Package | Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
BiochemicalReactionImpl |
class |
CatalysisImpl |
class |
ComplexAssemblyImpl |
class |
ControlImpl |
class |
ConversionImpl |
class |
DegradationImpl |
class |
GeneticInteractionImpl |
class |
InteractionImpl |
class |
ModulationImpl |
class |
MolecularInteractionImpl |
class |
PathwayImpl |
class |
ProcessImpl |
class |
TemplateReactionImpl |
class |
TemplateReactionRegulationImpl |
class |
TransportImpl |
class |
TransportWithBiochemicalReactionImpl |
Modifier and Type | Method and Description |
---|---|
Set<Process> |
ControlImpl.getControlled() |
Set<Process> |
PathwayImpl.getPathwayComponent() |
Set<Process> |
PathwayStepImpl.getStepProcess() |
Set<Process> |
BiochemicalPathwayStepImpl.getStepProcess() |
Modifier and Type | Method and Description |
---|---|
void |
ControlImpl.addControlled(Process controlled) |
void |
PathwayImpl.addPathwayComponent(Process component) |
void |
PathwayStepImpl.addStepProcess(Process processStep) |
void |
BiochemicalPathwayStepImpl.addStepProcess(Process process) |
protected boolean |
ModulationImpl.checkControlled(Process controlled) |
protected boolean |
ControlImpl.checkControlled(Process Controlled) |
protected boolean |
CatalysisImpl.checkControlled(Process controlled) |
void |
ControlImpl.removeControlled(Process controlled) |
void |
PathwayImpl.removePathwayComponent(Process component) |
void |
PathwayStepImpl.removeStepProcess(Process processStep) |
Modifier and Type | Method and Description |
---|---|
protected void |
ControlImpl.setControlled(Set<Process> controlled) |
protected void |
PathwayImpl.setPathwayComponent(Set<Process> pathwayComponent) |
Modifier and Type | Interface and Description |
---|---|
interface |
BiochemicalReaction
Definition: A conversion interaction in which one or more entities (substrates) undergo covalent
changes to become one or more other entities (products).
|
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 |
ComplexAssembly
Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
|
interface |
Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity,
i.e.
|
interface |
Conversion
Definition: An interaction in which molecules of one or more
PhysicalEntity pools are physically
transformed and become a member of one or more other PhysicalEntity pools. |
interface |
Degradation
Definition: A conversion in which a pool of macromolecules are degraded into their elementary
units.
|
interface |
GeneticInteraction
Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
|
interface |
Interaction
Definition: A biological relationship between two or more entities.
|
interface |
Modulation
Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
|
interface |
MolecularInteraction
Definition: An interaction in which at least one participant is a physical entity, e.g.
|
interface |
Pathway |
interface |
TemplateReaction |
interface |
TemplateReactionRegulation |
interface |
Transport |
interface |
TransportWithBiochemicalReaction |
Modifier and Type | Method and Description |
---|---|
Set<Process> |
Control.getControlled()
The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
|
Set<Process> |
Pathway.getPathwayComponent() |
Set<Process> |
PathwayStep.getStepProcess() |
Modifier and Type | Method and Description |
---|---|
void |
Control.addControlled(Process controlled)
The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
|
void |
Pathway.addPathwayComponent(Process components) |
void |
PathwayStep.addStepProcess(Process newSTEP_INTERACTIONS) |
void |
Control.removeControlled(Process controlled)
The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
|
void |
Pathway.removePathwayComponent(Process components) |
void |
PathwayStep.removeStepProcess(Process oldSTEP_INTERACTIONS) |
Copyright © 2015 BioPAX. All rights reserved.