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.util |
Package for several utility classes.
|
org.biopax.paxtools.query.wrapperL3 |
This package contains TODO annotate!
|
Modifier and Type | Class and Description |
---|---|
class |
BiochemicalReactionImpl |
class |
ComplexAssemblyImpl |
class |
ConversionImpl |
class |
DegradationImpl |
class |
TransportImpl |
class |
TransportWithBiochemicalReactionImpl |
Modifier and Type | Method and Description |
---|---|
Conversion |
BiochemicalPathwayStepImpl.getStepConversion() |
Modifier and Type | Method and Description |
---|---|
Class<? extends Conversion> |
ConversionImpl.getModelInterface() |
Modifier and Type | Method and Description |
---|---|
void |
BiochemicalPathwayStepImpl.setStepConversion(Conversion highLander)
This method sets the conversion of this BiochemicalPathwayStep to the
new Step_Conversion.
|
Modifier and Type | Method and Description |
---|---|
Conversion |
PEStateChange.getConv() |
Modifier and Type | Method and Description |
---|---|
static boolean |
Simplify.entityHasAChange(BioPAXElement target,
Conversion conv,
GroupMap groupMap,
Set<PEStateChange> peStateChanges) |
static boolean |
Simplify.entityHasAChange(BioPAXElement element,
Conversion conv,
GroupMap map,
Set<PEStateChange> changeSet,
Map<Conversion,Set<EntityReference>> extendedControls) |
Modifier and Type | Method and Description |
---|---|
static boolean |
Simplify.entityHasAChange(BioPAXElement element,
Conversion conv,
GroupMap map,
Set<PEStateChange> changeSet,
Map<Conversion,Set<EntityReference>> extendedControls) |
Constructor and Description |
---|
PEStateChange(SimplePhysicalEntity left,
SimplePhysicalEntity right,
PhysicalEntity leftRoot,
PhysicalEntity rightRoot,
BioPAXElement element,
Conversion conv) |
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 |
ComplexAssembly
Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
|
interface |
Degradation
Definition: A conversion in which a pool of macromolecules are degraded into their elementary
units.
|
interface |
Transport |
interface |
TransportWithBiochemicalReaction |
Modifier and Type | Method and Description |
---|---|
Conversion |
BiochemicalPathwayStep.getStepConversion()
This method returns the central conversion of this BiochemicalPathwayStep.
|
Modifier and Type | Method and Description |
---|---|
void |
BiochemicalPathwayStep.setStepConversion(Conversion stepConversion)
This method sets the conversion of this BiochemicalPathwayStep to the
new Step_Conversion.
|
Modifier and Type | Method and Description |
---|---|
protected ConversionDirectionType |
ConstraintAdapter.findDirectionInCatalysis(Conversion conv)
Searches the controlling catalysis for possible direction of the conversion.
|
protected ConversionDirectionType |
ConstraintAdapter.findDirectionInPathways(Conversion conv)
Searches pathways that contains this conversion for the possible directions.
|
protected Collection<BioPAXElement> |
InterToPartER.generate(Conversion conv,
InterToPartER.Direction direction,
Set<Entity> taboo)
Gets the related entity references of the given interaction,
|
protected Set<PhysicalEntity> |
ConstraintAdapter.getConvParticipants(Conversion conv,
RelType type)
Gets input ot output participants of the Conversion.
|
protected ConversionDirectionType |
ConstraintAdapter.getDirection(Conversion conv) |
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)
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 |
Blacklist.isUbique(PhysicalEntity pe,
Conversion conv,
ConversionDirectionType dir,
RelType context)
Checks if the given entity is blacklisted for the given Conversion assuming the Conversion
flows towards the given direction, and the entity is in given context.
|
Modifier and Type | Field and Description |
---|---|
protected Conversion |
ConversionWrapper.conv
Wrapped Conversion.
|
Modifier and Type | Method and Description |
---|---|
Conversion |
ConversionWrapper.getConversion() |
Modifier and Type | Method and Description |
---|---|
protected Set<Conversion> |
PhysicalEntityWrapper.getUpstreamConversions(Collection<Interaction> inters)
Gets the conversions at the upstream of this PhysicalEntity.
|
Constructor and Description |
---|
ConversionWrapper(Conversion conv,
GraphL3 graph)
Constructor with the Conversion to wrap and the owner graph.
|
Copyright © 2015 BioPAX. All rights reserved.