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

Class ReactionsPolisher

java.lang.Object

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

de.uni_halle.informatik.biodata.mp.polishing.ReactionsPolisher

All Implemented Interfaces:

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

public class ReactionsPolisher
extends AbstractPolisher
implements IPolishSBases<org.sbml.jsbml.Reaction>

This class provides methods to polish and validate SBML reactions according to specific rules and patterns. It includes functionality to: - Check and set SBO terms based on reaction ID patterns. - Polish species references and compartments. - Validate and set flux bounds and objectives. - Convert gene associations from reaction notes to FBCv2 format. - Check mass and atom balance of reactions.

The class operates on an SBML Reaction object and modifies it to conform to standards and conventions used in systems biology models, particularly those related to flux balance constraints.

Field Summary

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

polishingParameters, registry

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	polish(List<org.sbml.jsbml.Reaction> reactions)
void	polish(org.sbml.jsbml.Reaction reaction)	Polishes the reaction by applying various checks and modifications to ensure it conforms to the expected standards and conventions.

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

ReactionsPolisher

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

ReactionsPolisher

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

Method Details

polish

public void polish(List<org.sbml.jsbml.Reaction> reactions)

Specified by:

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

polish

public void polish(org.sbml.jsbml.Reaction reaction)

Polishes the reaction by applying various checks and modifications to ensure it conforms to the expected standards and conventions. This includes setting SBO terms, checking compartments, and ensuring proper setup of reactants and products.

Specified by:

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