org.sbolstandard.core2

Class Annotation

java.lang.Object

org.sbolstandard.core2.Annotation

All Implemented Interfaces:

Comparable<Annotation>

public class Annotation
extends Object
implements Comparable<Annotation>

Represents an Annotation object in the cSBOL data model.

Version:

2.1

Author:

Zhen Zhang, Matthew Pocock, Goksel Misirli, Chris Myers

Constructor Summary

Constructors

Constructor and Description
Annotation(QName qName, boolean literal) Constructs an annotation using the given qName and the boolean type literal.
Annotation(QName qName, double literal) Constructs an annotation using the given qName and the double type literal.
Annotation(QName qName, int literal) Constructs an annotation using the given qName and the integer type literal.
Annotation(QName qName, String literal) Constructs an annotation using the given qName and the string type literal.
Annotation(QName qName, URI literal) Constructs an annotation using the given qName and the URI type literal.

Method Summary

Modifier and Type	Method and Description
int	compareTo(Annotation annotation)
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.
boolean	equals(Object obj)
List<Annotation>	getAnnotations() Returns the list of Annotations of the nested value property.
Boolean	getBooleanValue() Returns a Boolean representation of the value property.
Double	getDoubleValue() Returns a Double representation of the value property.
Integer	getIntegerValue() Returns an Integer representation of the value property.
URI	getNestedIdentity() Returns the nested identity URI of the nested Annotation.
QName	getNestedQName() Returns the nested QName of the nested Annotation.
QName	getQName() Returns the QName of this Annotation instance.
String	getStringValue() Returns a string representation of the value property.
URI	getURIValue() Returns a URI representation of the value property.
int	hashCode()
boolean	isBooleanValue() Checks if the annotation has a boolean value property.
boolean	isDoubleValue() Checks if the annotation has a double value property.
boolean	isIntegerValue() Checks if the annotation has an integer value property.
boolean	isNestedAnnotations() Checks if the annotation has a nested value property.
boolean	isStringValue() Checks if the annotation has a string value property.
boolean	isURIValue() Checks if the annotation is a URI value property.
void	setAnnotations(List<Annotation> annotations) Sets the list of Annotations of the nested value property.
void	setBooleanValue(boolean literal) Sets the boolean representation of the value property.
void	setDoubleValue(double literal) Sets the double representation of the value property.
void	setIntegerValue(int literal) Sets the integer representation of the value property.
void	setNestedIdentity(URI uri) Sets the nested URI for this annotation.
void	setNestedQName(QName qName) Sets the nested QName for this annotation.
void	setQName(QName qName) Sets the QName of this annotation.
void	setStringValue(String literal) Sets the string representation of the value property.
void	setURIValue(URI literal) Sets the string representation of the value property.
String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Annotation

public Annotation(QName qName,
                  String literal)
           throws SBOLValidationException

Constructs an annotation using the given qName and the string type literal.

Parameters:

qName - the QName of this annotation

literal - a string type value

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12201, 12203

Annotation

public Annotation(QName qName,
                  int literal)
           throws SBOLValidationException

Constructs an annotation using the given qName and the integer type literal.

Parameters:

qName - the QName of this annotation

literal - an integer type value

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12201, 12203

Annotation

public Annotation(QName qName,
                  double literal)
           throws SBOLValidationException

Constructs an annotation using the given qName and the double type literal.

Parameters:

qName - the QName of this annotation

literal - a double type value

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12201, 12203

Annotation

public Annotation(QName qName,
                  boolean literal)
           throws SBOLValidationException

Constructs an annotation using the given qName and the boolean type literal.

Parameters:

qName - the QName of this annotation

literal - a boolean type value

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12201, 12203

Annotation

public Annotation(QName qName,
                  URI literal)
           throws SBOLValidationException

Constructs an annotation using the given qName and the URI type literal.

Parameters:

qName - the QName of this annotation

literal - a URI type value

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12201, 12203

Method Detail

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.

compareTo

public int compareTo(Annotation annotation)

Specified by:

compareTo in interface Comparable<Annotation>

getQName

public QName getQName()

Returns the QName of this Annotation instance.

Returns:

the QName of this Annotation instance

setQName

public void setQName(QName qName)
              throws SBOLValidationException

Sets the QName of this annotation.

Parameters:

qName - the QName for this annotation.

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12201

setBooleanValue

public void setBooleanValue(boolean literal)

Sets the boolean representation of the value property.

Parameters:

literal - the boolean representation of the value property

isBooleanValue

public boolean isBooleanValue()

Checks if the annotation has a boolean value property.

Returns:

true if the value property is a boolean, false otherwise.

getBooleanValue

public Boolean getBooleanValue()

Returns a Boolean representation of the value property.

Returns:

a Boolean representation of the value property if its value is a Boolean, null otherwise.

setDoubleValue

public void setDoubleValue(double literal)

Sets the double representation of the value property.

Parameters:

literal - the double representation of the value property

isDoubleValue

public boolean isDoubleValue()

Checks if the annotation has a double value property.

Returns:

true if the value property is a double integer, false otherwise

getDoubleValue

public Double getDoubleValue()

Returns a Double representation of the value property.

Returns:

a Double integer representation of the value property if its value is a Double integer, null otherwise.

setIntegerValue

public void setIntegerValue(int literal)

Sets the integer representation of the value property.

Parameters:

literal - the integer representation of the value property

isIntegerValue

public boolean isIntegerValue()

Checks if the annotation has an integer value property.

Returns:

true if the value property is an integer, false otherwise

getIntegerValue

public Integer getIntegerValue()

Returns an Integer representation of the value property.

Returns:

an Integer representation of the value property if its value is an Integer, null otherwise.

setStringValue

public void setStringValue(String literal)
                    throws SBOLValidationException

Sets the string representation of the value property.

Parameters:

literal - the string representation of the value property

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12203

isStringValue

public boolean isStringValue()

Checks if the annotation has a string value property.

Returns:

true if the value property is string type, false otherwise

getStringValue

public String getStringValue()

Returns a string representation of the value property.

Returns:

a string representation of the value property if it is a string, null otherwise.

setURIValue

public void setURIValue(URI literal)
                 throws SBOLValidationException

Sets the string representation of the value property.

Parameters:

literal - the URI representation of the value property

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12203

isURIValue

public boolean isURIValue()

Checks if the annotation is a URI value property.

Returns:

true if the annotation is a URI value property.

getURIValue

public URI getURIValue()

Returns a URI representation of the value property.

Returns:

a URI representation of the value property if it is a URI, null otherwise.

setNestedQName

public void setNestedQName(QName qName)
                    throws SBOLValidationException

Sets the nested QName for this annotation.

Parameters:

qName - the nested QName for this annotation.

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12204

getNestedQName

public QName getNestedQName()

Returns the nested QName of the nested Annotation.

Returns:

the nested QName if its value is nested Annotations, null otherwise.

getNestedIdentity

public URI getNestedIdentity()

Returns the nested identity URI of the nested Annotation.

Returns:

the nested identity URI of the nested nested Annotations if its value is nested Annotations, null otherwise.

setNestedIdentity

public void setNestedIdentity(URI uri)
                       throws SBOLValidationException

Sets the nested URI for this annotation.

Parameters:

uri - the nested uri for this annotation.

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12205

isNestedAnnotations

public boolean isNestedAnnotations()

Checks if the annotation has a nested value property.

Returns:

true if the value property is nested Annotations, false otherwise

setAnnotations

public void setAnnotations(List<Annotation> annotations)
                    throws SBOLValidationException

Sets the list of Annotations of the nested value property.

Parameters:

annotations - the list of Annotations for the nested value property.

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 12206

getAnnotations

public List<Annotation> getAnnotations()

Returns the list of Annotations of the nested value property.

Returns:

the list of Annotations if its value is nested Annotations, null otherwise.

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object