org.biopax.paxtools.io.sif.level3

Class InteractionRuleL3Adaptor

java.lang.Object

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

All Implemented Interfaces:

InteractionRule, InteractionRuleL3

Direct Known Subclasses:

ComponentRule, ConsecutiveCatalysisRule, ControlRule, ControlsTogetherRule, ExpressionRule, ParticipatesRule

public abstract class InteractionRuleL3Adaptor
extends Object
implements InteractionRuleL3

Base class for level 3 interactions rules.

Constructor Summary

Constructors

Constructor and Description
InteractionRuleL3Adaptor()

Method Summary

Modifier and Type	Method and Description
protected boolean	checkOption(Object key, Object value, Map options) Checks if the options map has the given option with the given value.
protected Set<BioPAXElement>	collectEntities(Set<PhysicalEntity> pes, InteractionSetL3 set)
protected void	createAndAdd(BioPAXElement source, BioPAXElement target, InteractionSetL3 is3, BinaryInteractionType type, BioPAXElement... mediators) Creates the binary interaction and adds to the inferred interaction list.
protected void	createClique(InteractionSetL3 interactionSet, List<BioPAXElement> components, BinaryInteractionType type, BioPAXElement... mediators) Creates an interactions between every ordered pair of components.
void	inferInteractions(InteractionSet interactionSet, BioPAXElement entity, Model model) Selects only PhysicalEntity as seed.
void	initOptions(Map options) Initializes the options.
protected void	initOptionsNotNull(Map options) Does nothing for this class.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biopax.paxtools.io.sif.level3.InteractionRuleL3

inferInteractionsFromPE

Methods inherited from interface org.biopax.paxtools.io.sif.InteractionRule

getRuleTypes

Constructor Detail

InteractionRuleL3Adaptor

public InteractionRuleL3Adaptor()

Method Detail

inferInteractions

public final void inferInteractions(InteractionSet interactionSet,
                                    BioPAXElement entity,
                                    Model model)

Selects only PhysicalEntity as seed.

Specified by:

inferInteractions in interface InteractionRule

Parameters:

interactionSet - inferred interactions

entity - this must be a PhysicalEntity for L3

model - BioPAX model

initOptions

public void initOptions(Map options)

Initializes the options.

Specified by:

initOptions in interface InteractionRule

Parameters:

options - options map

initOptionsNotNull

protected void initOptionsNotNull(Map options)

Does nothing for this class. Initializes the options where this is overwritten.

Parameters:

options - options map

checkOption

protected boolean checkOption(Object key,
                              Object value,
                              Map options)

Checks if the options map has the given option with the given value.

Parameters:

key - key of the option

value - value of the option

options - options map

Returns:

true if the options map has the given option with the given value

collectEntities

protected Set<BioPAXElement> collectEntities(Set<PhysicalEntity> pes,
                                             InteractionSetL3 set)

Parameters:

pes - physical entities

set - inferred binary interactions

Returns:

BioPAX objects

createClique

protected void createClique(InteractionSetL3 interactionSet,
                            List<BioPAXElement> components,
                            BinaryInteractionType type,
                            BioPAXElement... mediators)

Creates an interactions between every ordered pair of components.

Parameters:

interactionSet - inferred interactions

components - nodes of the clique

type - interaction type

mediators - mediator elements of te interaction

createAndAdd

protected void createAndAdd(BioPAXElement source,
                            BioPAXElement target,
                            InteractionSetL3 is3,
                            BinaryInteractionType type,
                            BioPAXElement... mediators)

Creates the binary interaction and adds to the inferred interaction list.

Parameters:

source - source of the interaction

target - target of the interaction

is3 - inferred interactions

type - interaction type

mediators - mediators of the interaction