org.biopax.paxtools.io.sif.level2

Class ParticipatesRule

java.lang.Object

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

org.biopax.paxtools.io.sif.level2.ParticipatesRule

All Implemented Interfaces:

InteractionRule, InteractionRuleL2

public class ParticipatesRule
extends InteractionRuleL2Adaptor

Finds pairs of molecules that are participants of the same interaction. User: demir Date: Dec 28, 2007 Time: 5:52:06 PM

Constructor Summary

Constructors

Constructor and Description
ParticipatesRule() Constructor with default values.
ParticipatesRule(int threshold) Constructor with participant number threshold.
ParticipatesRule(int threshold, boolean suppressExceptions) Constructor with participant number threshold and option to suppress exceptions.

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets a list of the rule types that this class implements.
void	inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity pe, Model model) Infer using given physicalEntity as source.
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

ParticipatesRule

public ParticipatesRule()

Constructor with default values.

ParticipatesRule

public ParticipatesRule(int threshold)

Constructor with participant number threshold.

Parameters:

threshold - participant number threshold

ParticipatesRule

public ParticipatesRule(int threshold,
                        boolean suppressExceptions)

Constructor with participant number threshold and option to suppress exceptions.

Parameters:

threshold - participant number threshold

suppressExceptions - option to just skip interactions with too many participants

Method Detail

initOptionsNotNull

public void initOptionsNotNull(Map options)

Initializes options.

Overrides:

initOptionsNotNull in class InteractionRuleL2Adaptor

Parameters:

options - options map

inferInteractionsFromPE

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

Infer using given physicalEntity as source.

Parameters:

interactionSet - to be populated

pe - source

model - BioPAX model

getRuleTypes

public List<BinaryInteractionType> getRuleTypes()

Description copied from interface: InteractionRule

Gets a list of the rule types that this class implements.

Returns:

supported rules