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.gsea |
This package contains a simple GSEA converter.
|
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<Provenance> |
ModelUtils.getDatasources(BioPAXElement biopaxElement)
Collects all Provenance objects
associated with this one as follows:
- if the element is Entity (has 'dataSource' property)
or is Provenence itself, get the values and quit;
- if the biopax element is PathwayStep or EntityReference,
traverse into some of its object/inverse properties to collect
dataSource values from associated entities.
|
Modifier and Type | Class and Description |
---|---|
class |
ProvenanceImpl |
Modifier and Type | Method and Description |
---|---|
Provenance |
ScoreImpl.getScoreSource() |
Modifier and Type | Method and Description |
---|---|
Set<Provenance> |
EntityImpl.getDataSource() |
Set<Provenance> |
L3ElementImpl.getDatasources()
Deprecated.
use getAnnotations() instead
|
Class<? extends Provenance> |
ProvenanceImpl.getModelInterface() |
Modifier and Type | Method and Description |
---|---|
void |
EntityImpl.addDataSource(Provenance dataSource) |
void |
EntityImpl.removeDataSource(Provenance dataSource) |
void |
ScoreImpl.setScoreSource(Provenance scoreSource) |
Modifier and Type | Method and Description |
---|---|
void |
EntityImpl.setDataSource(Set<Provenance> dataSource) |
Constructor and Description |
---|
GSEAConverter(String database,
boolean crossSpeciesCheckEnabled,
Set<Provenance> skipSubPathwaysOf)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
Provenance |
Score.getScoreSource()
This property defines the source of the scoring methodology.
|
Modifier and Type | Method and Description |
---|---|
Set<Provenance> |
Entity.getDataSource()
This method returns a set of free text descriptions of the source of this
data, e.g.
|
Modifier and Type | Method and Description |
---|---|
void |
Entity.addDataSource(Provenance dataSource)
This method adds the given value to the DATA_SOURCE set.
|
void |
Entity.removeDataSource(Provenance dataSource)
This method removes the given value from the DATA_SOURCE set.
|
void |
Score.setScoreSource(Provenance scoreSource)
This property defines the source of the scoring methodology.
|
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