org.biopax.paxtools.controller

Enum SimpleEditorMap

java.lang.Object

java.lang.Enum<SimpleEditorMap>

org.biopax.paxtools.controller.SimpleEditorMap

All Implemented Interfaces:

Serializable, Comparable<SimpleEditorMap>, EditorMap

public enum SimpleEditorMap
extends Enum<SimpleEditorMap>
implements EditorMap

Provides a simple editor map for a level with a given factory. This class initializes 3 singletons( 1 for each level) from a tab delimited text resources that lists the properties and their domains. This is done to remove any dependencies to Jena. The recommended usage is to use the get(org.biopax.paxtools.model.BioPAXLevel) method.

Author:

Emek Demir

Enum Constant Summary

Enum Constants

Enum Constant and Description
L2
L3

Method Summary

Modifier and Type	Method and Description
static EditorMap	buildCustomEditorMap(BioPAXLevel level, InputStream stream)
static SimpleEditorMap	get(BioPAXLevel level) To obtain a copy of the editor map for the corresponding level, use the
<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.
Iterator<PropertyEditor>	iterator()
static SimpleEditorMap	valueOf(String name) Returns the enum constant of this type with the specified name.
static SimpleEditorMap[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

L2

public static final SimpleEditorMap L2

L3

public static final SimpleEditorMap L3

Method Detail

values

public static SimpleEditorMap[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (SimpleEditorMap c : SimpleEditorMap.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static SimpleEditorMap valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

get

public static SimpleEditorMap get(BioPAXLevel level)

To obtain a copy of the editor map for the corresponding level, use the

Parameters:

level - the BioPAX level

Returns:

SimpleEditorMap implementation for the BioPAX L2 or L3

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

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

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

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

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.

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

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

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(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.

iterator

public Iterator<PropertyEditor> iterator()

Specified by:

iterator in interface EditorMap

Returns:

An iterator over all the properties in this EditorMap

buildCustomEditorMap

public static EditorMap buildCustomEditorMap(BioPAXLevel level,
                                             InputStream stream)