Package | Description |
---|---|
org.biopax.paxtools.controller |
This package contains various methods and algorithms for traversing and manipulating the model.
|
org.biopax.paxtools.impl.level3 |
This package contains the default implementation for BioPAX Level 3.
|
org.biopax.paxtools.model.level3 |
This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
|
org.biopax.paxtools.pattern.constraint |
Package for constraints.
|
org.biopax.paxtools.pattern.miner |
Package for pattern miner utility.
|
Modifier and Type | Method and Description |
---|---|
static Set<Pathway> |
ModelUtils.getParentPathways(BioPAXElement biopaxElement)
Collects all parent Pathway objects recursively
traversing the inverse object properties of the
biopax element.
|
Modifier and Type | Class and Description |
---|---|
class |
PathwayImpl |
Modifier and Type | Method and Description |
---|---|
Pathway |
PathwayStepImpl.getPathwayOrderOf() |
Modifier and Type | Method and Description |
---|---|
Class<? extends Pathway> |
PathwayImpl.getModelInterface() |
Set<Pathway> |
L3ElementImpl.getParentPathways()
Deprecated.
use getAnnotations() instead
|
Set<Pathway> |
ProcessImpl.getPathwayComponentOf() |
protected Set<Pathway> |
ControlImpl.getPathwayController() |
Modifier and Type | Method and Description |
---|---|
protected void |
PathwayStepImpl.setPathwayOrderOf(Pathway pathwayOrderOf) |
Modifier and Type | Method and Description |
---|---|
protected void |
ProcessImpl.setPathwayComponentOf(Set<Pathway> pathwayComponentOf) |
protected void |
ControlImpl.setPathwayController(Set<Pathway> pathwayController) |
Modifier and Type | Method and Description |
---|---|
Pathway |
PathwayStep.getPathwayOrderOf() |
Modifier and Type | Method and Description |
---|---|
Set<Pathway> |
Process.getPathwayComponentOf() |
Modifier and Type | Method and Description |
---|---|
protected ConversionDirectionType |
ConstraintAdapter.getDirection(Conversion conv,
Pathway pathway)
Gets the direction of the Control chain the the Interaction.
|
protected ConversionDirectionType |
ConstraintAdapter.getDirection(Conversion conv,
Pathway pathway,
Control cont)
Gets the direction of the Control chain the the Interaction.
|
Modifier and Type | Method and Description |
---|---|
Set<Pathway> |
SIFInteraction.getPathways()
Collects Pathway objects that the Interactions among the mediators are members.
|
Copyright © 2015 BioPAX. All rights reserved.