org.biopax.paxtools.io.sif.level3

Class ControlsTogetherRule

java.lang.Object

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

org.biopax.paxtools.io.sif.level3.ControlsTogetherRule

All Implemented Interfaces:

InteractionRule, InteractionRuleL3

public class ControlsTogetherRule
extends InteractionRuleL3Adaptor

Implements Co-Control rule, which means A and B have a control over the same interaction. This class performs a recursive search both downwards and and upwards of a control that A is a controller. Upwards search always proceed to upwards, i.e. never switch back to downwards at any point. If this is directly upwards of the first control that we start the search, then all reachable B have dependent activity to A. Downward search, however, is different. It can switch to an upwards search when possible, to infer independent controls. There appears three possible search patterns, starting from the first control (of A), each provides only dependent or independent relations:

• Upwards only --> dependent relation
• Downwards only --> dependent relation
• Downwards then upwards --> independent relation

Author:

Emek Demir, Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
ControlsTogetherRule()

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets a list of the rule types that this class implements.
void	inferInteractionsFromPE(InteractionSetL3 l3, PhysicalEntity pe, Model model) This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.

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

ControlsTogetherRule

public ControlsTogetherRule()

Method Detail

inferInteractionsFromPE

public void inferInteractionsFromPE(InteractionSetL3 l3,
                                    PhysicalEntity pe,
                                    Model model)

Description copied from interface: InteractionRuleL3

This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.

Parameters:

l3 - to be populated

pe - PhysicalEntity that will be the seed of the inference

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