org.biopax.paxtools.query.wrapperL3undirected

Class GraphL3Undirected

java.lang.Object

org.biopax.paxtools.query.model.AbstractGraph

org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected

All Implemented Interfaces:

Graph

public class GraphL3Undirected
extends AbstractGraph

Wrapper for L3 Graphs.

Author:

Ozgun Babur

Field Summary

Fields

Modifier and Type	Field and Description
protected List<Filter>	filters
protected org.apache.commons.logging.Log	log Log for logging.
protected Model	model The model to be wrapped.

Fields inherited from class org.biopax.paxtools.query.model.AbstractGraph

objectMap

Constructor Summary

Constructors

Constructor and Description
GraphL3Undirected(Model model, Filter... filters) Constructor with the model and the IDs of the ubiquitous molecules.

Method Summary

Modifier and Type	Method and Description
String	getKey(Object wrapped) RDF IDs of elements is used as key in the object map.
Model	getModel()
Set<Object>	getWrappedSet(Set<? extends GraphObject> wrappers) Gets the wrapped objects of the given wrappers.
Map<Object,Node>	getWrapperMap(Set<?> objects) Gets an element-to-wrapper map for the given elements.
Set<Node>	getWrapperSet(Set<?> objects) Gets wrappers of given elements
Node	wrap(Object obj) This method creates a wrapper for every wrappable L3 element.

Methods inherited from class org.biopax.paxtools.query.model.AbstractGraph

clear, getGraphObject, getGraphObject, getObjectMap

Methods inherited from class java.lang.Object

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

Field Detail

model

protected Model model

The model to be wrapped.

filters

protected List<Filter> filters

log

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

Log for logging.

Constructor Detail

GraphL3Undirected

public GraphL3Undirected(Model model,
                         Filter... filters)

Constructor with the model and the IDs of the ubiquitous molecules. IDs can be null, meaning no labeling is desired.

Parameters:

model - Model to wrap

filters - for filtering graph elements

Method Detail

wrap

public Node wrap(Object obj)

This method creates a wrapper for every wrappable L3 element.

Specified by:

wrap in class AbstractGraph

Parameters:

obj - Object to wrap

Returns:

The wrapper

getKey

public String getKey(Object wrapped)

RDF IDs of elements is used as key in the object map.

Specified by:

getKey in class AbstractGraph

Parameters:

wrapped - Object to wrap

Returns:

Key

getWrapperSet

public Set<Node> getWrapperSet(Set<?> objects)

Gets wrappers of given elements

Parameters:

objects - Wrapped objects

Returns:

wrappers

getWrapperMap

public Map<Object,Node> getWrapperMap(Set<?> objects)

Gets an element-to-wrapper map for the given elements.

Parameters:

objects - Wrapped objects

Returns:

object-to-wrapper map

getWrappedSet

public Set<Object> getWrappedSet(Set<? extends GraphObject> wrappers)

Gets the wrapped objects of the given wrappers.

Parameters:

wrappers - Wrappers

Returns:

Wrapped objects

getModel

public Model getModel()

Returns:

Wrapped model