Uses of Class
org.biopax.paxtools.io.sif.InteractionSet

Packages that use InteractionSet

Package	Description
org.biopax.paxtools.io.sif	This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format.
org.biopax.paxtools.io.sif.level2
org.biopax.paxtools.io.sif.level3	This package contains the SIF rules for BioPAX Level 3.

Uses of InteractionSet in org.biopax.paxtools.io.sif

Methods in org.biopax.paxtools.io.sif with parameters of type InteractionSet

Modifier and Type	Method and Description
void	InteractionRule.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.

Uses of InteractionSet in org.biopax.paxtools.io.sif.level2

Methods in org.biopax.paxtools.io.sif.level2 with parameters of type InteractionSet

Modifier and Type	Method and Description
void	InteractionRuleL2Adaptor.inferInteractions(InteractionSet interactionSet, BioPAXElement entity, Model model) Uses physicalEntity as source of the interaction.
void	ParticipatesRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity pe, Model model) Infer using given physicalEntity as source.
void	InteractionRuleL2.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity entity, Model model) This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.
void	ControlsTogetherRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity A, Model model) Infers interactions using A as source.
void	ControlRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity A, Model model) When options map is null, then all rules are generated.
void	ConsecutiveCatalysisRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity pe, Model model) Infers using the given physicalEntity as source.
void	ComponentRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity A, Model model) Infer starting from the given physicalEntity.
void	AffectsRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity pe, Model model) Infers interactions using the given physicalEntity as seed.

Uses of InteractionSet in org.biopax.paxtools.io.sif.level3

Subclasses of InteractionSet in org.biopax.paxtools.io.sif.level3

Modifier and Type	Class and Description
class	InteractionSetL3 Set of inferred interactions.

Methods in org.biopax.paxtools.io.sif.level3 with parameters of type InteractionSet

Modifier and Type	Method and Description
void	InteractionRuleL3Adaptor.inferInteractions(InteractionSet interactionSet, BioPAXElement entity, Model model) Selects only PhysicalEntity as seed.