org.biopax.paxtools.query.model

Class AbstractGraph

java.lang.Object

org.biopax.paxtools.query.model.AbstractGraph

All Implemented Interfaces:

Graph

Direct Known Subclasses:

GraphL3, GraphL3Undirected

public abstract class AbstractGraph
extends Object
implements Graph

Adapter class for a graph that is queried.

Author:

Ozgun Babur

Field Summary

Fields

Modifier and Type	Field and Description
protected Map<String,GraphObject>	objectMap Objects are stored in this map.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractGraph() Empty constructor that initializes the object map.

Method Summary

Modifier and Type	Method and Description
void	clear() Clears memory of all wrapper in the object map.
GraphObject	getGraphObject(Object obj) Gets the related wrapper for the given object, creates the wrapper if not created before.
GraphObject	getGraphObject(String id) Gets the wrapper object with its id (key).
abstract String	getKey(Object wrapped)
Map<String,GraphObject>	getObjectMap()
abstract Node	wrap(Object obj) Creates the wrapper for the given object.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biopax.paxtools.query.model.Graph

getWrappedSet, getWrapperMap, getWrapperSet

Field Detail

objectMap

protected Map<String,GraphObject> objectMap

Objects are stored in this map. getKey method of objects is used for generating the key.

Constructor Detail

AbstractGraph

protected AbstractGraph()

Empty constructor that initializes the object map.

Method Detail

getGraphObject

public GraphObject getGraphObject(Object obj)

Gets the related wrapper for the given object, creates the wrapper if not created before.

Specified by:

getGraphObject in interface Graph

Parameters:

obj - Object to wrap

Returns:

wrapper

getGraphObject

public GraphObject getGraphObject(String id)

Gets the wrapper object with its id (key).

Parameters:

id - Whatever getKey method return for the wrapped object.

Returns:

Wrapper

getObjectMap

public Map<String,GraphObject> getObjectMap()

Returns:

The object map

clear

public void clear()

Clears memory of all wrapper in the object map.

Specified by:

clear in interface Graph

getKey

public abstract String getKey(Object wrapped)

Parameters:

wrapped - Object to wrap

Returns:

A key for the object to map it to its wrapper

wrap

public abstract Node wrap(Object obj)

Creates the wrapper for the given object.

Parameters:

obj - Object to wrap

Returns:

The wrapper