org.biopax.paxtools.io.sif.level2

Class ComponentRule

java.lang.Object

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

org.biopax.paxtools.io.sif.level2.ComponentRule

All Implemented Interfaces:

InteractionRule, InteractionRuleL2

public class ComponentRule
extends InteractionRuleL2Adaptor

Component.InSame: A and B are components of same flattened complex structure, A and B are simple. Component.Of: A is component of B, B is complex, A may be nested multiple levels in B.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
ComponentRule() Constructor with default values.
ComponentRule(int threshold) Constructor with threshold
ComponentRule(int threshold, boolean suppressExceptions) Constructor with threshold and exception suppressing option.

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets supported interaction types.
void	inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity A, Model model) Infer starting from the given physicalEntity.
void	initOptionsNotNull(Map options) Initializes options.

Methods inherited from class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor

inferInteractions, initOptions

Methods inherited from class java.lang.Object

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

Constructor Detail

ComponentRule

public ComponentRule()

Constructor with default values.

ComponentRule

public ComponentRule(int threshold)

Constructor with threshold

Parameters:

threshold - limit for the member size of the complex to mine

ComponentRule

public ComponentRule(int threshold,
                     boolean suppressExceptions)

Constructor with threshold and exception suppressing option.

Parameters:

threshold - limit for the member size of the complex to mine

suppressExceptions - if true, does not throw exception for large complexes, just skips them

Method Detail

inferInteractionsFromPE

public void inferInteractionsFromPE(InteractionSet interactionSet,
                                    physicalEntity A,
                                    Model model)

Infer starting from the given physicalEntity.

Parameters:

interactionSet - to be populated

A - source of the interaction

model - BioPAX model

getRuleTypes

public List<BinaryInteractionType> getRuleTypes()

Gets supported interaction types.

Returns:

supported interaction types

initOptionsNotNull

public void initOptionsNotNull(Map options)

Initializes options.

Overrides:

initOptionsNotNull in class InteractionRuleL2Adaptor

Parameters:

options - options map