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

Class UnitPolisher

java.lang.Object

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

de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher

All Implemented Interfaces:

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

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

This class is responsible for ensuring that all necessary UnitDefinitions and Units are correctly defined and present in the SBML model. It handles the creation and verification of units used in the model, particularly focusing on the units related to growth, substance, time, and volume.

Additionally, this class is responsible for accurately assigning these defined units to specific components such as reactions, species, and parameters within the model as needed. This ensures that all these components adhere uniformly to the correct unit specifications, maintaining consistency and accuracy throughout the model's unit definitions.

Field Summary

Fields

Modifier and Type	Field	Description
static final org.sbml.jsbml.CVTerm	CV_TERM_DESCRIBED_BY_PUBMED_GROWTH_UNIT
static final org.sbml.jsbml.CVTerm	CV_TERM_IS_SUBSTANCE_UNIT
static final org.sbml.jsbml.CVTerm	CV_TERM_IS_TIME_UNIT
static final org.sbml.jsbml.CVTerm	CV_TERM_IS_UO_GRAM
static final org.sbml.jsbml.CVTerm	CV_TERM_IS_UO_HOUR
static final org.sbml.jsbml.CVTerm	CV_TERM_IS_UO_MMOL
static final org.sbml.jsbml.CVTerm	CV_TERM_IS_UO_SECOND
static final org.sbml.jsbml.CVTerm	CV_TERM_IS_VERSION_OF_UO_MOLE
static final org.sbml.jsbml.CVTerm	CV_TERM_IS_VERSION_OF_UO_SECOND
static final org.sbml.jsbml.CVTerm	CV_TERM_IS_VOLUME_UNIT
static final String	GROWTH_UNIT_ID
static final String	GROWTH_UNIT_NAME

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

polishingParameters, registry

Constructor Summary

Constructors

Constructor	Description
UnitPolisher(PolishingParameters parameters, Registry registry)
UnitPolisher(PolishingParameters parameters, Registry registry, List<ProgressObserver> observers)

Method Summary

Modifier and Type	Method	Description
void	polish(org.sbml.jsbml.Model model)	Ensures that all necessary UnitDefinitions and Units are present in the model.

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

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

polish

Field Details

CV_TERM_DESCRIBED_BY_PUBMED_GROWTH_UNIT

public static final org.sbml.jsbml.CVTerm CV_TERM_DESCRIBED_BY_PUBMED_GROWTH_UNIT

GROWTH_UNIT_ID

public static final String GROWTH_UNIT_ID

See Also:

• Constant Field Values

GROWTH_UNIT_NAME

public static final String GROWTH_UNIT_NAME

See Also:

• Constant Field Values

CV_TERM_IS_SUBSTANCE_UNIT

public static final org.sbml.jsbml.CVTerm CV_TERM_IS_SUBSTANCE_UNIT

CV_TERM_IS_TIME_UNIT

public static final org.sbml.jsbml.CVTerm CV_TERM_IS_TIME_UNIT

CV_TERM_IS_VOLUME_UNIT

public static final org.sbml.jsbml.CVTerm CV_TERM_IS_VOLUME_UNIT

CV_TERM_IS_UO_SECOND

public static final org.sbml.jsbml.CVTerm CV_TERM_IS_UO_SECOND

CV_TERM_IS_UO_HOUR

public static final org.sbml.jsbml.CVTerm CV_TERM_IS_UO_HOUR

CV_TERM_IS_UO_MMOL

public static final org.sbml.jsbml.CVTerm CV_TERM_IS_UO_MMOL

CV_TERM_IS_UO_GRAM

public static final org.sbml.jsbml.CVTerm CV_TERM_IS_UO_GRAM

CV_TERM_IS_VERSION_OF_UO_SECOND

public static final org.sbml.jsbml.CVTerm CV_TERM_IS_VERSION_OF_UO_SECOND

CV_TERM_IS_VERSION_OF_UO_MOLE

public static final org.sbml.jsbml.CVTerm CV_TERM_IS_VERSION_OF_UO_MOLE

Constructor Details

UnitPolisher

public UnitPolisher(PolishingParameters parameters,
 Registry registry)

UnitPolisher

public UnitPolisher(PolishingParameters parameters,
 Registry registry,
 List<ProgressObserver> observers)

Method Details

polish

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

Ensures that all necessary UnitDefinitions and Units are present in the model. If any are missing, they are created and added to the model. This method also sets the model's extent and substance units if they are not already set.

Specified by:

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