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.
|
Modifier and Type | Method and Description |
---|---|
BinaryInteractionType |
SimpleInteraction.getType()
Gets the type of the interaction.
|
static BinaryInteractionType |
BinaryInteractionType.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static BinaryInteractionType[] |
BinaryInteractionType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
List<BinaryInteractionType> |
InteractionRule.getRuleTypes()
Gets a list of the rule types that this class implements.
|
Modifier and Type | Method and Description |
---|---|
void |
SimpleInteraction.setType(BinaryInteractionType type)
Sets the type of the interaction.
|
Constructor and Description |
---|
SimpleInteraction(BioPAXElement source,
BioPAXElement target,
BinaryInteractionType type)
Constructor with parameters, without mediators.
|
SimpleInteraction(BioPAXElement source,
BioPAXElement target,
BinaryInteractionType type,
BioPAXElement... mediator)
Constructor with parameters, with mediators.
|
SimpleInteraction(BioPAXElement source,
BioPAXElement target,
BinaryInteractionType type,
Collection<BioPAXElement> mediator)
Constructor with parameters, with mediators.
|
Modifier and Type | Method and Description |
---|---|
List<BinaryInteractionType> |
ParticipatesRule.getRuleTypes() |
List<BinaryInteractionType> |
ControlsTogetherRule.getRuleTypes()
Gets supported interaction types.
|
List<BinaryInteractionType> |
ControlRule.getRuleTypes()
Gets supported interaction types.
|
List<BinaryInteractionType> |
ConsecutiveCatalysisRule.getRuleTypes()
Gets supported interaction types.
|
List<BinaryInteractionType> |
ComponentRule.getRuleTypes()
Gets supported interaction types.
|
List<BinaryInteractionType> |
AffectsRule.getRuleTypes()
Gets supported interactions types.
|
Modifier and Type | Method and Description |
---|---|
List<BinaryInteractionType> |
ParticipatesRule.getRuleTypes()
Gets supported interaction types.
|
List<BinaryInteractionType> |
ExpressionRule.getRuleTypes()
Gets a list of the rule types that this class implements.
|
List<BinaryInteractionType> |
ControlsTogetherRule.getRuleTypes() |
List<BinaryInteractionType> |
ControlRule.getRuleTypes()
Gets supported interaction types.
|
List<BinaryInteractionType> |
ConsecutiveCatalysisRule.getRuleTypes()
Gets supported interaction types.
|
List<BinaryInteractionType> |
ComponentRule.getRuleTypes()
Gets supported interaction types.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Copyright © 2015 BioPAX. All rights reserved.