Uses of Interface
org.biopax.paxtools.model.level3.Provenance

Packages that use Provenance

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.

Uses of Provenance in org.biopax.paxtools.controller

Methods in org.biopax.paxtools.controller that return types with arguments of type Provenance

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.

Uses of Provenance in org.biopax.paxtools.impl.level3

Classes in org.biopax.paxtools.impl.level3 that implement Provenance

Modifier and Type	Class and Description
class	ProvenanceImpl

Methods in org.biopax.paxtools.impl.level3 that return Provenance

Modifier and Type	Method and Description
Provenance	ScoreImpl.getScoreSource()

Methods in org.biopax.paxtools.impl.level3 that return types with arguments of type Provenance

Modifier and Type	Method and Description
Set<Provenance>	EntityImpl.getDataSource()
Set<Provenance>	L3ElementImpl.getDatasources() Deprecated. use getAnnotations() instead
Class<? extends Provenance>	ProvenanceImpl.getModelInterface()

Methods in org.biopax.paxtools.impl.level3 with parameters of type Provenance

Modifier and Type	Method and Description
void	EntityImpl.addDataSource(Provenance dataSource)
void	EntityImpl.removeDataSource(Provenance dataSource)
void	ScoreImpl.setScoreSource(Provenance scoreSource)

Method parameters in org.biopax.paxtools.impl.level3 with type arguments of type Provenance

Modifier and Type	Method and Description
void	EntityImpl.setDataSource(Set<Provenance> dataSource)

Uses of Provenance in org.biopax.paxtools.model.level3

Methods in org.biopax.paxtools.model.level3 that return Provenance

Modifier and Type	Method and Description
Provenance	Score.getScoreSource() This property defines the source of the scoring methodology.

Methods in org.biopax.paxtools.model.level3 that return types with arguments of type Provenance

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.

Methods in org.biopax.paxtools.model.level3 with parameters of type Provenance

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.