org.biopax.paxtools.controller

Class EditorMapImpl

java.lang.Object

org.biopax.paxtools.controller.EditorMapImpl

All Implemented Interfaces:

EditorMap

public class EditorMapImpl
extends Object
implements EditorMap

This is the base adapter for all editor maps. A PropertyEditor is an object that can manipulate a certain property. Editor maps are responsible for initializing these editors and providing them. The default level is the latest official release of BioPAX.

Field Summary

Fields

Modifier and Type	Field and Description
protected Map<Class<? extends BioPAXElement>,Map<String,PropertyEditor>>	classToEditorMap A map from classes to their registered editors.
protected Map<Class<? extends BioPAXElement>,Set<PropertyEditor>>	classToEditorSet Another map to keep editors as a set rather than a map.
protected Map<Class<? extends BioPAXElement>,Set<ObjectPropertyEditor>>	classToInverseEditorMap A map from classes to their registered inverse editors
protected BioPAXLevel	level
protected Map<String,Set<PropertyEditor>>	propertyToEditorMap A map from property names to actual property editors.

Constructor Summary

Constructors

Constructor and Description
EditorMapImpl(BioPAXLevel level)

Method Summary

Modifier and Type	Method and Description
protected PropertyEditor	createAndRegisterBeanEditor(String pName, Class domain, Map<Class<? extends BioPAXElement>,Set<Class<? extends BioPAXElement>>> rRestrictions)
<D extends BioPAXElement> PropertyEditor<? super D,?>	getEditorForProperty(String property, Class<D> javaClass) This method returns the editor intended to handle property named property of a class (javaClass).
Set<PropertyEditor>	getEditorsForProperty(String property) This method returns the set of editors intended to handle property named property.
Set<PropertyEditor>	getEditorsOf(BioPAXElement bpe) This method returns the set of editors whose domain subsumes the class of given BioPAX element.
Set<PropertyEditor>	getEditorsOf(Class<? extends BioPAXElement> domain) This method returns the set of editors whose domain subsumes the given class
Set<ObjectPropertyEditor>	getInverseEditorsOf(BioPAXElement bpe) Properties in BioPAX specification is unidirectional.
Set<ObjectPropertyEditor>	getInverseEditorsOf(Class<? extends BioPAXElement> domain) Properties in BioPAX specification is unidirectional.
<E extends BioPAXElement> Set<? extends Class<E>>	getKnownSubClassesOf(Class<E> javaClass) Returns a set of sub classes of a given class.
BioPAXLevel	getLevel() Returns the BioPAX level for which editor map is created.
<D extends BioPAXElement> Set<PropertyEditor<? extends D,?>>	getSubclassEditorsForProperty(String property, Class<D> domain) This method returns the set of editors intended to handle property named property.
protected boolean	isInBioPAXNameSpace(String nameSpace)
Iterator<PropertyEditor>	iterator()
protected void	registerEditorsWithSubClasses(PropertyEditor editor, Class<? extends BioPAXElement> domain) This method registers an editor with sub classes - i.e.
protected void	registerModelClass(String localName) This method inserts the class into internal hashmaps and initializes the value collections.

Methods inherited from class java.lang.Object

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

Field Detail

propertyToEditorMap

protected final Map<String,Set<PropertyEditor>> propertyToEditorMap

A map from property names to actual property editors. Since EditorMap keeps a separate editor for each target class( This is necessary to be able to validate class specific restrictions without instanceof checks), values are set of editors.

classToEditorMap

protected final Map<Class<? extends BioPAXElement>,Map<String,PropertyEditor>> classToEditorMap

A map from classes to their registered editors.

classToInverseEditorMap

protected final Map<Class<? extends BioPAXElement>,Set<ObjectPropertyEditor>> classToInverseEditorMap

A map from classes to their registered inverse editors

classToEditorSet

protected final Map<Class<? extends BioPAXElement>,Set<PropertyEditor>> classToEditorSet

Another map to keep editors as a set rather than a map. This is a small efficiency tweak as editors are create once objects, query multiple times objects.

level

protected final BioPAXLevel level

Constructor Detail

EditorMapImpl

public EditorMapImpl(BioPAXLevel level)

Method Detail

getEditorsOf

public Set<PropertyEditor> getEditorsOf(BioPAXElement bpe)

Description copied from interface: EditorMap

This method returns the set of editors whose domain subsumes the class of given BioPAX element.

Specified by:

getEditorsOf in interface EditorMap

Parameters:

bpe - BioPAX element for which the available editors will be returned

Returns:

empty set if there are no such editors

getEditorsOf

public Set<PropertyEditor> getEditorsOf(Class<? extends BioPAXElement> domain)

Description copied from interface: EditorMap

This method returns the set of editors whose domain subsumes the given class

Specified by:

getEditorsOf in interface EditorMap

Parameters:

domain - BioPAX model interface for which the available editors will be returned

Returns:

empty set if there are no such editors

getInverseEditorsOf

public Set<ObjectPropertyEditor> getInverseEditorsOf(BioPAXElement bpe)

Description copied from interface: EditorMap

Properties in BioPAX specification is unidirectional. e.g. entityReference property that links a PhysicalEntity to EntityReference has no defined corresponding inverse property that links EntityReferences to their corresponding entities. Most OWL reasoners can query the inverse of a property at no additional cost, but for most OO implementations this would require an expensive O(n) lookup. An OO implementation requires keeping additional properties for efficiency purposes. Inverse editors are read-only editors that captures these "inverse" part of the bidirectional properties specifically implemented in Paxtools. They have the pattern PropertyNameOf e.g. entityReferenceOf.

Specified by:

getInverseEditorsOf in interface EditorMap

Parameters:

bpe - BioPAX element for which the available inverse editors will be returned.

Returns:

all inverse editors for this entity's class type.

getInverseEditorsOf

public Set<ObjectPropertyEditor> getInverseEditorsOf(Class<? extends BioPAXElement> domain)

Description copied from interface: EditorMap

Properties in BioPAX specification is unidirectional. e.g. entityReference property that links a PhysicalEntity to EntityReference has no defined corresponding inverse property that links EntityReferences to their corresponding entities. Most OWL reasoners can query the inverse of a property at no additional cost, but for most OO implementations this would require an expensive O(n) lookup. An OO implementation requires keeping additional properties for efficiency purposes. Inverse editors are read-only editors that captures these "inverse" part of the bidirectional properties specifically implemented in Paxtools. They have the pattern PropertyNameOf e.g. entityReferenceOf.

Specified by:

getInverseEditorsOf in interface EditorMap

Parameters:

domain - of the inverse property

Returns:

all inverse editors for this class type.

getEditorForProperty

public <D extends BioPAXElement> PropertyEditor<? super D,?> getEditorForProperty(String property,
                                                                                  Class<D> javaClass)

Description copied from interface: EditorMap

This method returns the editor intended to handle property named property of a class (javaClass). This editor can then be used to modify the property of an element of class javaClass. To put in other words, this methods returns the editor of which domain includes javaClass, and the editor that can handle the property.

Specified by:

getEditorForProperty in interface EditorMap

Type Parameters:

D - domain

Parameters:

property - name of the property for which editor will be called

javaClass - class of the element

Returns:

null if there is no such editor

getSubclassEditorsForProperty

public <D extends BioPAXElement> Set<PropertyEditor<? extends D,?>> getSubclassEditorsForProperty(String property,
                                                                                                  Class<D> domain)

Description copied from interface: EditorMap

This method returns the set of editors intended to handle property named property. This editor can then be used to modify the property of an element which is in editor's domain list. In other words, this methods returns the set of the editors that can handle the property. Editors are not filtered for a specific domain class.

Specified by:

getSubclassEditorsForProperty in interface EditorMap

Type Parameters:

D - domain biopax type

Parameters:

property - name of the property for which editor will be called

domain - biopax type/class the property belongs to

Returns:

empty set if there are no such editors

getEditorsForProperty

public Set<PropertyEditor> getEditorsForProperty(String property)

Description copied from interface: EditorMap

This method returns the set of editors intended to handle property named property. This editor can then be used to modify the property of an element which is in editor's domain list. In other words, this methods returns the set of the editors that can handle the property. Editors are not filtered for a specific domain class.

Specified by:

getEditorsForProperty in interface EditorMap

Parameters:

property - name of the property for which editor will be called

Returns:

empty set if there are no such editors

getKnownSubClassesOf

public <E extends BioPAXElement> Set<? extends Class<E>> getKnownSubClassesOf(Class<E> javaClass)

Description copied from interface: EditorMap

Returns a set of sub classes of a given class. This method can be used for class filtering methods.

Specified by:

getKnownSubClassesOf in interface EditorMap

Type Parameters:

E - biopax type (biopax object model interface)

Parameters:

javaClass - the class whose subclasses will be returned

Returns:

an empty set if there are no such editors

isInBioPAXNameSpace

protected boolean isInBioPAXNameSpace(String nameSpace)

createAndRegisterBeanEditor

protected PropertyEditor createAndRegisterBeanEditor(String pName,
                                                     Class domain,
                                                     Map<Class<? extends BioPAXElement>,Set<Class<? extends BioPAXElement>>> rRestrictions)

registerEditorsWithSubClasses

protected void registerEditorsWithSubClasses(PropertyEditor editor,
                                             Class<? extends BioPAXElement> domain)

This method registers an editor with sub classes - i.e. inserts the editor to the proper value in editor maps.

Parameters:

editor - to be registered

domain - a subclass of the editor's original domain.

registerModelClass

protected void registerModelClass(String localName)

This method inserts the class into internal hashmaps and initializes the value collections.

Parameters:

localName - of the BioPAX class.

iterator

public Iterator<PropertyEditor> iterator()

Specified by:

iterator in interface EditorMap

Returns:

An iterator over all the properties in this EditorMap

getLevel

public BioPAXLevel getLevel()

Description copied from interface: EditorMap

Returns the BioPAX level for which editor map is created. Different BioPAX levels have different editor maps.

Specified by:

getLevel in interface EditorMap

Returns:

BioPAX Level