org.sbolstandard.core2

Class CombinatorialDerivation

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.TopLevel

org.sbolstandard.core2.CombinatorialDerivation

public class CombinatorialDerivation
extends TopLevel

Represents a CombinatorialDerivation object in the SBOL data model.

Version:

2.1

Author:

Zach Zundel, Igor Durovic

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
void	checkDescendantsURIcompliance() Check if this top-level object's and all of its descendants' URIs are all compliant.
void	clearVariableComponents() Removes all entries of this combinatorial derivation's list of variable components.
VariableComponent	createVariableComponent(String displayId, OperatorType operator, String variableId) Creates a child variable component for this combinatorial derivation with the given arguments, and then adds to this combinatorial derivation's list of variable components.
VariableComponent	createVariableComponent(String displayId, OperatorType operator, URI variable) Creates a child variable component for this combinatorial derivation with the given arguments, and then adds to this combinatorial derivation's list of variable components.
boolean	equals(Object obj)
StrategyType	getStrategy() Returns the strategy property.
ComponentDefinition	getTemplate() Returns the component definition referenced by this combinatorial derivation.
URI	getTemplateIdentity() Returns the component definition identity referenced by this combinatorial derivation.
URI	getTemplateURI() Returns the reference component definition URI.
VariableComponent	getVariableComponent(String displayId) Returns the variable component matching the given variable component's display ID.
VariableComponent	getVariableComponent(URI variableComponentURI) Returns the instance matching the given variable component's identity URI.
Set<VariableComponent>	getVariableComponents() Returns the set of variable components owned by this combinatorial derivation.
int	hashCode()
boolean	isSetStrategy() Checks if the strategy property is set.
boolean	removeVariableComponent(VariableComponent variableComponent) Removes the given variable component from the list of variable components.
void	setStrategy(StrategyType strategy) Sets the strategy property to the given one.
void	setTemplate(URI template) Sets the template property to the given one.
void	setVariableComponents(Set<VariableComponent> variableComponents) Clears the existing set of variable components first, and then adds the given set of the variable components to this combinatorial derivation.
String	toString()
void	unsetStrategy() Sets the strategy property of this combinatorial derivation to null.

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

isSetStrategy

public boolean isSetStrategy()

Checks if the strategy property is set.

Returns:

true if it is not null, false otherwise

removeVariableComponent

public boolean removeVariableComponent(VariableComponent variableComponent)

Removes the given variable component from the list of variable components.

Parameters:

variableComponent - the given variable component

Returns:

true if the matching variable component was removed successfully, false otherwise.

getVariableComponent

public VariableComponent getVariableComponent(URI variableComponentURI)

Returns the instance matching the given variable component's identity URI.

Parameters:

variableComponentURI - the identity URI of the variable component to be retrieved

Returns:

the matching variable component if present, or null otherwise.

getVariableComponent

public VariableComponent getVariableComponent(String displayId)

Returns the variable component matching the given variable component's display ID.

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

Parameters:

displayId - the display ID of the variable component to be retrieved

Returns:

the matching variable component if present, or null otherwise.

getVariableComponents

public Set<VariableComponent> getVariableComponents()

Returns the set of variable components owned by this combinatorial derivation.

Returns:

the set of variable components owned by this combinatorial derivation.

clearVariableComponents

public void clearVariableComponents()

Removes all entries of this combinatorial derivation's list of variable components. The list will be empty after this call returns.

This method calls removeVariableComponent(VariableComponent variableComponent) to iteratively remove each variable component.

setVariableComponents

public void setVariableComponents(Set<VariableComponent> variableComponents)
                           throws SBOLValidationException

Clears the existing set of variable components first, and then adds the given set of the variable components to this combinatorial derivation.

Parameters:

variableComponents - The set of variable components for this combinatorial derivation.

Throws:

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

• clearVariableComponents() or
• addVariableComponent(VariableComponent)

createVariableComponent

public VariableComponent createVariableComponent(String displayId,
                                                 OperatorType operator,
                                                 URI variable)
                                          throws SBOLValidationException

Creates a child variable component for this combinatorial derivation with the given arguments, and then adds to this combinatorial derivation's list of variable components.

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

Parameters:

displayId - the display ID for the variable component to be created

operator - the operator property for the variable component to be created

variable - the component URI referenced by the variable component to be created

Returns:

the created variable component

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 13002, 13003, 13004, 13005.

createVariableComponent

public VariableComponent createVariableComponent(String displayId,
                                                 OperatorType operator,
                                                 String variableId)
                                          throws SBOLValidationException

Creates a child variable component for this combinatorial derivation with the given arguments, and then adds to this combinatorial derivation's list of variable components.

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

Parameters:

displayId - the display ID for the variable component to be created

operator - the operator property for the variable component to be created

variableId - the component displayId referenced by the variable component to be created

Returns:

the created variable component

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 13002, 13003, 13004, 13005.

getTemplateURI

public URI getTemplateURI()

Returns the reference component definition URI.

Returns:

the reference component definition URI

getTemplateIdentity

public URI getTemplateIdentity()

Returns the component definition identity referenced by this combinatorial derivation.

Returns:

null if the associated SBOLDocument instance is null or no matching component definition referenced by this combinatorial derivation exists; or the matching component definition otherwise.

getTemplate

public ComponentDefinition getTemplate()

Returns the component definition referenced by this combinatorial derivation.

Returns:

null if the associated SBOLDocument instance is null or no matching component definition referenced by this combinatorial derivation; or the matching component definition otherwise.

setTemplate

public void setTemplate(URI template)
                 throws SBOLValidationException

Sets the template property to the given one.

Parameters:

template - the given template URI to set to

Throws:

SBOLValidationException - if either of the following SBOL validation rules was violated: 10602, 10604, 12905.

getStrategy

public StrategyType getStrategy()

Returns the strategy property.

Returns:

the strategy property

setStrategy

public void setStrategy(StrategyType strategy)
                 throws SBOLValidationException

Sets the strategy property to the given one.

Parameters:

strategy - the given strategy type to set to

Throws:

SBOLValidationException - on SBOL validation rule violation 12903.

unsetStrategy

public void unsetStrategy()

Sets the strategy property of this combinatorial derivation to null.

checkDescendantsURIcompliance

public void checkDescendantsURIcompliance()
                                   throws SBOLValidationException

Description copied from class: TopLevel

Check if this top-level object's and all of its descendants' URIs are all compliant.

Throws:

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

• URIcompliance.isChildURIcompliant(Identified, Identified).

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