org.sbolstandard.core2

Class Component

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.Measured

org.sbolstandard.core2.ComponentInstance

org.sbolstandard.core2.Component

public class Component
extends ComponentInstance

Represents a Component object in the SBOL data model.

Version:

2.1

Author:

Zhen Zhang, Nicholas Roehner, Chris Myers

Method Summary

Modifier and Type	Method and Description
Cut	addCut(String displayId, int at) Creates a cut with the given arguments and then adds it to this component's list of locations.
Cut	addCut(String displayId, int at, OrientationType orientation) Creates a cut with the given arguments and then adds it to this component's list of locations.
GenericLocation	addGenericLocation(String displayId) Creates a generic location with the given arguments and then adds it to this component's list of locations.
GenericLocation	addGenericLocation(String displayId, OrientationType orientation) Creates a generic location with the given arguments and then adds it to this component's list of locations.
GenericLocation	addGenericSourceLocation(String displayId) Creates a generic location with the given arguments and then adds it to this components's list of source locations.
GenericLocation	addGenericSourceLocation(String displayId, OrientationType orientation) Creates a generic location with the given arguments and then adds it to this component's list of source locations.
Range	addRange(String displayId, int start, int end) Creates a range with the given arguments and then adds it to this component's list of locations.
Range	addRange(String displayId, int start, int end, OrientationType orientation) Creates a range with the given arguments and then adds it to this component's list of locations.
boolean	addRole(URI roleURI) Adds the given role URI to this component's set of role URIs.
Cut	addSourceCut(String displayId, int at) Creates a cut with the given arguments and then adds it to this component's list of source locations.
Cut	addSourceCut(String displayId, int at, OrientationType orientation) Creates a cut with the given arguments and then adds it to this component's list of source locations.
Range	addSourceRange(String displayId, int start, int end) Creates a range with the given arguments and then adds it to this component's list of source locations.
Range	addSourceRange(String displayId, int start, int end, OrientationType orientation) Creates a range with the given arguments and then adds it to this component's list of source locations.
void	clearMapsTos() Removes all entries the list of mapsTos.
void	clearRoles() Removes all entries of this component's set of role URIs.
boolean	containsRole(URI roleURI) Checks if the given role URI is included in this component's set of role URIs.
MapsTo	createMapsTo(String displayId, RefinementType refinement, String localId, String remoteId) Creates a child mapsTo for this component with the given arguments, and then adds it to its list of mapsTos.
MapsTo	createMapsTo(String displayId, RefinementType refinement, URI local, URI remote) Creates a child mapsTo for this component with the given arguments, and then adds it to its list of mapsTos.
boolean	equals(Object obj)
Location	getLocation(String displayId) Returns the location owned by this component that matches the given display ID.
Location	getLocation(URI locationURI) Returns the location owned by this component that matches the given identity URI.
Set<Location>	getLocations() Returns the set of locations referenced by this component.
MapsTo	getMapsTo(String displayId) Returns the mapsTo that matches the given display ID.
MapsTo	getMapsTo(URI mapsToURI) Returns the mapsTo that matches the given URI.
Set<MapsTo>	getMapsTos() Returns the set of mapsTos owned by this instance.
Set<Location>	getPreciseLocations() Returns the set of Range/Cut locations referenced by this component.
Set<Location>	getPreciseSourceLocations() Returns the set of Range/Cut sourceLocations referenced by this component.
RoleIntegrationType	getRoleIntegration() Returns the roleIntegration property of this object.
Set<URI>	getRoles() Returns the set of role URIs owned by this component.
List<Location>	getSortedLocations() Returns a sorted list of locations owned by this component.
List<Location>	getSortedSourceLocations() Returns a sorted list of sourceLocations owned by this component.
Location	getSourceLocation(String displayId) Returns a source location owned by this component that matches the given display ID.
Location	getSourceLocation(URI sourceLocationURI) Returns a sourceLocation owned by this component that matches the given identity URI.
Set<Location>	getSourceLocations() Returns the set of sourceLocations referenced by this component.
int	hashCode()
boolean	isSetRoleIntegration() Test if the roleIntegration property is set.
boolean	removeLocation(Location location) Removes the given location from the list of locations.
boolean	removeMapsTo(MapsTo mapsTo) Removes the given mapsTo from the list of mapsTos.
boolean	removeRole(URI roleURI) Removes the given role URI from the set of roles.
boolean	removeSourceLocation(Location sourceLocation) Removes the given location from the list of source locations.
void	setDefinition(URI definition) Sets the definition property to the given one.
void	setRoleIntegration(RoleIntegrationType roleIntegration) Sets the roleIntegration property of this object to the given one.
void	setRoles(Set<URI> roles) Clears the existing set of roles first, and then adds the given set of the roles to this component.
String	toString()
void	unsetRoleIntegration() Sets the roleIntegration property of this object to null.

Methods inherited from class org.sbolstandard.core2.ComponentInstance

getAccess, getDefinition, getDefinitionIdentity, getDefinitionURI, setAccess

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

addRole

public boolean addRole(URI roleURI)
                throws SBOLValidationException

Adds the given role URI to this component's set of role URIs.

Parameters:

roleURI - the role URI to be added

Returns:

true if this set did not already contain the specified role, false otherwise.

Throws:

SBOLValidationException - if RoleIntegration is not set (10709).

removeRole

public boolean removeRole(URI roleURI)

Removes the given role URI from the set of roles.

Parameters:

roleURI - the given role URI to be removed

Returns:

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

setRoles

public void setRoles(Set<URI> roles)
              throws SBOLValidationException

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

Parameters:

roles - the set of roles to be set

Throws:

SBOLValidationException - if RoleIntegration is not set (10709).

getRoles

public Set<URI> getRoles()

Returns the set of role URIs owned by this component.

Returns:

the set of role URIs owned by this component.

containsRole

public boolean containsRole(URI roleURI)

Checks if the given role URI is included in this component's set of role URIs.

Parameters:

roleURI - the role URI to be checked

Returns:

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

clearRoles

public void clearRoles()

Removes all entries of this component's set of role URIs. The set will be empty after this call returns.

isSetRoleIntegration

public boolean isSetRoleIntegration()

Test if the roleIntegration property is set.

Returns:

true if it is not null

getRoleIntegration

public RoleIntegrationType getRoleIntegration()

Returns the roleIntegration property of this object.

Returns:

the roleIntegration property of this object.

setRoleIntegration

public void setRoleIntegration(RoleIntegrationType roleIntegration)
                        throws SBOLValidationException

Sets the roleIntegration property of this object to the given one.

Parameters:

roleIntegration - indicates how role is to be integrated with related roles.

Throws:

SBOLValidationException - if there are roles on this Component (10709).

unsetRoleIntegration

public void unsetRoleIntegration()
                          throws SBOLValidationException

Sets the roleIntegration property of this object to null.

Throws:

SBOLValidationException - if there are roles on this Component (10709).

createMapsTo

public MapsTo createMapsTo(String displayId,
                           RefinementType refinement,
                           String localId,
                           String remoteId)
                    throws SBOLValidationException

Creates a child mapsTo for this component with the given arguments, and then adds it to its list of mapsTos.

This method creates compliant local and remote URIs first. The compliant local URI is created with this component's persistent identity URI, followed by the given local component's display ID, followed by this component's version. The compliant remote URI is created following the same pattern. It then calls createMapsTo(String, RefinementType, URI, URI) with the given mapsTo's display ID, its refinement type, and the created compliant local and remote components' URIs.

This method calls ComponentDefinition.createComponent(String, AccessType, String, String) to automatically create a local component with the given display ID of referenced local component definition, AccessType.PUBLIC, and an empty version string, if all of the following conditions are satisfied:

• the associated SBOLDocument instance for this component is not null;
• if default components should be automatically created when not present in the associated SBOLDocument instance, i.e., SBOLDocument.isCreateDefaults() returns true;
• if this component's parent ComponentDefinition instance exists; and
• if this component's parent ComponentDefinition instance does not already have a component with the created compliant local URI.

This automatically created created component has the same display ID as its referenced component definition.

Parameters:

displayId - the display ID of the mapsTo to be created

refinement - the relationship between the local and remote components

localId - the display ID of the local component

remoteId - the display ID of the remote component

Returns:

the created mapsTo

Throws:

SBOLValidationException - if any of the following condition is satisfied:

• if either of the following SBOL validation rules was violated: 10204, 10206;
• an SBOL validation exception occurred in ComponentDefinition.createComponent(String, AccessType, String, String); or
• an SBOL validation exception occurred in createMapsTo(String, RefinementType, URI, URI).

createMapsTo

public MapsTo createMapsTo(String displayId,
                           RefinementType refinement,
                           URI local,
                           URI remote)
                    throws SBOLValidationException

Creates a child mapsTo for this component with the given arguments, and then adds it to its list of mapsTos.

This method creates a compliant URI for the mapsTo to be created. It starts with this component's persistent identity, followed by the mapsTo's display ID, and ends with this component's version.

Parameters:

displayId - the display ID of the mapsTo to be created

refinement - the relationship between the local and remote components

local - the identity URI of the local component

remote - the identity URI of the remote component

Returns:

the created mapsTo

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10526, 10802, 10803, 10804, 10805, 10807, 10808, 10809, 10811.

removeMapsTo

public boolean removeMapsTo(MapsTo mapsTo)

Removes the given mapsTo from the list of mapsTos.

Parameters:

mapsTo - a mapsTo to be removed

Returns:

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

getMapsTo

public MapsTo getMapsTo(String displayId)

Returns the mapsTo that matches the given display ID. ›

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

Parameters:

displayId - the display ID of the mapsTo to be retrieved

Returns:

the matching mapsTo

getMapsTo

public MapsTo getMapsTo(URI mapsToURI)

Returns the mapsTo that matches the given URI.

Parameters:

mapsToURI - The URI of the mapsTo to be retrieved

Returns:

the matching mapsTo

getMapsTos

public Set<MapsTo> getMapsTos()

Returns the set of mapsTos owned by this instance.

Returns:

the set of mapsTos owned by this instance.

clearMapsTos

public void clearMapsTos()

Removes all entries the list of mapsTos. The list will be empty after this call returns.

setDefinition

public void setDefinition(URI definition)
                   throws SBOLValidationException

Sets the definition property to the given one.

Overrides:

setDefinition in class ComponentInstance

Parameters:

definition - the given definition URI to set to

Throws:

SBOLValidationException - if either of the following SBOL validation rules was violated: 10604, 10605.

addGenericSourceLocation

public GenericLocation addGenericSourceLocation(String displayId)
                                         throws SBOLValidationException

Creates a generic location with the given arguments and then adds it to this components's list of source locations.

This method first creates a compliant URI for the generic location to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the generic location to be created

Returns:

the created generic location instance

Throws:

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

addGenericSourceLocation

public GenericLocation addGenericSourceLocation(String displayId,
                                                OrientationType orientation)
                                         throws SBOLValidationException

Creates a generic location with the given arguments and then adds it to this component's list of source locations.

This method first creates a compliant URI for the generic location to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the generic location to be created

orientation - the orientation type

Returns:

the created generic location instance

Throws:

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

addSourceCut

public Cut addSourceCut(String displayId,
                        int at)
                 throws SBOLValidationException

Creates a cut with the given arguments and then adds it to this component's list of source locations.

This method first creates a compliant URI for the cut to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the cut to be created

at - the at property for the cut to be created

Returns:

the created cut

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11202.

addSourceCut

public Cut addSourceCut(String displayId,
                        int at,
                        OrientationType orientation)
                 throws SBOLValidationException

Creates a cut with the given arguments and then adds it to this component's list of source locations.

This method first creates a compliant URI for the cut to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the cut to be created

at - the at property for the cut to be created

orientation - the orientation type

Returns:

the created cut

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11202.

addSourceRange

public Range addSourceRange(String displayId,
                            int start,
                            int end)
                     throws SBOLValidationException

Creates a range with the given arguments and then adds it to this component's list of source locations.

This method first creates a compliant URI for the range to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the range to be created

start - the start index for the range to be created

end - the end index for the range to be created

Returns:

the created range

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11102, 11103, 11104.

addSourceRange

public Range addSourceRange(String displayId,
                            int start,
                            int end,
                            OrientationType orientation)
                     throws SBOLValidationException

Creates a range with the given arguments and then adds it to this component's list of source locations.

This method first creates a compliant URI for the range to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the range to be created

start - the start index for the range to be created

end - the end index for the range to be created

orientation - the orientation type

Returns:

the created range

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11102, 11103, 11104.

removeSourceLocation

public boolean removeSourceLocation(Location sourceLocation)

Removes the given location from the list of source locations.

Parameters:

sourceLocation - the location to be removed

Returns:

true if the matching location was removed successfully, false otherwise

getSourceLocation

public Location getSourceLocation(String displayId)

Returns a source location owned by this component that matches the given display ID.

This method first creates a compliant URI. It starts with the component's persistent identity URI, followed by the given display ID, and ends with this component's version. This compliant URI is used to look up for the location to be retrieved.

Parameters:

displayId - the display ID of the location to be retrieved

Returns:

the matching location

getSourceLocation

public Location getSourceLocation(URI sourceLocationURI)

Returns a sourceLocation owned by this component that matches the given identity URI.

Parameters:

sourceLocationURI - the URI identity of the location to be retrieved

Returns:

the matching location

getSourceLocations

public Set<Location> getSourceLocations()

Returns the set of sourceLocations referenced by this component.

Returns:

the set of sourceLocations referenced by this component

getPreciseSourceLocations

public Set<Location> getPreciseSourceLocations()

Returns the set of Range/Cut sourceLocations referenced by this component.

Returns:

the set of Range/Cut sourceLocations referenced by this component

getSortedSourceLocations

public List<Location> getSortedSourceLocations()

Returns a sorted list of sourceLocations owned by this component.

Returns:

a sorted list of sourceLocations owned by this component

addGenericLocation

public GenericLocation addGenericLocation(String displayId)
                                   throws SBOLValidationException

Creates a generic location with the given arguments and then adds it to this component's list of locations.

This method first creates a compliant URI for the generic location to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the generic location to be created

Returns:

the created generic location instance

Throws:

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

addGenericLocation

public GenericLocation addGenericLocation(String displayId,
                                          OrientationType orientation)
                                   throws SBOLValidationException

Creates a generic location with the given arguments and then adds it to this component's list of locations.

This method first creates a compliant URI for the generic location to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the generic location to be created

orientation - the orientation type

Returns:

the created generic location instance

Throws:

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

addCut

public Cut addCut(String displayId,
                  int at)
           throws SBOLValidationException

Creates a cut with the given arguments and then adds it to this component's list of locations.

This method first creates a compliant URI for the cut to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the cut to be created

at - the at property for the cut to be created

Returns:

the created cut

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11202.

addCut

public Cut addCut(String displayId,
                  int at,
                  OrientationType orientation)
           throws SBOLValidationException

Creates a cut with the given arguments and then adds it to this component's list of locations.

This method first creates a compliant URI for the cut to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the cut to be created

at - the at property for the cut to be created

orientation - the orientation type

Returns:

the created cut

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11202.

addRange

public Range addRange(String displayId,
                      int start,
                      int end)
               throws SBOLValidationException

Creates a range with the given arguments and then adds it to this component's list of locations.

This method first creates a compliant URI for the range to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the range to be created

start - the start index for the range to be created

end - the end index for the range to be created

Returns:

the created range

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11102, 11103, 11104.

addRange

public Range addRange(String displayId,
                      int start,
                      int end,
                      OrientationType orientation)
               throws SBOLValidationException

Creates a range with the given arguments and then adds it to this component's list of locations.

This method first creates a compliant URI for the range to be created. It starts with this component's persistent identity URI, followed by the given display ID, and ends an empty string for version.

Parameters:

displayId - the display ID for the range to be created

start - the start index for the range to be created

end - the end index for the range to be created

orientation - the orientation type

Returns:

the created range

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11102, 11103, 11104.

removeLocation

public boolean removeLocation(Location location)

Removes the given location from the list of locations.

Parameters:

location - the location to be removed

Returns:

true if the matching location was removed successfully, false otherwise

getLocation

public Location getLocation(String displayId)

Returns the location owned by this component that matches the given display ID.

This method first creates a compliant URI. It starts with the component's persistent identity URI, followed by the given display ID, and ends with this component's version. This compliant URI is used to look up for the location to be retrieved.

Parameters:

displayId - the display ID of the location to be retrieved

Returns:

the matching location

getLocation

public Location getLocation(URI locationURI)

Returns the location owned by this component that matches the given identity URI.

Parameters:

locationURI - the URI identity of the location to be retrieved

Returns:

the matching location

getLocations

public Set<Location> getLocations()

Returns the set of locations referenced by this component.

Returns:

the set of locations referenced by this component

getPreciseLocations

public Set<Location> getPreciseLocations()

Returns the set of Range/Cut locations referenced by this component.

Returns:

the set of Range/Cut locations referenced by this component

getSortedLocations

public List<Location> getSortedLocations()

Returns a sorted list of locations owned by this component.

Returns:

a sorted list of locations owned by this component

hashCode

public int hashCode()

Overrides:

hashCode in class ComponentInstance

equals

public boolean equals(Object obj)

Overrides:

equals in class ComponentInstance

toString

public String toString()

Overrides:

toString in class ComponentInstance