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.
|
Modifier and Type | Class and Description |
---|---|
class |
DnaImpl |
class |
DnaRegionImpl |
class |
NucleicAcidImpl |
class |
ProteinImpl |
class |
RnaImpl |
class |
RnaRegionImpl |
class |
SimplePhysicalEntityImpl |
class |
SmallMoleculeImpl |
Modifier and Type | Method and Description |
---|---|
Set<SimplePhysicalEntity> |
EntityReferenceImpl.getEntityReferenceOf() |
Set<SimplePhysicalEntity> |
ComplexImpl.getSimpleMembers() |
protected Set<SimplePhysicalEntity> |
ComplexImpl.getSimpleMembers(Set<SimplePhysicalEntity> set) |
Modifier and Type | Method and Description |
---|---|
protected void |
ComplexImpl.collectSimpleMembersRecursive(PhysicalEntity pe,
Set<SimplePhysicalEntity> set) |
protected Set<SimplePhysicalEntity> |
ComplexImpl.getSimpleMembers(Set<SimplePhysicalEntity> set) |
protected void |
EntityReferenceImpl.setEntityReferenceOf(Set<SimplePhysicalEntity> entityReferenceOf) |
Modifier and Type | Method and Description |
---|---|
SimplePhysicalEntity |
PEStateChange.changedFrom(SimplePhysicalEntity source) |
SimplePhysicalEntity |
PEStateChange.changedInto(SimplePhysicalEntity source) |
SimplePhysicalEntity |
PEStateChange.getLeft() |
SimplePhysicalEntity |
PEStateChange.getRight() |
Modifier and Type | Method and Description |
---|---|
Set<SimplePhysicalEntity> |
ActivityNetworkAnalyzer.getPrecedingStates(SimplePhysicalEntity spe)
Deprecated.
|
Set<SimplePhysicalEntity> |
ActivityNetworkAnalyzer.getSucceedingStates(SimplePhysicalEntity spe)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
SimplePhysicalEntity |
PEStateChange.changedFrom(SimplePhysicalEntity source) |
SimplePhysicalEntity |
PEStateChange.changedInto(SimplePhysicalEntity source) |
Set<SimplePhysicalEntity> |
ActivityNetworkAnalyzer.getPrecedingStates(SimplePhysicalEntity spe)
Deprecated.
|
Set<SimplePhysicalEntity> |
ActivityNetworkAnalyzer.getSucceedingStates(SimplePhysicalEntity spe)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static void |
Simplify.getSimpleMembers(PhysicalEntity root,
Set<SimplePhysicalEntity> value) |
Constructor and Description |
---|
PEStateChange(SimplePhysicalEntity left,
SimplePhysicalEntity right,
PhysicalEntity leftRoot,
PhysicalEntity rightRoot,
BioPAXElement element,
Conversion conv) |
Modifier and Type | Interface and Description |
---|---|
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 |
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 |
SmallMolecule |
Modifier and Type | Method and Description |
---|---|
Set<SimplePhysicalEntity> |
EntityReference.getEntityReferenceOf()
Inverse of
getEntityReference() |
Set<SimplePhysicalEntity> |
Complex.getSimpleMembers()
Gets the member physical entities which are not complex.
|
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