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

Class BiGGSBMLAnnotator

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.BiGGSBMLAnnotator

All Implemented Interfaces:

IAnnotateSBases<org.sbml.jsbml.SBMLDocument>, IReportDiffs, IReportStatus

public class BiGGSBMLAnnotator
extends AbstractBiGGAnnotator
implements IAnnotateSBases<org.sbml.jsbml.SBMLDocument>

This class is responsible for annotating SBML models using data from the BiGG database. It handles the addition of annotations related to compartments, species, reactions, and gene products.

Field Summary

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

bigg, biGGAnnotationParameters, registry

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	annotate(org.sbml.jsbml.SBMLDocument doc)	Annotates an SBMLDocument using data from the BiGG Knowledgebase.

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

Methods inherited from interface de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases

annotate

Constructor Details

BiGGSBMLAnnotator

public BiGGSBMLAnnotator(BiGGDB bigg,
 BiGGAnnotationParameters parameters,
 SBOParameters sboParameters,
 Registry registry)

BiGGSBMLAnnotator

public BiGGSBMLAnnotator(BiGGDB bigg,
 BiGGAnnotationParameters parameters,
 SBOParameters sboParameters,
 Registry registry,
 List<ProgressObserver> observers)

Method Details

annotate

public void annotate(org.sbml.jsbml.SBMLDocument doc)
              throws SQLException,
AnnotationException

Annotates an SBMLDocument using data from the BiGG Knowledgebase. This method processes various components of the SBML model such as compartments, species, reactions, and gene products by adding relevant annotations from BiGG. It also handles the addition of publications and notes related to the model.

Specified by:

annotate in interface IAnnotateSBases<org.sbml.jsbml.SBMLDocument>

Parameters:

doc - The SBMLDocument that contains the model to be annotated.

Throws:

SQLException

AnnotationException