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.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.
|
Modifier and Type | Method and Description |
---|---|
static void |
ModelUtils.copySimplePointers(Model model,
Named source,
Named target)
Copies names and xrefs from source to target
biopax object; it does not copy unification xrefs
but instead adds relationship xrefs using the same
db and id values as source's unification xrefs.
|
Modifier and Type | Class and Description |
---|---|
class |
Group
This class represents a grouping of EntityReferences strictly used by SIF rules for handling generics and complexes.
|
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 |
BioSource
Definition: The biological source of an entity (e.g.
|
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 |
DnaReference
A DNA reference is a grouping of several DNA entities that are common in
sequence and genomic position.
|
interface |
DnaRegion
Definition: A region on a DNA molecule.
|
interface |
DnaRegionReference
Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and
genomic position.
|
interface |
Entity
This class represents a discrete biological unit used when describing
pathways.
|
interface |
EntityReference
Definition: An entity reference is a grouping of several physical entities across different
contexts and molecular states, that share common physical properties and often named and treated
as a single entity with multiple states by biologists.
|
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 |
NucleicAcidReference
Role interface for NucleicAcidReferences, namely DNA and RNA.
|
interface |
NucleicAcidRegionReference |
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 |
ProteinReference
Description: A protein reference is a grouping of several protein entities that are encoded by the same
genetic sequence.
|
interface |
Provenance
Definition: The direct source of a pathway data or score.
|
interface |
Rna |
interface |
RnaReference |
interface |
RnaRegion
Definition: A region on a RNA molecule.
|
interface |
RnaRegionReference
A RNA region reference
|
interface |
SequenceEntity
Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
|
interface |
SequenceEntityReference
Tagger interface for protein, dna and rna entities
|
interface |
SimplePhysicalEntity
Tagger interface for non-complex physical entities
|
interface |
SmallMolecule |
interface |
SmallMoleculeReference |
interface |
TemplateReaction |
interface |
TemplateReactionRegulation |
interface |
Transport |
interface |
TransportWithBiochemicalReaction |
Copyright © 2015 BioPAX. All rights reserved.