org.sbml.libsbml
Class SBMLUnitsConverter

java.lang.Object
  org.sbml.libsbml.SBMLConverter
      org.sbml.libsbml.SBMLUnitsConverter

public class SBMLUnitsConverter
extends SBMLConverter

SBML converter to convert a model's units to SI units.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. It is a class used in the implementation of extra functionality provided by libSBML.

This SBML converter converts the units in a model to base SI units, namely metre, kilogram, second, Ampere, Kelvin, mole and candela.

Unit conversion will only be performed on models that are fully unit consistent; that is, all objects have associated units, and there are no literal numbers with no units specified. In the case of an SBML Level 3 model involving math expressions, this means that the timeUnits attribute on the Model object must be set, and if there are any reactions in the model, the extentUnits attribute on the Model object must also be set.

This converter has the additional Boolean property 'removeUnusedUnits' that can be used to tell the converter whether to remove any UnitDefinition objects that are not referred to, after conversion is complete. You can set this value by adding the property using

prop.addOption('removeUnusedUnits', false);

The converter's default behavior is to remove the unused UnitDefinition objects in the model.

See Also:

SBMLFunctionDefinitionConverter, SBMLLevelVersionConverter, SBMLRuleConverter, SBMLStripPackageConverter, SBMLUnitsConverter

Constructor Summary

SBMLUnitsConverter()

SBMLUnitsConverter(SBMLUnitsConverter obj)

Method Summary

SBMLConverter	cloneObject() Creates and returns a deep copy of this SBMLConverter object.
int	convert() Perform the conversion.
void	delete() Explicitly deletes the underlying native object.
ConversionProperties	getDefaultProperties() Returns the default properties of this converter.
static void	init()
boolean	matchesProperties(ConversionProperties props) Predicate returning true if this converter's properties matches a given set of configuration properties.

Methods inherited from class org.sbml.libsbml.SBMLConverter

getDocument, getProperties, getTargetNamespaces, setDocument, setProperties, swigReleaseOwnership, swigTakeOwnership

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SBMLUnitsConverter

public SBMLUnitsConverter()

SBMLUnitsConverter

public SBMLUnitsConverter(SBMLUnitsConverter obj)

Method Detail

delete

public void delete()

Explicitly deletes the underlying native object.

In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the SBMLUnitsConverter.delete() method on the libSBML object.

This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke SBMLUnitsConverter.delete() themselves.

Overrides:

delete in class SBMLConverter

init

public static void init()

cloneObject

public SBMLConverter cloneObject()

Creates and returns a deep copy of this SBMLConverter object.

Overrides:

cloneObject in class SBMLConverter

Returns:

a (deep) copy of this SBMLConverter object.

matchesProperties

public boolean matchesProperties(ConversionProperties props)

Predicate returning true if this converter's properties matches a given set of configuration properties.

Overrides:

matchesProperties in class SBMLConverter

Parameters:

props - the configuration properties to match.

Returns:

true if this converter's properties match, false otherwise.

convert

public int convert()

Perform the conversion.

This method causes the converter to do the actual conversion work, that is, to convert the SBMLDocument object set by SBMLConverter.setDocument(SBMLDocument doc) and with the configuration options set by SBMLConverter.setProperties(ConversionProperties props).

Overrides:

convert in class SBMLConverter

Returns:

integer value indicating the success/failure of the operation. The set of possible values that may be returned depends on the converter subclass; please consult the documentation for the relevant class to find out what the possibilities are.

getDefaultProperties

public ConversionProperties getDefaultProperties()

Returns the default properties of this converter.

A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method returns the default property settings for this converter. It is meant to be called in order to discover all the settings for the converter object. The run-time properties of the converter object can be adjusted by using the method SBMLConverter.setProperties(ConversionProperties props).

Overrides:

getDefaultProperties in class SBMLConverter

Returns:

the default properties for the converter.

See Also:

SBMLConverter.setProperties(ConversionProperties props), SBMLUnitsConverter.matchesProperties(ConversionProperties props)