org.biopax.paxtools.controller

Class AbstractPropertyEditor<D extends BioPAXElement,R>

java.lang.Object

org.biopax.paxtools.controller.PropertyAccessorAdapter<D,R>

org.biopax.paxtools.controller.SimplePropertyAccessor<D,R>

org.biopax.paxtools.controller.AbstractPropertyEditor<D,R>

All Implemented Interfaces:

PropertyAccessor<D,R>, PropertyEditor<D,R>

Direct Known Subclasses:

EnumeratedPropertyEditor, ObjectPropertyEditor, PrimitivePropertyEditor, StringPropertyEditor

public abstract class AbstractPropertyEditor<D extends BioPAXElement,R>
extends SimplePropertyAccessor<D,R>
implements PropertyEditor<D,R>

This is the base class for all property editors. Each property controller is responsible for manipulating a certain property for a given class of objects (domain).

Field Summary

Fields

Modifier and Type	Field and Description
protected Method	addMethod This variable stores the method to invoke for adding the given value to the property managed by this commander.
static ThreadLocal<Boolean>	checkRestrictions
protected static org.apache.commons.logging.Log	log
protected String	property Local OWL name of the property
protected Method	removeMethod This variable stores the method for removing the value of the property on a given bean.
protected Method	setMethod This variable stores the method to invoke for setting a property to the to the given value.

Fields inherited from class org.biopax.paxtools.controller.SimplePropertyAccessor

getMethod

Fields inherited from class org.biopax.paxtools.controller.PropertyAccessorAdapter

domain, multipleCardinality, range

Constructor Summary

Constructors

Constructor and Description
AbstractPropertyEditor(String property, Method getMethod, Class<D> domain, Class<R> range, boolean multipleCardinality) Constructor.

Method Summary

Modifier and Type	Method and Description
void	addMaxCardinalityRestriction(Class<? extends D> domain, int max) Sets a maximum cardinality for a domain.
protected void	checkRestrictions(R value, D bean) Checks if the bean and the value are consistent with the cardinality rules of the model.
static <D extends BioPAXElement,R> PropertyEditor<D,R>	createPropertyEditor(Class<D> domain, String property) This method creates a property reflecting on the domain and property.
protected static Class	detectRange(Method getMethod) Given the multiple cardinality feature, the range of the get method is returned.
Method	getAddMethod()
Method	getGetMethod()
Integer	getMaxCardinality(Class<? extends D> restrictedDomain) Return the maximum cardinality that is defined for the property to which editor is belong.
Method	getPrimarySetMethod() Returns the primary set method of the editor.
String	getProperty()
Method	getRemoveMethod()
Method	getSetMethod()
R	getUnknown() Gets the unknown value.
protected void	invokeMethod(Method method, D bean, R value) Calls the method onto bean with the value as its parameter.
protected boolean	isInstanceOfAtLeastOne(Set<Class<? extends BioPAXElement>> classes, Object value) Checks if value is an instance of one of the classes given in a set.
protected R	parseValueFromString(String value)
void	removeValueFromBean(R value, D bean) Removes the value from the bean using the default removeMethod, if such method is defined (i.e., it's a multiple cardinality property), otherwise sets unknown value using PropertyEditor.setValueToBean(Object, org.biopax.paxtools.model.BioPAXElement) (but only if )
void	removeValueFromBean(Set<R> values, D bean) Removes the values from the bean using the PropertyEditor.removeValueFromBean(Object, org.biopax.paxtools.model.BioPAXElement) for each value in the set.
void	setValueToBean(R value, D bean) Sets the value to the bean using the default setMethod if value is not null.
void	setValueToBean(Set<R> values, D bean)
String	toString()

Methods inherited from class org.biopax.paxtools.controller.SimplePropertyAccessor

getValueFromBean, isMultipleCardinality, isUnknown

Methods inherited from class org.biopax.paxtools.controller.PropertyAccessorAdapter

getDomain, getRange, getValueFromBeans, isMultipleCardinality

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biopax.paxtools.controller.PropertyAccessor

getDomain, getRange, getValueFromBean, getValueFromBeans, isMultipleCardinality, isUnknown

Field Detail

log

protected static final org.apache.commons.logging.Log log

setMethod

protected Method setMethod

This variable stores the method to invoke for setting a property to the to the given value. If multiple cardinality, the returned method is expected to have a Set as its only parameter.

addMethod

protected Method addMethod

This variable stores the method to invoke for adding the given value to the property managed by this commander. In the case of multiple cardinality, the method is expected to have a PropertyAccessorAdapter.range as its only parameter, otherwise expected to be null.

removeMethod

protected Method removeMethod

This variable stores the method for removing the value of the property on a given bean. In the case of multiple cardinality, this method is expected to have a PropertyAccessorAdapter.range as its only parameter, otherwise expected to be null

property

protected final String property

Local OWL name of the property

checkRestrictions

public static ThreadLocal<Boolean> checkRestrictions

Constructor Detail

AbstractPropertyEditor

public AbstractPropertyEditor(String property,
                              Method getMethod,
                              Class<D> domain,
                              Class<R> range,
                              boolean multipleCardinality)

Constructor.

Parameters:

property - biopax property name

getMethod - getter

domain - class the property belongs to

range - property values type/class

multipleCardinality - whether more than one value is allowed

Method Detail

toString

public String toString()

Specified by:

toString in interface PropertyEditor<D extends BioPAXElement,R>

Overrides:

toString in class SimplePropertyAccessor<D extends BioPAXElement,R>

createPropertyEditor

public static <D extends BioPAXElement,R> PropertyEditor<D,R> createPropertyEditor(Class<D> domain,
                                                                                   String property)

This method creates a property reflecting on the domain and property. Proper subclass is chosen based on the range of the property.

Type Parameters:

D - domain

R - range

Parameters:

domain - paxtools level2 interface that maps to the corresponding owl level2.

property - to be managed by the constructed controller.

Returns:

a property controller to manipulate the beans for the given property.

detectRange

protected static Class detectRange(Method getMethod)

Given the multiple cardinality feature, the range of the get method is returned.

Parameters:

getMethod - default method

Returns:

the range as a class

getAddMethod

public Method getAddMethod()

Specified by:

getAddMethod in interface PropertyEditor<D extends BioPAXElement,R>

Returns:

the add method.

getGetMethod

public Method getGetMethod()

Specified by:

getGetMethod in interface PropertyEditor<D extends BioPAXElement,R>

Returns:

the get method

getProperty

public String getProperty()

Specified by:

getProperty in interface PropertyEditor<D extends BioPAXElement,R>

Returns:

the proterty name as a string

getRemoveMethod

public Method getRemoveMethod()

Specified by:

getRemoveMethod in interface PropertyEditor<D extends BioPAXElement,R>

Returns:

the remove method

getSetMethod

public Method getSetMethod()

Specified by:

getSetMethod in interface PropertyEditor<D extends BioPAXElement,R>

Returns:

the set method

addMaxCardinalityRestriction

public void addMaxCardinalityRestriction(Class<? extends D> domain,
                                         int max)

Description copied from interface: PropertyEditor

Sets a maximum cardinality for a domain.

Specified by:

addMaxCardinalityRestriction in interface PropertyEditor<D extends BioPAXElement,R>

Parameters:

domain - domain on which restriction will be set

max - cardinality

See Also:

PropertyAccessor.isMultipleCardinality()

getMaxCardinality

public Integer getMaxCardinality(Class<? extends D> restrictedDomain)

Description copied from interface: PropertyEditor

Return the maximum cardinality that is defined for the property to which editor is belong.

Specified by:

getMaxCardinality in interface PropertyEditor<D extends BioPAXElement,R>

Parameters:

restrictedDomain - domain to be checked for the cardinality

Returns:

an integer indicating the maximum cardinality

isInstanceOfAtLeastOne

protected boolean isInstanceOfAtLeastOne(Set<Class<? extends BioPAXElement>> classes,
                                         Object value)

Checks if value is an instance of one of the classes given in a set. This method becomes useful, when the restrictions have to be checked for a set of objects. e.g. check if the value is in the range of the editor.

Parameters:

classes - a set of classes to be checked

value - value whose class will be checked

Returns:

true if value belongs to one of the classes in the set

getUnknown

public R getUnknown()

Description copied from interface: PropertyEditor

Gets the unknown value. In an object property or enumeration context a value is regarded to be unknown if it is null (unset); in a primitive property context it depends (can be e.g., BioPAXElement.UNKNOWN_FLOAT)

Specified by:

getUnknown in interface PropertyEditor<D extends BioPAXElement,R>

Returns:

null or what it means that the property value is unknown

removeValueFromBean

public void removeValueFromBean(R value,
                                D bean)

Description copied from interface: PropertyEditor

Removes the value from the bean using the default removeMethod, if such method is defined (i.e., it's a multiple cardinality property), otherwise sets unknown value using PropertyEditor.setValueToBean(Object, org.biopax.paxtools.model.BioPAXElement) (but only if )

Specified by:

removeValueFromBean in interface PropertyEditor<D extends BioPAXElement,R>

Parameters:

value - to be removed from the bean

bean - bean from which the value is going to be removed

removeValueFromBean

public void removeValueFromBean(Set<R> values,
                                D bean)

Description copied from interface: PropertyEditor

Removes the values from the bean using the PropertyEditor.removeValueFromBean(Object, org.biopax.paxtools.model.BioPAXElement) for each value in the set.

Specified by:

removeValueFromBean in interface PropertyEditor<D extends BioPAXElement,R>

Parameters:

values - to be removed from the bean

bean - bean from which the value is going to be removed

invokeMethod

protected void invokeMethod(Method method,
                            D bean,
                            R value)

Calls the method onto bean with the value as its parameter. In this context method can be one of these three: set, add, or remove.

Parameters:

method - method that is going to be called

bean - bean onto which the method is going to be applied

value - the value which is going to be used by method

parseValueFromString

protected R parseValueFromString(String value)

setValueToBean

public void setValueToBean(R value,
                           D bean)

Description copied from interface: PropertyEditor

Sets the value to the bean using the default setMethod if value is not null.

Specified by:

setValueToBean in interface PropertyEditor<D extends BioPAXElement,R>

Parameters:

value - to be set to the bean

bean - to which the value is to be set

setValueToBean

public void setValueToBean(Set<R> values,
                           D bean)

Specified by:

setValueToBean in interface PropertyEditor<D extends BioPAXElement,R>

checkRestrictions

protected void checkRestrictions(R value,
                                 D bean)

Checks if the bean and the value are consistent with the cardinality rules of the model. This method is important for validations.

Parameters:

value - Value that is related to the object

bean - Object that is related to the value

getPrimarySetMethod

public Method getPrimarySetMethod()

Description copied from interface: PropertyEditor

Returns the primary set method of the editor. It is the setMethod for a property of single cardinality, and the addMethod method for a property of multiple cardinality.

Specified by:

getPrimarySetMethod in interface PropertyEditor<D extends BioPAXElement,R>

Returns:

the method to be primarily used for setting a value to an object.