Interface AnnotationType
- All Known Implementing Classes:
AnnotationType.Abstract
,AnnotationType.Impl
Annotation
.
AnnotationType
instances can be used to validate an
Annotation
to check that it has the appropriate
properties and that they are of the right type.
Common Usage
// annType is going to define ID as being a single String and // AC as being a list of Strings and accept any other properties at all AnnotationType annType = new AnnotationType.Impl(); annType.setDefaultConstraints(PropertyConstraint.ANY, Cardinality.ANY) annType.setConstraints("ID", new PropertyConstraint.ByClass(String.class), CardinalityConstraint.ONE ); annType.setConstraint("AC", new PropertyConstraint.ByClass(String.class), CardinalityConstraint.ANY ); Annotation ann = ...; if(annType.accepts(ann)) { // we have proved that ann contains one ID property that is a String System.out.println("ID: " + (String) ann.getProperty("ID")); // we know that the AC property is potentialy more than one String - // let's use getProperty on AnnotationType to make sure that the // values get unpacked cleanly System.out.println("AC:"); for(Iterator i = annType.getProperty(ann, "AC"); i.hasNext(); ) { System.out.println("\t" + (String) i.next()); } } else { throw new IllegalArgumentException( "Expecting an annotation conforming to: " annType + " but got: " + ann ); }
Description
AnnotationType is a constraint-based language for describing sets of Annotation bundles. It works by assuming that any given Annotation may have any set of properties defined. If it matches a particular AnnotationType instance, then each defined property must be of a value that is acceptable to the type, and each undefined property must be allowed to be absend in the type.
AnnotationType
imposes a data model on Annotations
where the value of each `slot' is considered as a Collection
.
Values which aren't actually Collection
instances are treated
as singleton sets. Undefined properties are treated as Collection.EMPTY_SET
.
The logic to validate a complete slot in an Annotation
is
encapsulated by a CollectionConstraint
object. In the common case,
slots are validated by CollectionConstraint.AllValuesIn
which
ensures that all members of the collection match a specified PropertyConstraint
,
and that the size of the collection matches a cardinality constraint. This is the
most important type of constraint when defining datatypes. However, when using
AnnotationTypes
to specify a query over a set of Annotations, it may be more
useful to ask whether a slot contains a given value: For example
// Test that gene_name contains the value "BRCA2", ignoring other values (synonyms) // which might be present in that slot. AnnotationType at = new AnnotationType.Impl(); at.setConstraint( "gene_name", new CollectionConstraint.Contains( new PropertyConstraint.ExactValue("BRCA2"), CardinalityConstraint.ONE ) );
It is usually left up to the AnnotationType instance to work out how multiple values should be packed into a single property slot in an Annotation instance. Commonly, things that are allowed a cardinality of 1 will store one value directly in the slot. Things that allow multiple values (and optionaly things with one value) will usualy store them within a Collection in the slot. This complexity is hidden from you if you use the accessor methods built into AnnotationType, setProperty(), addProperty(), removeProperty() and getProperty().
Using AnnotationType instances that you have been provided with e.g. from UnigeneTools.LIBRARY_ANNOTATIONAnnotationType
instances can be used as queries
to select from a set of Annotations based on the value of one
or more properties. Commonly, this is used in conjunction
with FeatureFilter.ByAnnotationType
.
Make AnnotationType instances that describe what should and
should not appear in an Annotation bundle
Constrain FeatureFilter schemas by Annotation associated with
the features
Provide meta-data to the tag-value parser for automatically
generating object representations of flat-files
Implementing your own AnnotationType implementations to reflect
frame, schema or ontology definitions. For example, dynamically
reflect an RDMBS schema or DAML/Oil deffinition as an
AnnotationType.- Since:
- 1.3
- Author:
- Matthew Pocock, Keith James (docs), Thomas Down
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic class
An abstract base class useful for implementing AnnotationType instances.static class
An implementation ofAnnotationType
. -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final AnnotationType
The type that accepts all annotations and is the supertype of all other annotations.static final AnnotationType
The type that accepts no annotations at all and is the subtype of all other annotations. -
Method Summary
Modifier and TypeMethodDescriptionvoid
addProperty
(Annotation ann, Object property, Object value) Add a value to the specified property slot.Get the comment for the whole AnnotationType.getComment
(Object property) Get the comment for a particular property.getConstraint
(Object key) Retrieve the constraint that will be applied to all properties with a given key.Get the CollectionConstraint that will be applied to all properties without an explicit binding.Retrieve the set of properties for which constraints have been explicity specified.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 property, Object value) Remove a value from the specified property slot.void
setComment
(Object property, String comment) Set the comment for a particular property.void
setComment
(String comment) Set the comment for the whole AnnotationType.void
setConstraint
(Object key, CollectionConstraint con) Specifies the constraint to apply to the specified property.void
setConstraints
(Object key, PropertyConstraint con, Location card) Set the constraints associated with a property.void
Specifies the default constraint to apply to properties where no other constraint is specified.void
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.
-
Field Details
-
ANY
The type that accepts all annotations and is the supertype of all other annotations. Only an empty annotation is an exact instance of this type. Use this whenever an AnnotationType is needed by an API and you don't want to constrain anything -
NONE
The type that accepts no annotations at all and is the subtype of all other annotations. Use this whenever an AnnotationType is needed by an API and you want to make sure that all Annotation objects get rejected
-
-
Method Details
-
instanceOf
Validate an Annotation against this AnnotationType. Any time you wish to see if an Annotation bundle conforms to a type- Parameters:
ann
- the Annotation to validate.- Returns:
- true if ann conforms to this type and false if it doesn't.
-
subTypeOf
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.
- Parameters:
subType
- an AnnotationType to check.- Returns:
- true if subType is a sub-type of this type.
-
getConstraint
Retrieve the constraint that will be applied to all properties with a given key.
For an
If you want to find out exactly what constraints will be applied to a particular propery keyAnnotation
to be accepted, each key in getProperties() must be present in the annotation and each of the values associated with those properties must match the constraint.- Parameters:
key
- the property to be validated.- Returns:
- PropertyConstraint the constraint by which the values must be accepted.
-
setConstraints
Set the constraints associated with a property. This method constrains the value of the specified property such that all members must matchcon
, and the number of members must matchcard
. It implicitly constructs aCollectionConstraint.AllValuesIn
instance.When you are building your own AnnotationType
- Parameters:
key
- the name of the property to constraincon
- the PropertyConstraint to enforcecard
- the CardinalityConstraint to enforce
-
setConstraint
Specifies the constraint to apply to the specified property.- Parameters:
key
- the name of the property to constraincon
- the constraint to apply to this slot.
-
setDefaultConstraints
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 matchcon
, and the number of members must matchcard
. It implicitly constructs aCollectionConstraint.AllValuesIn
instance.- Parameters:
pc
- the default PropertyConstraintcc
- the default CardinalityConstraint
-
setDefaultConstraint
Specifies the default constraint to apply to properties where no other constraint is specified.- Parameters:
cc
- The default constraint.
-
getDefaultConstraint
Get the CollectionConstraint that will be applied to all properties without an explicit binding. This defaults to CollectionConstraint.ALL.If you want to find out exactly what constraint will be applied to properties with no explicitly defined constraints
- Returns:
- the default CollectionConstraint
-
getProperties
Retrieve the set of properties for which constraints have been explicity specified. Discover which properties have explicit constraints- Returns:
- the Set of properties to validate.
-
setProperty
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.- Parameters:
ann
- the Annotation to modifyproperty
- the property key Objectvalue
- 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
-
addProperty
Add a value to the specified property slot.- Parameters:
ann
- the Annotation to modifyproperty
- the property key Objectvalue
- 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
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.- Parameters:
ann
- the Annotation to accessproperty
- the property key Object- Returns:
- a Collection of values
- Throws:
ChangeVetoException
- if the value could not be removed
-
removeProperty
Remove a value from the specified property slot.- Parameters:
ann
- the Annotation to modifyproperty
- the property key Objectvalue
- the property value Object- Throws:
ChangeVetoException
- if the Annotation could not be modified
-
setComment
Set the comment for the whole AnnotationType. This is human-readable text.- Parameters:
comment
- the new comment
-
getComment
Get the comment for the whole AnnotationType. This is human-readable text.- Returns:
- the comment
-
setComment
Set the comment for a particular property. This is a human-readable description of the property.- Parameters:
property
- the property to comment oncomment
- the comment
-
getComment
Get the comment for a particular property. This is a human-readable description of the property.- Parameters:
property
- the property to get a comment for- Returns:
- the comment
-