org.biopax.paxtools.io.sif.level3

Class ConsecutiveCatalysisRule

java.lang.Object

org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

org.biopax.paxtools.io.sif.level3.ConsecutiveCatalysisRule

All Implemented Interfaces:

InteractionRule, InteractionRuleL3

public class ConsecutiveCatalysisRule
extends InteractionRuleL3Adaptor

This class creates an interaction between two entities if they are catalyzing consecutive conversions. Conversions are considered consecutive if one of the RIGHT participants of one reaction is the LEFT of the other and if the directions of catalysis and control matches.

Author:

Emek Demir

Constructor Summary

Constructors

Constructor and Description
ConsecutiveCatalysisRule()

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets supported interaction types.
void	inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) Infers interactions using the given PhysicalEntity as seed.

Methods inherited from class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

checkOption, collectEntities, createAndAdd, createClique, inferInteractions, initOptions, initOptionsNotNull

Methods inherited from class java.lang.Object

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

Constructor Detail

ConsecutiveCatalysisRule

public ConsecutiveCatalysisRule()

Method Detail

inferInteractionsFromPE

public void inferInteractionsFromPE(InteractionSetL3 interactionSet,
                                    PhysicalEntity pe,
                                    Model model)

Infers interactions using the given PhysicalEntity as seed.

Parameters:

interactionSet - to be populated

pe - PhysicalEntity that will be the seed of the inference

model - BioPAX model

getRuleTypes

public List<BinaryInteractionType> getRuleTypes()

Gets supported interaction types.

Returns:

supported interaction types