org.sbolstandard.core2

Class SequenceAnnotation

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.SequenceAnnotation

All Implemented Interfaces:

Comparable<SequenceAnnotation>

public class SequenceAnnotation
extends Identified
implements Comparable<SequenceAnnotation>

Represents a SequenceAnnotation 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 sequence annotation'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 sequence annotation's list of locations.
GenericLocation	addGenericLocation(String displayId) Creates a generic location with the given arguments and then adds it to this sequence annotation's list of locations.
GenericLocation	addGenericLocation(String displayId, OrientationType orientation) Creates a generic location with the given arguments and then adds it to this sequence annotation's list of locations.
Range	addRange(String displayId, int start, int end) Creates a range with the given arguments and then adds it to this sequence annotation'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 sequence annotation's list of locations.
boolean	addRole(URI roleURI) Adds the given role to this sequence annotation's set of roles.
void	clearRoles() Removes all entries of this sequence annotation's set of roles.
int	compareTo(SequenceAnnotation sa)
boolean	containsRole(URI roleURI) Checks if the given role is included in this sequence annotation's set of roles.
boolean	equals(Object obj)
Component	getComponent() Returns the component this sequence annotation refers to.
ComponentDefinition	getComponentDefinition() Returns the component definition for the component annotated by this sequence annotation.
URI	getComponentIdentity() Returns the component identity this sequence annotation refers to.
URI	getComponentURI() Returns the component that this sequence annotation refers to.
Location	getLocation(String displayId) Returns the location owned by this sequence annotation that matches the given display ID.
Location	getLocation(URI locationURI) Returns the location owned by this sequence annotation that matches the given identity URI.
Set<Location>	getLocations() Returns the set of locations referenced by this sequence annotation.
Set<Location>	getPreciseLocations() Returns the set of Range/Cut locations referenced by this sequence annotation.
Set<URI>	getRoles() Returns this sequence annotation's set of roles.
List<Location>	getSortedLocations() Returns a sorted list of locations owned by this sequence annotation.
int	hashCode()
boolean	isSetComponent() Test if the reference component is set.
boolean	removeLocation(Location location) Removes the given location from the list of locations.
boolean	removeRole(URI roleURI) Removes the given role from this sequence annotation's set of roles.
void	setComponent(String displayId) Sets this sequence annotation's reference component (its identity URI) to the one matching the given display ID.
void	setComponent(URI componentURI) Sets the reference component's identity URI to the given URI.
void	setRoles(Set<URI> roles) Clears the existing set of roles first, and then adds the given set of the roles to this sequence annotation.
String	toString()
void	unsetComponent() Sets the reference component to null.

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

addGenericLocation

public GenericLocation addGenericLocation(String displayId)
                                   throws SBOLValidationException

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

This method first creates a compliant URI for the generic location to be created. It starts with this sequence annotation'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 sequence annotation's list of locations.

This method first creates a compliant URI for the generic location to be created. It starts with this sequence annotation'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 sequence annotation's list of locations.

This method first creates a compliant URI for the cut to be created. It starts with this sequence annotation'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 sequence annotation's list of locations.

This method first creates a compliant URI for the cut to be created. It starts with this sequence annotation'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 sequence annotation's list of locations.

This method first creates a compliant URI for the range to be created. It starts with this sequence annotation'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 sequence annotation's list of locations.

This method first creates a compliant URI for the range to be created. It starts with this sequence annotation'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)
                       throws SBOLValidationException

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

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 10902

getLocation

public Location getLocation(String displayId)

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

This method first creates a compliant URI. It starts with the sequence annotation's persistent identity URI, followed by the given display ID, and ends with this sequence annotation'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 sequence annotation 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 sequence annotation.

Returns:

the set of locations referenced by this sequence annotation

getPreciseLocations

public Set<Location> getPreciseLocations()

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

Returns:

the set of Range/Cut locations referenced by this sequence annotation

getSortedLocations

public List<Location> getSortedLocations()

Returns a sorted list of locations owned by this sequence annotation.

Returns:

a sorted list of locations owned by this sequence annotation

isSetComponent

public boolean isSetComponent()

Test if the reference component is set.

Returns:

true if this sequence annotation refers to a component, false otherwise

getComponentURI

public URI getComponentURI()

Returns the component that this sequence annotation refers to.

Returns:

the component that this sequence annotation refers to

getComponentIdentity

public URI getComponentIdentity()

Returns the component identity this sequence annotation refers to.

If this sequence annotation's parent component definition is null, this method returns null. Otherwise, it returns its child component which is also referenced by this sequence annotation.

Returns:

the component identity this sequence annotation refers to

getComponent

public Component getComponent()

Returns the component this sequence annotation refers to.

If this sequence annotation's parent component definition is null, this method returns null. Otherwise, it returns its child component which is also referenced by this sequence annotation.

Returns:

the component this sequence annotation refers to

setComponent

public void setComponent(String displayId)
                  throws SBOLValidationException

Sets this sequence annotation's reference component (its identity URI) to the one matching the given display ID.

This method first creates a compliant URI for the reference component. It starts with this sequence annotation's parent component defintion's persistent identity URI, followed by the given display ID, and ends with this sequence annotation's parent component defintion's version.

Parameters:

displayId - the given display ID for the reference component

Throws:

SBOLValidationException - if either of the following conditions is satisfied:

• either of the following SBOL validation rules was violated: 10204, 10206; or
• if an SBOL validation rule violation occurred in any of the following constructors or methods:
  • ComponentDefinition.createComponent(String, AccessType, String, String), or
  • setComponent(URI).

setComponent

public void setComponent(URI componentURI)
                  throws SBOLValidationException

Sets the reference component's identity URI to the given URI.

Parameters:

componentURI - the given component identity URI

Throws:

SBOLValidationException - if either of the following SBOL validation rules was violated: 10522, 10905, 10909.

unsetComponent

public void unsetComponent()

Sets the reference component to null.

addRole

public boolean addRole(URI roleURI)
                throws SBOLValidationException

Adds the given role to this sequence annotation's set of roles.

Parameters:

roleURI - the role to be added

Returns:

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

Throws:

SBOLValidationException - if component property is already set

removeRole

public boolean removeRole(URI roleURI)

Removes the given role from this sequence annotation's set of roles.

Parameters:

roleURI - the given role to be removed

Returns:

true if the matching role 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 sequence annotation.

Parameters:

roles - the set of roles to be set

Throws:

SBOLValidationException - if component property is already set

getRoles

public Set<URI> getRoles()

Returns this sequence annotation's set of roles.

Returns:

this sequence annotation's set of roles

containsRole

public boolean containsRole(URI roleURI)

Checks if the given role is included in this sequence annotation's set of roles.

Parameters:

roleURI - the role to be checked

Returns:

true if this set contains the given role, false otherwise

clearRoles

public void clearRoles()

Removes all entries of this sequence annotation's set of roles. The set will be empty after this call returns.

hashCode

public int hashCode()

Overrides:

hashCode in class Identified

equals

public boolean equals(Object obj)

Overrides:

equals in class Identified

getComponentDefinition

public ComponentDefinition getComponentDefinition()

Returns the component definition for the component annotated by this sequence annotation.

If the parent component definition for this sequence annotation is not set, then this method returns null. The component definition returned is the definition of the component that is referenced by the "component" field of this sequence annotation.

Returns:

the component definition for the component annotated by this sequence annotation

toString

public String toString()

Overrides:

toString in class Identified

compareTo

public int compareTo(SequenceAnnotation sa)

Specified by:

compareTo in interface Comparable<SequenceAnnotation>