org.sbolstandard.core2

Class VariableComponent

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.VariableComponent

public class VariableComponent
extends Identified

Represents a VariableComponent in the SBOL data model

Version:

2.1

Author:

Zach Zundel, Igor Durovic

Method Summary

Modifier and Type	Method and Description
void	addVariant(String uriPrefix, String displayId, String version) Adds the given variant to the list of variants.
void	addVariant(URI variant) Adds the given variant URI to the list of variant URIs.
void	addVariantCollection(String uriPrefix, String displayId, String version) Adds the given variant collection to the list of variant collections.
void	addVariantCollection(URI variantCollection) Adds the given variant collection URI to the list of variant collection URIs.
void	addVariantDerivation(String uriPrefix, String displayId, String version) Adds the given variant derivation to the list of variant derivations.
void	addVariantDerivation(URI variantDerivation) Adds the given variant derivation URI to the list of variant derivations URIs.
void	clearVariantCollections() removes all entries of this variable component's set of variant collection URIs.
void	clearVariantDerivations() removes all entries of this variable component's set of variant derivation URIs.
void	clearVariants() removes all entries of this variable component's set of variant URIs.
OperatorType	getOperator() Returns the operator of the given variable component.
Component	getVariable() Returns the instance matching the given variable component's variable.
URI	getVariableURI() Returns the URI of the instance matching the given variable component's variable.
Set<Collection>	getVariantCollections() Returns a set of collections belonging to the variable component.
Set<URI>	getVariantCollectionURIs() Returns a set of collection URIs belonging to the variable component.
Set<CombinatorialDerivation>	getVariantDerivations() Returns a set of combinatorial derivations belonging to the variable component.
Set<URI>	getVariantDerivationURIs() Returns a set of combinatorial derivation URIs belonging to the variable component.
Set<ComponentDefinition>	getVariants() Returns a set of component definitions belonging to the variable component.
Set<URI>	getVariantURIs() Returns a set of component definition URIs belonging to the variable component.
boolean	removeVariant(ComponentDefinition variant) Removes the given component definition from the list of variants.
boolean	removeVariant(URI variantURI) Removes the component definition with the given URI from the list of variants.
boolean	removeVariantCollection(Collection variantCollection) Removes the given collection from the list of variantCollections.
boolean	removeVariantCollection(URI variantCollectionURI) Removes the collection with the given URI from the list of variantCollections.
boolean	removeVariantDerivation(CombinatorialDerivation variantDerivation) Removes the given combinatorial derivation from the list of variant derivations.
boolean	removeVariantDerivation(URI variantDerivationURI) Removes the combinatorial derivation with the given URI from the list of variant derivations.
void	setCombinatorialDerivation(CombinatorialDerivation combinatorialDerivation) Sets the parent combinatorial derivation to the given one.
void	setOperator(OperatorType operator) Sets the operator property to the given one.
void	setVariable(URI variable) Sets the variable property to the given one.
void	setVariantCollections(Set<URI> variantCollections) Clears the existing set of variant collections first, and then adds the given set of the variant collections to this variable component.
void	setVariantDerivations(Set<URI> variantDerivations) Clears the existing set of variant derivations first, and then adds the given set of the variant derivations to this variable component.
void	setVariants(Set<URI> variants) Clears the existing set of variants first, and then adds the given set of the variants to this variable component.
String	toString()

Methods inherited from class org.sbolstandard.core2.Identified

addWasDerivedFrom, addWasGeneratedBy, clearAnnotations, clearWasDerivedFroms, clearWasGeneratedBys, containsWasDerivedFrom, containsWasGeneratedBy, createAnnotation, createAnnotation, createAnnotation, createAnnotation, createAnnotation, createAnnotation, equals, getAnnotation, getAnnotations, getDescription, getDisplayId, getIdentity, getName, getPersistentIdentity, getVersion, getWasDerivedFrom, getWasDerivedFroms, getWasGeneratedBys, hasAnnotations, hashCode, 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

setCombinatorialDerivation

public void setCombinatorialDerivation(CombinatorialDerivation combinatorialDerivation)

Sets the parent combinatorial derivation to the given one.

Parameters:

combinatorialDerivation - the given combinatorial derivation to set to

addVariant

public void addVariant(URI variant)
                throws SBOLValidationException

Adds the given variant URI to the list of variant URIs.

Parameters:

variant - variant to be added

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 13008

addVariantCollection

public void addVariantCollection(URI variantCollection)
                          throws SBOLValidationException

Adds the given variant collection URI to the list of variant collection URIs.

Parameters:

variantCollection - variant collection to be added

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 13010

addVariantDerivation

public void addVariantDerivation(URI variantDerivation)
                          throws SBOLValidationException

Adds the given variant derivation URI to the list of variant derivations URIs.

Parameters:

variantDerivation - variant derivation to be added

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 13014

getVariable

public Component getVariable()

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

Returns:

the matching component if present, or null otherwise.

getVariableURI

public URI getVariableURI()

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

Returns:

the matching component if present, or null otherwise.

setVariable

public void setVariable(URI variable)
                 throws SBOLValidationException

Sets the variable property to the given one.

Parameters:

variable - the given component to set to

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 13004, 13005

getOperator

public OperatorType getOperator()

Returns the operator of the given variable component.

Returns:

the matching operator if present, or null otherwise.

setOperator

public void setOperator(OperatorType operator)
                 throws SBOLValidationException

Sets the operator property to the given one.

Parameters:

operator - the given operator type to set to

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 13002

getVariants

public Set<ComponentDefinition> getVariants()

Returns a set of component definitions belonging to the variable component.

Returns:

the matching set of component definitions

getVariantURIs

public Set<URI> getVariantURIs()

Returns a set of component definition URIs belonging to the variable component.

Returns:

the matching set of component definition URIs

getVariantCollections

public Set<Collection> getVariantCollections()

Returns a set of collections belonging to the variable component.

Returns:

the matching set of collections

getVariantCollectionURIs

public Set<URI> getVariantCollectionURIs()

Returns a set of collection URIs belonging to the variable component.

Returns:

the matching set of collection URIs

getVariantDerivations

public Set<CombinatorialDerivation> getVariantDerivations()

Returns a set of combinatorial derivations belonging to the variable component.

Returns:

the matching set of combinatorial derivations

getVariantDerivationURIs

public Set<URI> getVariantDerivationURIs()

Returns a set of combinatorial derivation URIs belonging to the variable component.

Returns:

the matching set of combinatorial derivation URIs

setVariants

public void setVariants(Set<URI> variants)
                 throws SBOLValidationException

Clears the existing set of variants first, and then adds the given set of the variants to this variable component.

Parameters:

variants - The set of variants

Throws:

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

• clearVariants()
• addVariant(URI), or

setVariantCollections

public void setVariantCollections(Set<URI> variantCollections)
                           throws SBOLValidationException

Clears the existing set of variant collections first, and then adds the given set of the variant collections to this variable component.

Parameters:

variantCollections - The set of variant collections

Throws:

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

• clearVariantCollections()
• addVariantCollection(URI), or

setVariantDerivations

public void setVariantDerivations(Set<URI> variantDerivations)
                           throws SBOLValidationException

Clears the existing set of variant derivations first, and then adds the given set of the variant derivations to this variable component.

Parameters:

variantDerivations - The set of variant derivations

Throws:

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

• clearVariantDerivations()
• addVariantDerivation(URI), or

addVariant

public void addVariant(String uriPrefix,
                       String displayId,
                       String version)
                throws SBOLValidationException

Adds the given variant to the list of variants.

Parameters:

uriPrefix - URI prefix for variant

displayId - display id for variant

version - version for variant

Throws:

SBOLValidationException - if the following SBOL validation rule was violated:

addVariantCollection

public void addVariantCollection(String uriPrefix,
                                 String displayId,
                                 String version)
                          throws SBOLValidationException

Adds the given variant collection to the list of variant collections.

Parameters:

uriPrefix - URI prefix for variant collection

displayId - display id for variant collection

version - version for variant collection

Throws:

SBOLValidationException - if the following SBOL validation rule was violated:

addVariantDerivation

public void addVariantDerivation(String uriPrefix,
                                 String displayId,
                                 String version)
                          throws SBOLValidationException

Adds the given variant derivation to the list of variant derivations.

Parameters:

uriPrefix - URI prefix for variant derivation

displayId - display id for variant derivation

version - version for variant derivation

Throws:

SBOLValidationException - if the following SBOL validation rule was violated:

removeVariant

public boolean removeVariant(ComponentDefinition variant)

Removes the given component definition from the list of variants.

Parameters:

variant - a component definition be removed

Returns:

true if the matching component definition is removed successfully, false otherwise.

removeVariant

public boolean removeVariant(URI variantURI)

Removes the component definition with the given URI from the list of variants.

Parameters:

variantURI - a component definition URI be removed

Returns:

true if the matching component definition is removed successfully, false otherwise.

clearVariants

public void clearVariants()

removes all entries of this variable component's set of variant URIs.

removeVariantCollection

public boolean removeVariantCollection(Collection variantCollection)

Removes the given collection from the list of variantCollections.

Parameters:

variantCollection - a collection to be removed

Returns:

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

removeVariantCollection

public boolean removeVariantCollection(URI variantCollectionURI)

Removes the collection with the given URI from the list of variantCollections.

Parameters:

variantCollectionURI - a collection URI to be removed

Returns:

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

clearVariantCollections

public void clearVariantCollections()

removes all entries of this variable component's set of variant collection URIs.

removeVariantDerivation

public boolean removeVariantDerivation(CombinatorialDerivation variantDerivation)

Removes the given combinatorial derivation from the list of variant derivations.

Parameters:

variantDerivation - a combinatorial derivation to be removed

Returns:

true if the matching combinatorial derivation is removed successfully, false otherwise.

removeVariantDerivation

public boolean removeVariantDerivation(URI variantDerivationURI)

Removes the combinatorial derivation with the given URI from the list of variant derivations.

Parameters:

variantDerivationURI - a combinatorial derivation URI to be removed

Returns:

true if the matching combinatorial derivation is removed successfully, false otherwise.

clearVariantDerivations

public void clearVariantDerivations()

removes all entries of this variable component's set of variant derivation URIs.

toString

public String toString()

Overrides:

toString in class Identified