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

Class FBCReactionPolisher

java.lang.Object

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

de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher

All Implemented Interfaces:

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

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

Field Summary

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

polishingParameters, registry

Constructor Summary

Constructors

Constructor	Description
FBCReactionPolisher(org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlugin, PolishingParameters polishingParameters, SBOParameters sboParameters, Registry registry)
FBCReactionPolisher(org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlugin, 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)
void	setFluxBoundSBOTerm(org.sbml.jsbml.Parameter bound)	Polishes the SBO term of a flux bound parameter based on its ID.

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

FBCReactionPolisher

public FBCReactionPolisher(org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlugin,
 PolishingParameters polishingParameters,
 SBOParameters sboParameters,
 Registry registry)

FBCReactionPolisher

public FBCReactionPolisher(org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlugin,
 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)

Specified by:

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

setFluxBoundSBOTerm

public void setFluxBoundSBOTerm(org.sbml.jsbml.Parameter bound)

Polishes the SBO term of a flux bound parameter based on its ID. If the parameter's ID matches the default flux bound pattern, it sets the SBO term to 626. Otherwise, it sets the SBO term to 625.

Parameters:

bound - The parameter representing a flux bound.