Package org.biopax.paxtools.io.sif.level3

This package contains the SIF rules for BioPAX Level 3.

See: Description

Interface Summary

Interface	Description
InteractionRuleL3	This interface defines a rule which can be run on BioPAX model L2 to derive simple interactions.

Class Summary

Class	Description
ActivityNetworkAnalyzer	Deprecated
ComponentRule	This rule class mines complex membership relations.
ConsecutiveCatalysisRule	This class creates an interaction between two entities if they are catalyzing consecutive conversions.
ControlRule	A controls a conversion which B is at left or right or both.
ControlsTogetherRule	Implements Co-Control rule, which means A and B have a control over the same interaction.
ExpressionRule	This rule mines the transctivation and transinhibition relations between entities.
Group	This class represents a grouping of EntityReferences strictly used by SIF rules for handling generics and complexes.
Grouper
GroupMap
InteractionRuleL3Adaptor	Base class for level 3 interactions rules.
InteractionSetL3	Set of inferred interactions.
ParticipatesRule	Finds pairs of molecules that are participants of the same interaction for the INTERACTS_WITH type, and participants of the same Conversion for the REACTS_WITH type.
PEStateChange	This experimental class is used by Activity Network Analyzer to capture state change events.
Simplify

Enum Summary

Enum	Description
ChangeType	This enum handles types of modifications and contains utility methods for extracting them.

Package org.biopax.paxtools.io.sif.level3 Description

This package contains the SIF rules for BioPAX Level 3.