org.biopax.paxtools.controller

Class PathAccessor

java.lang.Object

org.biopax.paxtools.controller.PropertyAccessorAdapter<BioPAXElement,Object>

org.biopax.paxtools.controller.PathAccessor

All Implemented Interfaces:

PropertyAccessor<BioPAXElement,Object>

public class PathAccessor
extends PropertyAccessorAdapter<BioPAXElement,Object>

This class is a composite property accessor that allows users to chain multiple property accessors to define paths in the BioPAX object graph. The path can be defined by either explicitly providing a set of property accessors or by an xPath like syntax. The path can contain transitive and or restricted sub paths: A transitive sub-path is traversed recursively as many times as possible. e.g. Complex/component* will return all components of the complex and the components of the components if those components are complex recursively. A restricted subpath is restricted with a class and only follows through the domains that are assignable from the the restriction class. e.g. Control/controlled:Pathway/name will only return the names of the pathways that are being controlled, but not interactions.

Field Summary

Fields

Modifier and Type	Field and Description
static org.apache.commons.logging.Log	log

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

multipleCardinality, range

Constructor Summary

Constructors

Constructor and Description
PathAccessor(List<PropertyAccessor<? extends BioPAXElement,?>> objectAccessors, BioPAXLevel level) Constructor for defining the access path with a list of accessors.
PathAccessor(String path) This constructor defaults to BioPAX Level 3.
PathAccessor(String path, BioPAXLevel level) Constructor for defining the access path via a XPath like string.

Method Summary

Modifier and Type	Method and Description
boolean	applies(BioPAXElement bpe)
Set	getValueFromBean(BioPAXElement bean) Returns the value of the bean using the default getMethod.
Set	getValueFromBeans(Collection<? extends BioPAXElement> beans) Returns the values for a collection of beans using the default getMethod.
Set	getValueFromModel(Model model) This method runs the path query on all the elements within the model.
boolean	isUnknown(Object value) Checks if the value is unkown.

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

getDomain, getRange, isMultipleCardinality

Methods inherited from class java.lang.Object

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

Field Detail

log

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

Constructor Detail

PathAccessor

public PathAccessor(List<PropertyAccessor<? extends BioPAXElement,?>> objectAccessors,
                    BioPAXLevel level)

Constructor for defining the access path with a list of accessors. All of the accessors must be of the same level. In the case one accessor's range can not be assigned by the domain of the next( broken path), this accessor will return an empty set.

Parameters:

objectAccessors - A list of object accessors.

level - biopax level

PathAccessor

public PathAccessor(String path,
                    BioPAXLevel level)

Constructor for defining the access path via a XPath like string.

Parameters:

path - The string defining the path. The following operators can be used:

• The first token is the class name of the starting domain.
• The next tokens are names of the properties, separated by "/"
• A property step can be restricted to a domain by defining the restriction class with ":" after the property
• A property step can be declared transitive by adding a "*" at the end.
• Two accessors can be joined by "|" (Currently not implemented)
• A subpath can be defined by a substring enclosed in "(" ")"
• Subpaths can also be restricted or made transitive

level - BioPAX level that this path is defined in.

PathAccessor

public PathAccessor(String path)

This constructor defaults to BioPAX Level 3.

Parameters:

path - The string defining the path. The following operators can be used:

• The first token is the class name of the starting domain.
• The next tokens are names of the properties, separated by "/"
• A property step can be restricted to a domain by defining the restriction class with ":" after the property
• A property step can be declared transitive by adding a "*" at the end.
• Two accessors can be joined by "|" (Currently not implemented)
• A subpath can be defined by a substring enclosed in "(" ")"
• Subpaths can also be restricted or made transitive

Method Detail

getValueFromBean

public Set getValueFromBean(BioPAXElement bean)
                     throws IllegalBioPAXArgumentException

Description copied from interface: PropertyAccessor

Returns the value of the bean using the default getMethod.

Parameters:

bean - the object whose property is requested

Returns:

an object as the value

Throws:

IllegalBioPAXArgumentException

getValueFromBeans

public Set getValueFromBeans(Collection<? extends BioPAXElement> beans)
                      throws IllegalBioPAXArgumentException

Description copied from interface: PropertyAccessor

Returns the values for a collection of beans using the default getMethod.

Specified by:

getValueFromBeans in interface PropertyAccessor<BioPAXElement,Object>

Overrides:

getValueFromBeans in class PropertyAccessorAdapter<BioPAXElement,Object>

Parameters:

beans - collection of BioPAX objects

Returns:

an object as the value

Throws:

IllegalBioPAXArgumentException

getValueFromModel

public Set getValueFromModel(Model model)

This method runs the path query on all the elements within the model.

Parameters:

model - to be queried

Returns:

a merged set of all values that is reachable by the paths starting from all applicable objects in the model. For example running ProteinReference/xref:UnificationXref on the model will get all the unification xrefs of all ProteinReferences.

isUnknown

public boolean isUnknown(Object value)

Description copied from interface: PropertyAccessor

Checks if the value is unkown. In this context a value is regarded to be unknown if it is null (unset).

Parameters:

value - the value to be checked

Returns:

true if the value is unknown

applies

public boolean applies(BioPAXElement bpe)

Parameters:

bpe - BioPAXElement to be checked.

Returns:

true if bpe is an instance of the domain of this accessor.