org.biojava.bio

Class AnnotationType.Abstract

java.lang.Object

org.biojava.bio.AnnotationType.Abstract

All Implemented Interfaces:

AnnotationType

Direct Known Subclasses:

AnnotationType.Impl

Enclosing interface:

AnnotationType

public abstract static class AnnotationType.Abstract
extends Object
implements AnnotationType

An abstract base class useful for implementing AnnotationType instances.

This provides deffinitions for the logical operators (validate(), subTypeOf()), the mutators (setProperty(), getProperty() and deleteProperty()) and toString() that you may not want to write yourself. It leaves the data-related methods up to you.

Since:

1.3

Author:

Matthew Pocock, Thomas Down

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.AnnotationType

AnnotationType.Abstract, AnnotationType.Impl

Field Summary

Fields inherited from interface org.biojava.bio.AnnotationType

ANY, NONE

Constructor Summary

Constructors

Constructor and Description
AnnotationType.Abstract()

Method Summary

Methods

Modifier and Type	Method and Description
void	addProperty(Annotation ann, Object key, Object value) Add a value to the specified property slot.
Collection	getProperty(Annotation ann, Object property) Get the Collection of values associated with an Annotation bundle according to the type we believe it to be.
boolean	instanceOf(Annotation ann) Validate an Annotation against this AnnotationType.
void	removeProperty(Annotation ann, Object key, Object value) Remove a value from the specified property slot.
void	setConstraints(Object key, PropertyConstraint pc, Location cc) Set the constraints associated with a property.
void	setDefaultConstraints(PropertyConstraint pc, Location cc) Set the constraints that will apply to all properties without an explicitly defined set of constraints.
void	setProperty(Annotation ann, Object property, Object value) Set the property in an annotation bundle according to the type we believe it should be.
boolean	subTypeOf(AnnotationType subType) See if an AnnotationType is a specialisation of this type.
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.bio.AnnotationType

getComment, getComment, getConstraint, getDefaultConstraint, getProperties, setComment, setComment, setConstraint, setDefaultConstraint

Constructor Detail

AnnotationType.Abstract

public AnnotationType.Abstract()

Method Detail

setConstraints

public void setConstraints(Object key,
                  PropertyConstraint pc,
                  Location cc)

Description copied from interface: AnnotationType

Set the constraints associated with a property. This method constrains the value of the specified property such that all members must match con, and the number of members must match card. It implicitly constructs a CollectionConstraint.AllValuesIn instance.

When you are building your own AnnotationType

Specified by:

setConstraints in interface AnnotationType

Parameters:

key - the name of the property to constrain

pc - the PropertyConstraint to enforce

cc - the CardinalityConstraint to enforce

setDefaultConstraints

public void setDefaultConstraints(PropertyConstraint pc,
                         Location cc)

Description copied from interface: AnnotationType

Set the constraints that will apply to all properties without an explicitly defined set of constraints. This method constrains the value of the specified property such that all members must match con, and the number of members must match card. It implicitly constructs a CollectionConstraint.AllValuesIn instance.

Specified by:

setDefaultConstraints in interface AnnotationType

Parameters:

pc - the default PropertyConstraint

cc - the default CardinalityConstraint

instanceOf

public boolean instanceOf(Annotation ann)

Description copied from interface: AnnotationType

Validate an Annotation against this AnnotationType. Any time you wish to see if an Annotation bundle conforms to a type

Specified by:

instanceOf in interface AnnotationType

Parameters:

ann - the Annotation to validate.

Returns:

true if ann conforms to this type and false if it doesn't.

setProperty

public final void setProperty(Annotation ann,
               Object property,
               Object value)
                       throws ChangeVetoException

Description copied from interface: AnnotationType

Set the property in an annotation bundle according to the type we believe it should be. This will take care of any neccisary packing or unpacking to Collections.

Specified by:

setProperty in interface AnnotationType

Parameters:

ann - the Annotation to modify

property - the property key Object

value - the property value Object

Throws:

ChangeVetoException - if the value could not be accepted by this annotation type for that property key, or if the Annotation could not be modified

getProperty

public final Collection getProperty(Annotation ann,
                     Object property)
                             throws ChangeVetoException

Description copied from interface: AnnotationType

Get the Collection of values associated with an Annotation bundle according to the type we believe it to be. This will take care of any neccisary packing or unpacking to Collections. Properties with no values will return empty Collections.

Specified by:

getProperty in interface AnnotationType

Parameters:

ann - the Annotation to access

property - the property key Object

Returns:

a Collection of values

Throws:

ChangeVetoException - if the value could not be removed

addProperty

public final void addProperty(Annotation ann,
               Object key,
               Object value)
                       throws ChangeVetoException

Description copied from interface: AnnotationType

Add a value to the specified property slot.

Specified by:

addProperty in interface AnnotationType

Parameters:

ann - the Annotation to modify

key - the property key Object

value - the property value Object

Throws:

ChangeVetoException - if the value could not be accepted by this annotation type for that property key, or if the Annotation could not be modified

removeProperty

public final void removeProperty(Annotation ann,
                  Object key,
                  Object value)
                          throws ChangeVetoException

Description copied from interface: AnnotationType

Remove a value from the specified property slot.

Specified by:

removeProperty in interface AnnotationType

Parameters:

ann - the Annotation to modify

key - the property key Object

value - the property value Object

Throws:

ChangeVetoException - if the Annotation could not be modified

toString

public String toString()

Overrides:

toString in class Object

subTypeOf

public boolean subTypeOf(AnnotationType subType)

Description copied from interface: AnnotationType

See if an AnnotationType is a specialisation of this type.

An AnnotationType is a sub-type if it restricts each of the properties of the super-type to a type that can be cast to the type in the super-type. Note that this is not always a cast in the pure Java sense; it may include checks on the number and type of members in collections or other criteria.

Specified by:

subTypeOf in interface AnnotationType

Parameters:

subType - an AnnotationType to check.

Returns:

true if subType is a sub-type of this type.