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 |
ComplexImpl |
class |
DnaImpl |
class |
DnaRegionImpl |
class |
NucleicAcidImpl |
class |
PathwayImpl |
class |
PhysicalEntityImpl |
class |
ProteinImpl |
class |
RnaImpl |
class |
RnaRegionImpl |
class |
SimplePhysicalEntityImpl |
class |
SmallMoleculeImpl |
Modifier and Type | Method and Description |
---|---|
Set<Controller> |
ControlImpl.getController() |
Modifier and Type | Method and Description |
---|---|
void |
ControlImpl.addController(Controller controller) |
void |
CatalysisImpl.addController(Controller controller) |
void |
ControlImpl.removeController(Controller controller) |
Modifier and Type | Interface and Description |
---|---|
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 |
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 |
NucleicAcid
Tagger interface for DNA and RNA
|
interface |
Pathway |
interface |
PhysicalEntity |
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 |
Modifier and Type | Method and Description |
---|---|
Set<Controller> |
Control.getController()
The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
Control.addController(Controller controller)
The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.
|
void |
Control.removeController(Controller controller)
The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.
|
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