Uses of Interface
org.biopax.paxtools.io.sif.InteractionRule

Packages that use InteractionRule

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 InteractionRule in org.biopax.paxtools.io.sif

Methods in org.biopax.paxtools.io.sif that return types with arguments of type InteractionRule

Modifier and Type	Method and Description
static List<InteractionRule>	SimpleInteractionConverter.getRules(BioPAXLevel level) Deprecated. Gets all available interaction rules for the given level.

Constructors in org.biopax.paxtools.io.sif with parameters of type InteractionRule

Constructor and Description
SimpleInteractionConverter(InteractionRule... rules) Deprecated. Constructor with the mining rules to use.
SimpleInteractionConverter(Map options, InteractionRule... rules) Deprecated. Constructor with mining rules and options.
SimpleInteractionConverter(Map options, Set<String> blackList, InteractionRule... rules) Deprecated. Constructor with mining rules, options, and black list.

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

Subinterfaces of InteractionRule in org.biopax.paxtools.io.sif.level2

Modifier and Type	Interface and Description
interface	InteractionRuleL2 This interface defines a rule which can be run on BioPAX model L2 to derive simple interactions.

Classes in org.biopax.paxtools.io.sif.level2 that implement InteractionRule

Modifier and Type	Class and Description
class	AffectsRule This is an experimental rule that mines ACTIVATES and INHIBITS relations between molecules.
class	InteractionRuleL2Adaptor Base class for level 2 rules.

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

Subinterfaces of InteractionRule in org.biopax.paxtools.io.sif.level3

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

Classes in org.biopax.paxtools.io.sif.level3 that implement InteractionRule

Modifier and Type	Class and Description
class	ComponentRule This rule class mines complex membership relations.
class	ConsecutiveCatalysisRule This class creates an interaction between two entities if they are catalyzing consecutive conversions.
class	ControlRule A controls a conversion which B is at left or right or both.
class	ControlsTogetherRule Implements Co-Control rule, which means A and B have a control over the same interaction.
class	ExpressionRule This rule mines the transctivation and transinhibition relations between entities.
class	InteractionRuleL3Adaptor Base class for level 3 interactions rules.
class	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.