org.biopax.paxtools.io.sif

Interface InteractionRule

All Known Subinterfaces:

InteractionRuleL2, InteractionRuleL3

All Known Implementing Classes:

AffectsRule, ComponentRule, ComponentRule, ConsecutiveCatalysisRule, ConsecutiveCatalysisRule, ControlRule, ControlRule, ControlsTogetherRule, ControlsTogetherRule, ExpressionRule, InteractionRuleL2Adaptor, InteractionRuleL3Adaptor, ParticipatesRule, ParticipatesRule

public interface InteractionRule

This interface defines a rule which can be run on BioPAX model to derive simple interactions. All new rules should implement this interface. User: demir Date: Dec 28, 2007 Time: 3:49:46 PM

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets a list of the rule types that this class implements.
void	inferInteractions(InteractionSet set, BioPAXElement entity, Model model) This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.
void	initOptions(Map options) Uses the parameter map as options for the rule.

Method Detail

inferInteractions

void inferInteractions(InteractionSet set,
                       BioPAXElement entity,
                       Model model)

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

Parameters:

set - to be populated

entity - this must be a physicalEntity for L2, and PhysicalEntity for L3

model - BioPAX model

getRuleTypes

List<BinaryInteractionType> getRuleTypes()

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

Returns:

supported rules

initOptions

void initOptions(Map options)

Uses the parameter map as options for the rule. Each rule defines its possible keys for the options map. Values are always Boolean.

Parameters:

options - options map