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.model.level3 |
This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
|
Modifier and Type | Method and Description |
---|---|
static Set<BioSource> |
ModelUtils.getOrganisms(BioPAXElement biopaxElement)
Collects BioSource objects from this or
related elements (where it makes sense;
though the biopax element might have no
or empty 'organism' property at all.
|
Modifier and Type | Class and Description |
---|---|
class |
BioSourceImpl |
Modifier and Type | Method and Description |
---|---|
BioSource |
SequenceEntityReferenceImpl.getOrganism() |
BioSource |
PathwayImpl.getOrganism() |
BioSource |
GeneImpl.getOrganism() |
Modifier and Type | Method and Description |
---|---|
Class<? extends BioSource> |
BioSourceImpl.getModelInterface() |
Set<BioSource> |
L3ElementImpl.getOrganisms()
Deprecated.
use getAnnotations() instead
|
Modifier and Type | Method and Description |
---|---|
void |
SequenceEntityReferenceImpl.setOrganism(BioSource organism) |
void |
PathwayImpl.setOrganism(BioSource organism) |
void |
GeneImpl.setOrganism(BioSource source) |
Modifier and Type | Method and Description |
---|---|
BioSource |
SequenceEntityReference.getOrganism()
An organism, e.g.
|
BioSource |
Pathway.getOrganism()
An organism, e.g.
|
BioSource |
Gene.getOrganism()
An organism, e.g.
|
Modifier and Type | Method and Description |
---|---|
void |
SequenceEntityReference.setOrganism(BioSource source)
An organism, e.g.
|
void |
Pathway.setOrganism(BioSource source)
An organism, e.g.
|
void |
Gene.setOrganism(BioSource source)
An organism, e.g.
|
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