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

Class ModelPolisher

java.lang.Object

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

de.uni_halle.informatik.biodata.mp.polishing.ModelPolisher

All Implemented Interfaces:

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

public class ModelPolisher
extends AbstractPolisher
implements IPolishSBases<org.sbml.jsbml.Model>

This class provides functionality to polish an SBML (Systems Biology Markup Language) document. Polishing involves enhancing the document with additional annotations, setting appropriate SBO (Systems Biology Ontology) terms, and ensuring the document adheres to certain standards and conventions useful for computational models in systems biology. The class supports operations such as checking the document's structure, polishing individual model components, and processing external resources linked within the document.

Field Summary

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

polishingParameters, registry

Constructor Summary

Constructors

Constructor	Description
ModelPolisher(PolishingParameters polishingParameters, SBOParameters sboParameters, Registry registry)
ModelPolisher(PolishingParameters polishingParameters, SBOParameters sboParameters, Registry registry, List<ProgressObserver> observers)

Method Summary

Modifier and Type	Method	Description
void	polish(org.sbml.jsbml.Model model)	This method orchestrates the polishing of an SBML model by delegating tasks to specific polishing methods for different components of the model.
String	toString()

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

equals, getObservers, hashCode, statusReport

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSBases

polish

Constructor Details

ModelPolisher

public ModelPolisher(PolishingParameters polishingParameters,
 SBOParameters sboParameters,
 Registry registry)

ModelPolisher

public ModelPolisher(PolishingParameters polishingParameters,
 SBOParameters sboParameters,
 Registry registry,
 List<ProgressObserver> observers)

Method Details

polish

public void polish(org.sbml.jsbml.Model model)

This method orchestrates the polishing of an SBML model by delegating tasks to specific polishing methods for different components of the model. It initializes a progress bar to track and display the progress of the polishing process.

Specified by:

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

Parameters:

model - The SBML Model to be polished.

toString

public String toString()

Overrides:

toString in class AbstractPolisher