation for the GenericTopLevel type in URI

See Also:

Constant Field Values

ACTIVITY

public static final String ACTIVITY

The abbreviation for the Activity type in URI

See Also:

Constant Field Values

AGENT

public static final String AGENT

The abbreviation for the Agent type in URI

See Also:

Constant Field Values

PLAN

public static final String PLAN

The abbreviation for the Plan type in URI

See Also:

Constant Field Values

COMBINATORIAL_DERIVATION

public static final String COMBINATORIAL_DERIVATION

The abbreviation for the CombinatorialDerivation type in URI

See Also:

Constant Field Values

IMPLEMENTATION

public static final String IMPLEMENTATION

The abbreviation for the Implementation type in URI

See Also:

Constant Field Values

ATTACHMENT

public static final String ATTACHMENT

The abbreviation for the Attachment type in URI

See Also:

Constant Field Values

ANNOTATION

public static final String ANNOTATION

The abbreviation for the Annotation type in URI

See Also:

Constant Field Values

EXPERIMENT

public static final String EXPERIMENT

The abbreviation for the Experiment type in URI

See Also:

Constant Field Values

EXPERIMENTAL_DATA

public static final String EXPERIMENTAL_DATA

The abbreviation for the Experimental_DATA type in URI

See Also:

Constant Field Values

Method Detail

hashCode

public int hashCode()

Overrides:

hashCode in class Identified

equals

public boolean equals(Object obj)

Overrides:

equals in class Identified

addAttachment

public boolean addAttachment(Attachment attachment)
                      throws SBOLValidationException

Adds the URI of the given Attachment instance to this top level's set of attachment URIs. This method calls addAttachment(URI) with this Attachment URI.

Parameters:

attachment - the Attachment instance whose identity URI to be added

Returns:

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

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: TODO

addAttachment

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

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

This method creates a compliant sequence URI with the default URI prefix, which was set in the SBOLDocument instance hosting this top level, the given display ID and version. It then calls addAttachment(URI) with this Attachment URI.

Parameters:

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

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

Returns:

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

Throws:

SBOLValidationException - see addAttachment(URI)

addAttachment

public boolean addAttachment(String displayId)
                      throws SBOLValidationException

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

Parameters:

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

Returns:

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

Throws:

SBOLValidationException - see addAttachment(String, String)

getAttachments

public Set<Attachment> getAttachments()

Returns the set of attachments referenced by this top level.

Returns:

the set of attachments referenced by this top level

getAttachmentURIs

public Set<URI> getAttachmentURIs()

Returns the set of attachment URIs referenced by this top level.

Returns:

the set of attachment URIs referenced by this top level

clearAttachments

public void clearAttachments()

Removes all entries of this top level's list of attachments. The list will be empty after this call returns.

containsAttachment

public boolean containsAttachment(URI attachmentURI)

Checks if the given attachment URI is included in this top level's set of attachment URIs.

Parameters:

attachmentURI - the attachment URI to be checked

Returns:

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

removeAttachment

public boolean removeAttachment(URI attachment)

Removes the given attachment from the list of attachments.

Parameters:

attachment - an attachment uri be removed

Returns:

true if the matching attachment is removed successfully, false otherwise.

setAttachments

public void setAttachments(Set<URI> attachments)
                    throws SBOLValidationException

Clears the existing set of attachments first, and then adds the given set of the attachments to this top level.

Parameters:

attachments - The set of attachments for this top level.

Throws:

SBOLValidationException - if an SBOL validation rule violation occurred in any of the following methods:

• clearAttachments() or
• addAttachment(Attachment)