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.
|
org.biopax.paxtools.pattern.constraint |
Package for constraints.
|
Modifier and Type | Class and Description |
---|---|
class |
BiochemicalReactionImpl |
class |
CatalysisImpl |
class |
ComplexAssemblyImpl |
class |
ComplexImpl |
class |
ControlImpl |
class |
ConversionImpl |
class |
DegradationImpl |
class |
DnaImpl |
class |
DnaRegionImpl |
class |
EntityImpl |
class |
GeneImpl |
class |
GeneticInteractionImpl |
class |
InteractionImpl |
class |
ModulationImpl |
class |
MolecularInteractionImpl |
class |
NucleicAcidImpl |
class |
PathwayImpl |
class |
PhysicalEntityImpl |
class |
ProcessImpl |
class |
ProteinImpl |
class |
RnaImpl |
class |
RnaRegionImpl |
class |
SimplePhysicalEntityImpl |
class |
SmallMoleculeImpl |
class |
TemplateReactionImpl |
class |
TemplateReactionRegulationImpl |
class |
TransportImpl |
class |
TransportWithBiochemicalReactionImpl |
Modifier and Type | Method and Description |
---|---|
Entity |
ExperimentalFormImpl.getExperimentalFormEntity() |
Modifier and Type | Method and Description |
---|---|
Set<Entity> |
InteractionImpl.getParticipant() |
Modifier and Type | Method and Description |
---|---|
void |
MolecularInteractionImpl.addParticipant(Entity participant) |
void |
InteractionImpl.addParticipant(Entity aParticipant) |
void |
InteractionImpl.removeParticipant(Entity aParticipant) |
void |
ExperimentalFormImpl.setExperimentalFormEntity(Entity experimentalFormEntity) |
Modifier and Type | Method and Description |
---|---|
protected void |
InteractionImpl.setParticipant(Set<Entity> participant) |
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 |
Complex
Definition: A physical entity whose structure is comprised of other physical entities bound to each other
non-covalently, at least one of which is a macromolecule (e.g.
|
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 |
Controller
This is a role interface for pathway elements that can control processes, namely
Pathway and PhysicalEntity . |
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 |
Dna
Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic
acid.
|
interface |
DnaRegion
Definition: A region on a DNA molecule.
|
interface |
Gene
Definition: A continuant that encodes information that can be inherited through replication.
|
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 |
NucleicAcid
Tagger interface for DNA and RNA
|
interface |
Pathway |
interface |
PhysicalEntity |
interface |
Process
Tagging interface for entities that can participate in a pathway
and can be targeted by a control : Pathway and Interaction
|
interface |
Protein |
interface |
Rna |
interface |
RnaRegion
Definition: A region on a RNA molecule.
|
interface |
SequenceEntity
Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
|
interface |
SimplePhysicalEntity
Tagger interface for non-complex physical entities
|
interface |
SmallMolecule |
interface |
TemplateReaction |
interface |
TemplateReactionRegulation |
interface |
Transport |
interface |
TransportWithBiochemicalReaction |
Modifier and Type | Method and Description |
---|---|
Entity |
ExperimentalForm.getExperimentalFormEntity() |
Modifier and Type | Method and Description |
---|---|
Set<Entity> |
Interaction.getParticipant()
The entities that participate in this interaction.
|
Modifier and Type | Method and Description |
---|---|
void |
Interaction.addParticipant(Entity participant)
The entities that participate in this interaction.
|
void |
Interaction.removeParticipant(Entity participant)
The entities that participate in this interaction.
|
void |
ExperimentalForm.setExperimentalFormEntity(Entity newPARTICIPANT) |
Modifier and Type | Method and Description |
---|---|
protected Collection<BioPAXElement> |
InterToPartER.generate(Conversion conv,
InterToPartER.Direction direction,
Set<Entity> taboo)
Gets the related entity references of the given interaction,
|
protected Collection<BioPAXElement> |
InterToPartER.generate(Interaction inter,
Set<Entity> taboo)
Gets the related entity references of the given interaction.
|
Copyright © 2015 BioPAX. All rights reserved.