Package de.uni_halle.informatik.biodata.mp.polishing

Class CompartmentPolisher

java.lang.Object

de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher

de.uni_halle.informatik.biodata.mp.polishing.CompartmentPolisher

All Implemented Interfaces:

IPolishSBases<org.sbml.jsbml.Compartment>, IReportStatus

public class CompartmentPolisher
extends AbstractPolisher
implements IPolishSBases<org.sbml.jsbml.Compartment>

This class is responsible for polishing the properties of a compartment in an SBML model to ensure compliance with standards and completeness. It handles the annotation processing, ID and name setting, and ensures that necessary attributes like units and spatial dimensions are appropriately set.

Field Summary

Fields inherited from class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher

polishingParameters, registry

Constructor Summary

Constructors

Constructor	Description
CompartmentPolisher(PolishingParameters polishingParameters, Registry registry, List<ProgressObserver> observers)

Method Summary

Modifier and Type	Method	Description
void	polish(List<org.sbml.jsbml.Compartment> compartments)	Polishes all compartments in the given SBML model.
void	polish(org.sbml.jsbml.Compartment compartment)	Polishes the properties of a compartment to ensure compliance with standards and completeness.

Methods inherited from class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher

equals, getObservers, hashCode, statusReport, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

CompartmentPolisher

public CompartmentPolisher(PolishingParameters polishingParameters,
 Registry registry,
 List<ProgressObserver> observers)

Method Details

polish

public void polish(List<org.sbml.jsbml.Compartment> compartments)

Polishes all compartments in the given SBML model. This method iterates through each compartment in the model, updates the progress display, and applies polishing operations defined in the CompartmentPolishing class.

Specified by:

polish in interface IPolishSBases<org.sbml.jsbml.Compartment>

polish

public void polish(org.sbml.jsbml.Compartment compartment)

Polishes the properties of a compartment to ensure compliance with standards and completeness. This method processes annotations, sets default values for missing identifiers, names, and meta identifiers, and ensures that the compartment has appropriate units and other necessary attributes set.

Specified by:

polish in interface IPolishSBases<org.sbml.jsbml.Compartment>