org.biopax.paxtools.io.sif.level3

Class ControlRule

java.lang.Object

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

org.biopax.paxtools.io.sif.level3.ControlRule

All Implemented Interfaces:

InteractionRule, InteractionRuleL3

public class ControlRule
extends InteractionRuleL3Adaptor

A controls a conversion which B is at left or right or both. - Controls.StateChange (B at both sides (one side may be as a member of a complex), or B is complex) - Controls.MetabolicChange (B at one side only)

Author:

Ozgun Babur Date: Dec 29, 2007 Time: 1:27:55 AM

Constructor Summary

Constructors

Constructor and Description
ControlRule()

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets supported interaction types.
void	inferInteractionsFromPE(InteractionSetL3 is3, PhysicalEntity pe, Model model) When options map is null, then all rules are generated.
void	initOptionsNotNull(Map options) Initializes options.

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

checkOption, collectEntities, createAndAdd, createClique, inferInteractions, initOptions

Methods inherited from class java.lang.Object

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

Constructor Detail

ControlRule

public ControlRule()

Method Detail

initOptionsNotNull

public void initOptionsNotNull(Map options)

Initializes options.

Overrides:

initOptionsNotNull in class InteractionRuleL3Adaptor

Parameters:

options - options map

inferInteractionsFromPE

public void inferInteractionsFromPE(InteractionSetL3 is3,
                                    PhysicalEntity pe,
                                    Model model)

When options map is null, then all rules are generated. Otherwise only rules that are contained in the options map as a key are generated.

Parameters:

is3 - set to fill in

model - biopax graph - may be null, has no use here

pe - PhysicalEntity that will be the seed of the inference

getRuleTypes

public List<BinaryInteractionType> getRuleTypes()

Gets supported interaction types.

Returns:

supported interaction types