Package org.biopax.paxtools.converter

Class LevelUpgrader

java.lang.Object

org.biopax.paxtools.controller.Traverser

org.biopax.paxtools.controller.AbstractTraverser

org.biopax.paxtools.converter.LevelUpgrader

All Implemented Interfaces:

ModelFilter, Visitor

public final class LevelUpgrader
extends AbstractTraverser
implements ModelFilter

Upgrades BioPAX L1 and L2 to Level 3. Notes: - it does not fix existing BioPAX errors - most but not all things are converted (e.g., complex.ORGANISM property cannot...) - phy. entities "clones" - because, during L1 or L2 data read, all re-used pEPs are duplicated... (TODO filter after the conversion)

Author:

rodch

Field Summary

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

visited

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

editorMap, filters, visitor

Constructor Summary

Constructors

Constructor	Description
LevelUpgrader()	Default Constructor that also loads 'classesmap' and 'propsmap' from the properties files.
LevelUpgrader(BioPAXFactory factory)	Constructor

Method Summary

Modifier and Type	Method	Description
Model	filter(Model model)	Converts a BioPAX Model, Level 1 or 2, to the Level 3.
static String	getLocalId(BioPAXElement bpe)	Gets the local part of the BioPAX element ID.
protected Object	getMatchingEnum(Object o)
protected void	preparePep2PEIDMap(Model model)
protected void	visit(Object value, BioPAXElement parent, Model newModel, PropertyEditor editor)	This is to implement a real action here: do something, return or even to continue (traverse) into the child (range) element's properties if it's a BioPAX object.

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

reset, traverse, visit

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

filter, getVisitor, setVisitor, traverseElements

Methods inherited from class java.lang.Object

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

Constructor Details

LevelUpgrader

public LevelUpgrader()

Default Constructor that also loads 'classesmap' and 'propsmap' from the properties files.

LevelUpgrader

public LevelUpgrader(BioPAXFactory factory)

Constructor

Parameters:

factory - BioPAX objects factory implementation

Method Details

filter

public Model filter(Model model)

Converts a BioPAX Model, Level 1 or 2, to the Level 3.

Specified by:

filter in interface ModelFilter

Parameters:

model - BioPAX model to upgrade

Returns:

new Level3 model

visit

protected void visit(Object value,
 BioPAXElement parent,
 Model newModel,
 PropertyEditor editor)

Description copied from class: AbstractTraverser

This is to implement a real action here: do something, return or even to continue (traverse) into the child (range) element's properties if it's a BioPAX object.

Specified by:

visit in class AbstractTraverser

Parameters:

value - property value

parent - parent/owner BioPAX element

newModel - the BioPAX model of interest

editor - the property editor

getLocalId

public static String getLocalId(BioPAXElement bpe)

Gets the local part of the BioPAX element ID.

Parameters:

bpe - BioPAX object

Returns:

id - local part of the URI

getMatchingEnum

protected Object getMatchingEnum(Object o)

preparePep2PEIDMap

protected void preparePep2PEIDMap(Model model)