Package de.uni_halle.informatik.biodata.mp.annotation.bigg

Class AbstractBiGGAnnotator

java.lang.Object

de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator

de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator

All Implemented Interfaces:

IReportDiffs, IReportStatus

Direct Known Subclasses:

BiGGCompartmentsAnnotator, BiGGCVTermAnnotator, BiGGFBCAnnotator, BiGGFBCSpeciesAnnotator, BiGGModelAnnotator, BiGGPublicationsAnnotator, BiGGSBMLAnnotator

public abstract class AbstractBiGGAnnotator
extends AbstractAnnotator

Field Summary

Fields

Modifier and Type	Field	Description
protected final BiGGDB	bigg
protected final BiGGAnnotationParameters	biGGAnnotationParameters
protected final Registry	registry

Constructor Summary

Constructors

Constructor	Description
AbstractBiGGAnnotator(BiGGDB bigg, BiGGAnnotationParameters biGGAnnotationParameters, Registry registry)
AbstractBiGGAnnotator(BiGGDB bigg, BiGGAnnotationParameters biGGAnnotationParameters, Registry registry, List<ProgressObserver> observers)

Method Summary

Modifier and Type	Method	Description
Optional<BiGGId>	getBiGGIdFromResources(List<String> resources, String type)	Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase.

Methods inherited from class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator

diffReport, getObservers, statusReport

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

bigg

protected final BiGGDB bigg

registry

protected final Registry registry

biGGAnnotationParameters

protected final BiGGAnnotationParameters biGGAnnotationParameters

Constructor Details

AbstractBiGGAnnotator

public AbstractBiGGAnnotator(BiGGDB bigg,
 BiGGAnnotationParameters biGGAnnotationParameters,
 Registry registry)

AbstractBiGGAnnotator

public AbstractBiGGAnnotator(BiGGDB bigg,
 BiGGAnnotationParameters biGGAnnotationParameters,
 Registry registry,
 List<ProgressObserver> observers)

Method Details

getBiGGIdFromResources

public Optional<BiGGId> getBiGGIdFromResources(List<String> resources,
 String type)
                                        throws SQLException

Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase. This method processes annotations for biological entities such as Species, Reaction, or GeneProduct. Each entity's annotations are provided as a list of URIs, which are then parsed to retrieve the BiGG ID.

Parameters:

resources - A list of URIs containing annotations for the biological entity.

type - The type of the biological entity, which can be one of the following: BiGGDBContract.Constants.TYPE_SPECIES, BiGGDBContract.Constants.TYPE_REACTION, or BiGGDBContract.Constants.TYPE_GENE_PRODUCT.

Returns:

An containing the BiGG ID if it could be successfully retrieved, otherwise Optional.empty().

Throws:

SQLException