Identified

java.lang.Object
- org.sbolstandard.core2.Identified

Direct Known Subclasses:

Association, Location, MapsTo, Measure, Measured, SequenceAnnotation, SequenceConstraint, TopLevel, Usage, VariableComponent
```
public abstract class Identified
extends Object
```
Represents an Identified object in the SBOL data model.

Version:

2.1

Author:

Zhen Zhang, Nicholas Roehner, Chris Myers

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`boolean`	`addWasDerivedFrom(URI wasDerivedFromURI)` Adds the given wasDerivedFrom URI to the set of wasDerivedFrom URIs.
`boolean`	`addWasGeneratedBy(URI wasGeneratedByURI)` Adds the given wasGeneratedBy URI to the set of wasGeneratedBy URIs.
`void`	`clearAnnotations()` Removes all entries of this instance's list of annotations.
`void`	`clearWasDerivedFroms()` Removes all entries from the set of wasDerivedFrom URIs.
`void`	`clearWasGeneratedBys()` Removes all entries from the set of wasGeneratedBy URIs.
`boolean`	`containsWasDerivedFrom(URI wasDerivedFromURI)` Checks if the given wasDerivedFrom URI is included in the set of wasDerivedFrom URIs.
`boolean`	`containsWasGeneratedBy(URI wasGeneratedByURI)` Checks if the given wasGeneratedBy URI is included in the set of wasGeneratedBy URIs.
`Annotation`	`createAnnotation(QName qName, boolean literal)` Creates an annotation using the given arguments, and then adds to the list of annotaions.
`Annotation`	`createAnnotation(QName qName, double literal)` Creates an annotation using the given arguments, then adds to this instance's list of annotations.
`Annotation`	`createAnnotation(QName qName, int literal)` Creates an annotation using the given arguments, then adds to this instance's list of annotations.
`Annotation`	`createAnnotation(QName qName, QName nestedQName, String nestedId, List<Annotation> annotations)` Creates an annotation with nested annotations using the given arguments, and then adds to this instance's list of annotations.
`Annotation`	`createAnnotation(QName qName, String literal)` Creates an annotation using the given arguments, then adds to this instance's list of annotations.
`Annotation`	`createAnnotation(QName qName, URI literal)` Creates an annotation using the given arguments, then adds to this instance's list of annotations.
`boolean`	`equals(Object obj)`
`Annotation`	`getAnnotation(QName qName)` Returns the annotation matching the given QName.
`List<Annotation>`	`getAnnotations()` Returns the list of annotations owned by this instance.
`String`	`getDescription()` Returns the description property of this instance.
`String`	`getDisplayId()` Returns the display ID of this instance.
`URI`	`getIdentity()` Returns the identity URI of this instance.
`String`	`getName()` Returns the name property of this instance.
`URI`	`getPersistentIdentity()` Returns the persistent identity URI of this instance.
`String`	`getVersion()` Returns this instance's version.
`URI`	`getWasDerivedFrom()` Deprecated.
`Set<URI>`	`getWasDerivedFroms()` Returns the set of wasDerivedFrom URIs.
`Set<URI>`	`getWasGeneratedBys()` Returns the set of wasGeneratedBy URIs.
`boolean`	`hasAnnotations()` Test if this instance has any annotations.
`int`	`hashCode()`
`boolean`	`isSetDescription()` Test if the description property is set.
`boolean`	`isSetDisplayId()` Test if the display ID is set.
`boolean`	`isSetName()` Test if the name property is set.
`boolean`	`isSetPersistentIdentity()` Test if the persistent identity URI is set.
`boolean`	`isSetVersion()` Test if the version is set.
`boolean`	`isSetWasDerivedFrom()` Deprecated.
`boolean`	`removeAnnotation(Annotation annotation)` Removes the given annotation from the list of annotations owned by this instance.
`boolean`	`removeWasDerivedFrom(URI wasDerivedFromURI)` Removes the given wasDerivedFrom URI from the set of wasDerivedFroms.
`boolean`	`removeWasGeneratedBy(URI wasGeneratedByURI)` Removes the given wasGeneratedBy URI from the set of wasGeneratedBys.
`void`	`setDescription(String description)` Sets the description property for this instance.
`void`	`setName(String name)` Sets the name property for this instance.
`void`	`setWasDerivedFrom(URI wasDerivedFrom)` Deprecated.
`void`	`setWasDerivedFroms(Set<URI> wasDerivedFroms)` Clears the existing set of wasDerivedFroms first, and then adds the given set of the wasDerivedFroms.
`void`	`setWasGeneratedBys(Set<URI> wasGeneratedBys)` Clears the existing set of wasGeneratedBys first, and then adds the given set of the wasGeneratedBys.
`String`	`toString()`
`void`	`unsetDescription()` Sets the description property to `null`.
`void`	`unsetName()` Sets the name of this instance to `null`.
`void`	`unsetWasDerivedFrom()` Deprecated.

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait

- Method Detail
  - getIdentity
```
public URI getIdentity()
```
    Returns the identity URI of this instance.
    
    Returns:
    
    the identity URI of this instance.
  - isSetPersistentIdentity
```
public boolean isSetPersistentIdentity()
```
    Test if the persistent identity URI is set.
    
    Returns:
    
    true if it is not null, or false otherwise
  - getPersistentIdentity
```
public URI getPersistentIdentity()
```
    Returns the persistent identity URI of this instance. If its persistent identity is not set, this method returns the identity URI.
    
    Returns:
    
    the persistent identity URI of this instance if it is set, or the identity URI otherwise
  - isSetVersion
```
public boolean isSetVersion()
```
    Test if the version is set.
    
    Returns:
    
    true if it is not null, or false otherwise
  - isSetWasDerivedFrom
```
@Deprecated
public boolean isSetWasDerivedFrom()
```
    Deprecated.
    
    Test if the wasDerivedFrom property is set.
    
    Returns:
    
    true if it is not null, or false otherwise
  - getVersion
```
public String getVersion()
```
    Returns this instance's version.
    
    Returns:
    
    this instance's version.
  - isSetDisplayId
```
public boolean isSetDisplayId()
```
    Test if the display ID is set.
    
    Returns:
    
    true if it is not null, or false otherwise
  - getDisplayId
```
public String getDisplayId()
```
    Returns the display ID of this instance.
    
    Returns:
    
    the display ID of this instance.
  - addWasDerivedFrom
```
public boolean addWasDerivedFrom(URI wasDerivedFromURI)
                          throws SBOLValidationException
```
    Adds the given wasDerivedFrom URI to the set of wasDerivedFrom URIs.
    
    Parameters:
    
    wasDerivedFromURI - the wasDerivedFrom URI to be added
    
    Returns:
    
    true if this set did not already contain the specified wasDerivedFrom, false otherwise.
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rules was violated: 10305.
  - removeWasDerivedFrom
```
public boolean removeWasDerivedFrom(URI wasDerivedFromURI)
```
    Removes the given wasDerivedFrom URI from the set of wasDerivedFroms.
    
    Parameters:
    
    wasDerivedFromURI - the given wasDerivedFrom URI to be removed
    
    Returns:
    
    true if the matching wasDerivedFrom reference was removed successfully, false otherwise.
  - containsWasDerivedFrom
```
public boolean containsWasDerivedFrom(URI wasDerivedFromURI)
```
    Checks if the given wasDerivedFrom URI is included in the set of wasDerivedFrom URIs.
    
    Parameters:
    
    wasDerivedFromURI - the wasDerivedFrom URI to be checked
    
    Returns:
    
    true if this set contains the given wasDerivedFrom URI, false otherwise.
  - clearWasDerivedFroms
```
public void clearWasDerivedFroms()
```
    Removes all entries from the set of wasDerivedFrom URIs. The set will be empty after this call returns.
  - getWasDerivedFroms
```
public Set<URI> getWasDerivedFroms()
```
    Returns the set of wasDerivedFrom URIs.
    
    Returns:
    
    the set of wasDerivedFrom URIs.
  - getWasDerivedFrom
```
@Deprecated
public URI getWasDerivedFrom()
```
    Deprecated.
    
    Returns the wasDerivedFrom property of this instance.
    
    Returns:
    
    the wasDerivedFrom property of this instance.
  - setWasDerivedFrom
```
@Deprecated
public void setWasDerivedFrom(URI wasDerivedFrom)
                                   throws SBOLValidationException
```
    Deprecated.
    
    Sets the wasDerivedFrom property of this instance to the given one.
    
    Parameters:
    
    wasDerivedFrom - the wasDerivedFrom property to set to
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rules was violated: 10303, 10304, 10305.
  - setWasDerivedFroms
```
public void setWasDerivedFroms(Set<URI> wasDerivedFroms)
                        throws SBOLValidationException
```
    Clears the existing set of wasDerivedFroms first, and then adds the given set of the wasDerivedFroms.
    
    Parameters:
    
    wasDerivedFroms - the set of wasDerivedFroms to set to
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rules was violated: 10305.
  - addWasGeneratedBy
```
public boolean addWasGeneratedBy(URI wasGeneratedByURI)
                          throws SBOLValidationException
```
    Adds the given wasGeneratedBy URI to the set of wasGeneratedBy URIs.
    
    Parameters:
    
    wasGeneratedByURI - the wasGeneratedBy URI to be added
    
    Returns:
    
    true if this set did not already contain the specified wasGeneratedBy, false otherwise.
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 10222
  - removeWasGeneratedBy
```
public boolean removeWasGeneratedBy(URI wasGeneratedByURI)
```
    Removes the given wasGeneratedBy URI from the set of wasGeneratedBys.
    
    Parameters:
    
    wasGeneratedByURI - the given wasGeneratedBy URI to be removed
    
    Returns:
    
    true if the matching wasGeneratedBy reference was removed successfully, false otherwise.
  - containsWasGeneratedBy
```
public boolean containsWasGeneratedBy(URI wasGeneratedByURI)
```
    Checks if the given wasGeneratedBy URI is included in the set of wasGeneratedBy URIs.
    
    Parameters:
    
    wasGeneratedByURI - the wasGeneratedBy URI to be checked
    
    Returns:
    
    true if this set contains the given wasGeneratedBy URI, false otherwise.
  - clearWasGeneratedBys
```
public void clearWasGeneratedBys()
```
    Removes all entries from the set of wasGeneratedBy URIs. The set will be empty after this call returns.
  - getWasGeneratedBys
```
public Set<URI> getWasGeneratedBys()
```
    Returns the set of wasGeneratedBy URIs.
    
    Returns:
    
    the set of wasGeneratedBy URIs.
  - setWasGeneratedBys
```
public void setWasGeneratedBys(Set<URI> wasGeneratedBys)
                        throws SBOLValidationException
```
    Clears the existing set of wasGeneratedBys first, and then adds the given set of the wasGeneratedBys.
    
    Parameters:
    
    wasGeneratedBys - the set of wasGeneratedBys to set to
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rules was violated: 10222
  - hasAnnotations
```
public boolean hasAnnotations()
```
    Test if this instance has any annotations.
    
    Returns:
    
    true if this instance has any annotations, or false otherwise
  - createAnnotation
```
public Annotation createAnnotation(QName qName,
                                   String literal)
                            throws SBOLValidationException
```
    Creates an annotation using the given arguments, then adds to this instance's list of annotations.
    
    Parameters:
    
    qName - the QName of the annotation to be created
    
    literal - the literal string
    
    Returns:
    
    the created annotation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10401, 10501, 10701, 10801, 10901, 11101, 11201, 11301, 11401, 11501, 11601, 11701, 11801, 11901, 12001, 12101, 12301.
  - createAnnotation
```
public Annotation createAnnotation(QName qName,
                                   double literal)
                            throws SBOLValidationException
```
    Creates an annotation using the given arguments, then adds to this instance's list of annotations.
    
    Parameters:
    
    qName - the QName of the annotation to be created
    
    literal - the double type literal
    
    Returns:
    
    the created annotation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10401, 10501, 10701, 10801, 10901, 11101, 11201, 11301, 11401, 11501, 11601, 11701, 11801, 11901, 12001, 12101, 12301.
  - createAnnotation
```
public Annotation createAnnotation(QName qName,
                                   int literal)
                            throws SBOLValidationException
```
    Creates an annotation using the given arguments, then adds to this instance's list of annotations.
    
    Parameters:
    
    qName - the QName of the annotation to be created
    
    literal - the integer type literal
    
    Returns:
    
    the created annotation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10401, 10501, 10701, 10801, 10901, 11101, 11201, 11301, 11401, 11501, 11601, 11701, 11801, 11901, 12001, 12101, 12301.
  - createAnnotation
```
public Annotation createAnnotation(QName qName,
                                   boolean literal)
                            throws SBOLValidationException
```
    Creates an annotation using the given arguments, and then adds to the list of annotaions.
    
    Parameters:
    
    qName - the QName of the annotation to be created
    
    literal - a boolean type literal
    
    Returns:
    
    the created annotation instance
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rule was violated: 10401, 10501, 10701, 10801, 10901, 11101, 11201, 11301, 11401, 11501, 11601, 11701, 11801, 11901, 12001, 12101
  - createAnnotation
```
public Annotation createAnnotation(QName qName,
                                   URI literal)
                            throws SBOLValidationException
```
    Creates an annotation using the given arguments, then adds to this instance's list of annotations.
    
    Parameters:
    
    qName - the QName of the annotation to be created
    
    literal - the literal URI
    
    Returns:
    
    the created annotation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10401, 10501, 10701, 10801, 10901, 11101, 11201, 11301, 11401, 11501, 11601, 11701, 11801, 11901, 12001, 12101, 12301.
  - createAnnotation
```
public Annotation createAnnotation(QName qName,
                                   QName nestedQName,
                                   String nestedId,
                                   List<Annotation> annotations)
                            throws SBOLValidationException
```
    Creates an annotation with nested annotations using the given arguments, and then adds to this instance's list of annotations.
    
    Parameters:
    
    qName - the QName of the annotation to be created
    
    nestedQName - the QName of the nested annotation
    
    nestedId - the id for the nested annotation
    
    annotations - the list of annotations used to construct the nested annotation
    
    Returns:
    
    the created annotation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10401, 10501, 10701, 10801, 10901, 11101, 11201, 11301, 11401, 11501, 11601, 11701, 11801, 11901, 12001, 12101, 12301.
  - removeAnnotation
```
public boolean removeAnnotation(Annotation annotation)
```
    Removes the given annotation from the list of annotations owned by this instance.
    
    Parameters:
    
    annotation - the annotation to be removed
    
    Returns:
    
    true if the matching annotation was removed successfully, or false otherwise.
  - getAnnotations
```
public List<Annotation> getAnnotations()
```
    Returns the list of annotations owned by this instance.
    
    Returns:
    
    the list of annotations owned by this instance.
  - getAnnotation
```
public Annotation getAnnotation(QName qName)
```
    Returns the annotation matching the given QName.
    
    Parameters:
    
    qName - the QName of the annotation to be retrieved
    
    Returns:
    
    the annotation matching the given QName
  - clearAnnotations
```
public void clearAnnotations()
```
    Removes all entries of this instance's list of annotations. The set will be empty after this call returns.
  - unsetWasDerivedFrom
```
@Deprecated
public void unsetWasDerivedFrom()
```
    Deprecated.
    
    Sets the wasDerivedFrom property to null.
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - isSetName
```
public boolean isSetName()
```
    Test if the name property is set.
    
    Returns:
    
    true if it is not null, or false otherwise
  - getName
```
public String getName()
```
    Returns the name property of this instance.
    
    Returns:
    
    the name property of this instance.
  - setName
```
public void setName(String name)
```
    Sets the name property for this instance.
    
    Parameters:
    
    name - the name property to set to
  - unsetName
```
public void unsetName()
```
    Sets the name of this instance to null.
  - isSetDescription
```
public boolean isSetDescription()
```
    Test if the description property is set.
    
    Returns:
    
    true if it is not null, or false otherwise
  - getDescription
```
public String getDescription()
```
    Returns the description property of this instance.
    
    Returns:
    
    the description property of this instance.
  - setDescription
```
public void setDescription(String description)
```
    Sets the description property for this instance.
    
    Parameters:
    
    description - the description to set to
  - unsetDescription
```
public void unsetDescription()
```
    Sets the description property to null.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class Identified

Method Summary

Methods inherited from class java.lang.Object

Method Detail

getIdentity

isSetPersistentIdentity

getPersistentIdentity

isSetVersion

isSetWasDerivedFrom

getVersion

isSetDisplayId

getDisplayId

addWasDerivedFrom

removeWasDerivedFrom

containsWasDerivedFrom

clearWasDerivedFroms

getWasDerivedFroms

getWasDerivedFrom

setWasDerivedFrom

setWasDerivedFroms

addWasGeneratedBy

removeWasGeneratedBy

containsWasGeneratedBy

clearWasGeneratedBys

getWasGeneratedBys

setWasGeneratedBys

hasAnnotations

createAnnotation

createAnnotation

createAnnotation

createAnnotation

createAnnotation

createAnnotation

removeAnnotation

getAnnotations

getAnnotation

clearAnnotations

unsetWasDerivedFrom

hashCode

equals

isSetName

getName

setName

unsetName

isSetDescription

getDescription

setDescription

unsetDescription

toString