org.biopax.paxtools.io.sif.level2

Class InteractionRuleL2Adaptor

java.lang.Object

org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor

All Implemented Interfaces:

InteractionRule, InteractionRuleL2

Direct Known Subclasses:

AffectsRule, ComponentRule, ConsecutiveCatalysisRule, ControlRule, ControlsTogetherRule, ParticipatesRule

public abstract class InteractionRuleL2Adaptor
extends Object
implements InteractionRuleL2

Base class for level 2 rules.

Constructor Summary

Constructors

Constructor and Description
InteractionRuleL2Adaptor()

Method Summary

Modifier and Type	Method and Description
void	inferInteractions(InteractionSet interactionSet, BioPAXElement entity, Model model) Uses physicalEntity as source of the interaction.
void	initOptions(Map options) Initializes options.
protected void	initOptionsNotNull(Map options) Does nothing here.

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.io.sif.level2.InteractionRuleL2

inferInteractionsFromPE

Methods inherited from interface org.biopax.paxtools.io.sif.InteractionRule

getRuleTypes

Constructor Detail

InteractionRuleL2Adaptor

public InteractionRuleL2Adaptor()

Method Detail

inferInteractions

public void inferInteractions(InteractionSet interactionSet,
                              BioPAXElement entity,
                              Model model)

Uses physicalEntity as source of the interaction.

Specified by:

inferInteractions in interface InteractionRule

Parameters:

interactionSet - to populate

entity - this must be a physicalEntity for L2, and PhysicalEntity for L3

model - BioPAX model

initOptions

public void initOptions(Map options)

Initializes options.

Specified by:

initOptions in interface InteractionRule

Parameters:

options - options map

initOptionsNotNull

protected void initOptionsNotNull(Map options)

Does nothing here. Overridden in children. options is guaranteed to be not null.

Parameters:

options - options map