org.sbml.libsbml
Class SBMLConverter

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

Direct Known Subclasses:

SBMLFunctionDefinitionConverter, SBMLInitialAssignmentConverter, SBMLLevelVersionConverter, SBMLRuleConverter, SBMLStripPackageConverter, SBMLUnitsConverter

public class SBMLConverter
extends Object

Base class for SBML converters.

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.

The SBMLConverter class is the base class for the various SBML converters: classes of objects that transform or convert SBML documents. These transformations can involve essentially anything that can be written algorithmically; examples include converting the units of measurement in a model, or converting from one Level+Version combination of SBML to another.

LibSBML provides a number of built-in converters, and applications can create their own by subclassing SBMLConverter and following the examples of the existing converters. The following are the built-in converters in libSBML 5.8.0:

• SBMLFunctionDefinitionConverter
• SBMLInitialAssignmentConverter
• SBMLLevelVersionConverter
• SBMLRuleConverter
• SBMLStripPackageConverter
• SBMLUnitsConverter

Many converters provide the ability to configure their behavior to some extent. This is realized through the use of properties that offer different options. Two related classes implement these features: ConversionProperties and ConversionOptions. The default property values for each converter can be interrogated using the method SBMLConverter.getDefaultProperties() on the converter class.

Constructor Summary

SBMLConverter()
Creates a new SBMLConverter object.

SBMLConverter(SBMLConverter c)
Copy constructor; creates a copy of an SBMLConverter object.

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.
SBMLDocument	getDocument() Returns the SBML document that is the subject of the conversions.
ConversionProperties	getProperties() Returns the current properties in effect for this converter.
SBMLNamespaces	getTargetNamespaces() Returns the target SBML namespaces of the currently set properties.
boolean	matchesProperties(ConversionProperties props) Predicate returning true if this converter's properties matches a given set of configuration properties.
int	setDocument(SBMLDocument doc) Sets the current SBML document to the given SBMLDocument object.
int	setProperties(ConversionProperties props) Sets the configuration properties to be used by this converter.
void	swigReleaseOwnership()
void	swigTakeOwnership()

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLConverter

public SBMLConverter()

Creates a new SBMLConverter object.

SBMLConverter

public SBMLConverter(SBMLConverter c)

Copy constructor; creates a copy of an SBMLConverter object.

Parameters:

c - the SBMLConverter object to copy.

Throws:

SBMLConstructorException - Thrown if the argument orig is null.

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 SBMLConverter.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 SBMLConverter.delete() themselves.

swigReleaseOwnership

public void swigReleaseOwnership()

swigTakeOwnership

public void swigTakeOwnership()

cloneObject

public SBMLConverter cloneObject()

Creates and returns a deep copy of this SBMLConverter object.

Returns:

a (deep) copy of this SBMLConverter object.

getDocument

public SBMLDocument getDocument()

Returns the SBML document that is the subject of the conversions.

Returns:

the current SBMLDocument object.

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).

Returns:

the default properties for the converter.

See Also:

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

getTargetNamespaces

public SBMLNamespaces getTargetNamespaces()

Returns the target SBML namespaces of the currently set properties.

SBML namespaces are used by libSBML to express the Level+Version of the SBML document (and, possibly, any SBML Level 3 packages in use). Some converters' behavior is affected by the SBML namespace configured in the converter. For example, the actions of SBMLLevelVersionConverter, the converter for converting SBML documents from one Level+Version combination to another, are fundamentally dependent on the SBML namespaces being targeted.

Returns:

the SBMLNamespaces object that describes the SBML namespaces in effect.

matchesProperties

public boolean matchesProperties(ConversionProperties props)

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

Parameters:

props - the configuration properties to match.

Returns:

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

setDocument

public int setDocument(SBMLDocument doc)

Sets the current SBML document to the given SBMLDocument object.

Parameters:

doc - the document to use for this conversion.

Returns:

integer value indicating the success/failure of the operation. The set of possible values that may be returned ultimately depends on the specific subclass of SBMLConverter being used, but the default method can return the following values:

• LIBSBML_OPERATION_SUCCESS

setProperties

public int setProperties(ConversionProperties props)

Sets the configuration properties to be used by 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 sets the current properties for this converter.

Parameters:

props - the ConversionProperties object defining the properties to set.

Returns:

integer value indicating the success/failure of the operation. The set of possible values that may be returned ultimately depends on the specific subclass of SBMLConverter being used, but the default method can return the following values:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

See Also:

SBMLConverter.getProperties(), SBMLConverter.matchesProperties(ConversionProperties props)

getProperties

public ConversionProperties getProperties()

Returns the current properties in effect for 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 current properties for this converter; in other words, the settings in effect at this moment. To change the property values, you can use SBMLConverter.setProperties(ConversionProperties props).

Returns:

the currently set configuration properties.

See Also:

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

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).

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.