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

Class BiGGCVTermAnnotator<T extends org.sbml.jsbml.SBase>

java.lang.Object

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

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

de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCVTermAnnotator<T>

All Implemented Interfaces:

IReportDiffs, IReportStatus

Direct Known Subclasses:

BiGGGeneProductAnnotator, BiGGReactionsAnnotator, BiGGSpeciesAnnotator

public abstract class BiGGCVTermAnnotator<T extends org.sbml.jsbml.SBase>
extends AbstractBiGGAnnotator

Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms. This class defines the basic structure and operations for adding annotations to SBML elements based on BiGG IDs. It includes methods to check the validity of BiGG IDs, add annotations to SBML elements, and specifically handle annotations for Species and Reactions using data from BiGG and other databases.

Field Summary

Fields inherited from class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator

bigg, biGGAnnotationParameters, registry

Constructor Summary

Constructors

Constructor	Description
BiGGCVTermAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry)
BiGGCVTermAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry, List<ProgressObserver> observers)

Method Summary

Modifier and Type	Method	Description
protected abstract BiGGId	findBiGGId(T element)	Abstract method to check the validity of a BiGG ID.

Methods inherited from class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator

getBiGGIdFromResources

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

Constructor Details

BiGGCVTermAnnotator

public BiGGCVTermAnnotator(BiGGDB bigg,
 BiGGAnnotationParameters parameters,
 Registry registry)

BiGGCVTermAnnotator

public BiGGCVTermAnnotator(BiGGDB bigg,
 BiGGAnnotationParameters parameters,
 Registry registry,
 List<ProgressObserver> observers)

Method Details

findBiGGId

protected abstract BiGGId findBiGGId(T element)
                              throws SQLException

Abstract method to check the validity of a BiGG ID. Implementations should return an Optional containing the BiGG ID if it is valid, or an empty Optional if not.

Returns:

Optional containing the valid BiGG ID or empty if the ID is invalid.

Throws:

SQLException