Package | Description |
---|---|
org.biopax.paxtools.io.sif.level3 |
This package contains the SIF rules for BioPAX Level 3.
|
Modifier and Type | Method and Description |
---|---|
protected Set<BioPAXElement> |
InteractionRuleL3Adaptor.collectEntities(Set<PhysicalEntity> pes,
InteractionSetL3 set) |
protected void |
InteractionRuleL3Adaptor.createAndAdd(BioPAXElement source,
BioPAXElement target,
InteractionSetL3 is3,
BinaryInteractionType type,
BioPAXElement... mediators)
Creates the binary interaction and adds to the inferred interaction list.
|
protected void |
InteractionRuleL3Adaptor.createClique(InteractionSetL3 interactionSet,
List<BioPAXElement> components,
BinaryInteractionType type,
BioPAXElement... mediators)
Creates an interactions between every ordered pair of components.
|
void |
ParticipatesRule.inferInteractionsFromPE(InteractionSetL3 interactionSet,
PhysicalEntity pe,
Model model)
Infers interactions starting from the given PhysicalEntity.
|
void |
InteractionRuleL3.inferInteractionsFromPE(InteractionSetL3 interactionSet,
PhysicalEntity pe,
Model model)
This method populates the interactionSet with simple interactions that can
be derived from the model based on this rule.
|
void |
ExpressionRule.inferInteractionsFromPE(InteractionSetL3 interactionSet,
PhysicalEntity pe,
Model model)
Searches the transcriptional relations using the pattern, then decides the interaction type
according to the type of the Control.
|
void |
ControlsTogetherRule.inferInteractionsFromPE(InteractionSetL3 l3,
PhysicalEntity pe,
Model model) |
void |
ControlRule.inferInteractionsFromPE(InteractionSetL3 is3,
PhysicalEntity pe,
Model model)
When options map is null, then all rules are generated.
|
void |
ConsecutiveCatalysisRule.inferInteractionsFromPE(InteractionSetL3 interactionSet,
PhysicalEntity pe,
Model model)
Infers interactions using the given PhysicalEntity as seed.
|
void |
ComponentRule.inferInteractionsFromPE(InteractionSetL3 interactionSet,
PhysicalEntity pe,
Model model)
Infer interactions where A = the given PhysicalEntity.
|
Copyright © 2015 BioPAX. All rights reserved.