Package | Description |
---|---|
org.biopax.paxtools.impl.level3 |
This package contains the default implementation for BioPAX Level 3.
|
org.biopax.paxtools.io.sif.level3 |
This package contains the SIF rules 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.
|
org.biopax.paxtools.query.wrapperL3 |
This package contains TODO annotate!
|
org.biopax.paxtools.query.wrapperL3undirected |
This package contains TODO annotate!
|
Modifier and Type | Class and Description |
---|---|
class |
CatalysisImpl |
class |
ControlImpl |
class |
ModulationImpl |
class |
TemplateReactionRegulationImpl |
Modifier and Type | Method and Description |
---|---|
Set<Control> |
ProcessImpl.getControlledOf() |
Set<Control> |
PhysicalEntityImpl.getControllerOf() |
Set<Control> |
PathwayImpl.getControllerOf() |
Class<? extends Control> |
ControlImpl.getModelInterface() |
Modifier and Type | Method and Description |
---|---|
protected void |
ProcessImpl.setControlledOf(Set<Control> controlledOf) |
protected void |
PhysicalEntityImpl.setControllerOf(Set<Control> controllerOf) |
protected void |
PathwayImpl.setControllerOf(Set<Control> controllerOf) |
Modifier and Type | Method and Description |
---|---|
Map<Control,Boolean> |
PEStateChange.getDeltaControls() |
Modifier and Type | Interface and Description |
---|---|
interface |
Catalysis
Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion
interaction by lowering its activation energy.
|
interface |
Modulation
Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
|
interface |
TemplateReactionRegulation |
Modifier and Type | Method and Description |
---|---|
Set<Control> |
Process.getControlledOf() |
Set<Control> |
Controller.getControllerOf()
This method returns the list of
Control interactions that this entity controls. |
Modifier and Type | Method and Description |
---|---|
protected List<Control> |
ConstraintAdapter.getControlChain(Control control,
Interaction inter)
Gets the chain of Control, staring from the given Control, leading to the given Interaction.
|
Modifier and Type | Method and Description |
---|---|
protected ConversionDirectionType |
ConstraintAdapter.getCatalysisDirection(Control cont)
Gets the direction of the Control, if exists.
|
protected List<Control> |
ConstraintAdapter.getControlChain(Control control,
Interaction inter)
Gets the chain of Control, staring from the given Control, leading to the given Interaction.
|
protected ConversionDirectionType |
ConstraintAdapter.getDirection(Conversion conv,
Control cont)
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 |
---|---|
boolean |
MinerAdapter.isInhibition(Control ctrl)
Checks if the type of a Control is inhibition.
|
protected int |
MinerAdapter.sign(Control ctrl)
Identifies negative and positive controls.
|
Modifier and Type | Field and Description |
---|---|
protected Control |
ControlWrapper.ctrl
Wrapped control.
|
Modifier and Type | Method and Description |
---|---|
Control |
ControlWrapper.getControl()
Gets the wrapped Control.
|
Constructor and Description |
---|
ControlWrapper(Control ctrl,
Graph graph)
Constructor with the Control and the owner graph.
|
Modifier and Type | Field and Description |
---|---|
protected Control |
ControlWrapper.ctrl
Wrapped control.
|
Modifier and Type | Method and Description |
---|---|
Control |
ControlWrapper.getControl()
Gets the wrapped Control.
|
Constructor and Description |
---|
ControlWrapper(Control ctrl,
Graph graph)
Constructor with the Control and the owner graph.
|
Copyright © 2015 BioPAX. All rights reserved.