org.sbml.libsbml

Class SBMLLocalParameterConverter

java.lang.Object

org.sbml.libsbml.SBMLConverter

org.sbml.libsbml.SBMLLocalParameterConverter

public class SBMLLocalParameterConverter
extends SBMLConverter

Converter to turn local parameters into global ones.

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 converter essentially promotes local parameters to global parameters. It works by examining every Reaction object for LocalParameter objects, then creating Parameter objects on the model for each one found, and finally removing the original LocalParameter objects. It creates new identifiers for the fresh Parameter objects by concatenating the identifier of the reaction with the identifier of the original LocalParameter object.

This converter can be useful for software applications that do not have the ability to handle local parameters on reactions. Such applications could check incoming models for local parameters and run those models through this converter before proceeding with other steps.

Configuration and use of SBMLLocalParameterConverter

SBMLLocalParameterConverter is enabled by creating a ConversionProperties object with the option 'promoteLocalParameters', and passing this properties object to SBMLDocument.convert(ConversionProperties). The converter offers no other options.

General information about the use of SBML converters

The use of all the converters follows a similar approach. First, one creates a ConversionProperties object and calls ConversionProperties.addOption(ConversionOption) on this object with one argument: a text string that identifies the desired converter. (The text string is specific to each converter; consult the documentation for a given converter to find out how it should be enabled.)

Next, for some converters, the caller can optionally set some converter-specific properties using additional calls to ConversionProperties.addOption(ConversionOption). Many converters provide the ability to configure their behavior to some extent; this is realized through the use of properties that offer different options. The default property values for each converter can be interrogated using the method SBMLConverter.getDefaultProperties() on the converter class in question .

Finally, the caller should invoke the method SBMLDocument.convert(ConversionProperties) with the ConversionProperties object as an argument.

Example of invoking an SBML converter

The following code fragment illustrates an example using SBMLReactionConverter, which is invoked using the option string 'replaceReactions':

ConversionProperties props = new ConversionProperties();
if (props != null) {
  props.addOption('replaceReactions');
} else {
  // Deal with error.
}

In the case of SBMLReactionConverter, there are no options to affect its behavior, so the next step is simply to invoke the converter on an SBMLDocument object. Continuing the example code:

  // Assume that the variable 'document' has been set to an SBMLDocument object.
  status = document.convert(config);
  if (status != libsbml.LIBSBML_OPERATION_SUCCESS)
  {
    // Handle error somehow.
    System.out.println('Error: conversion failed due to the following:');
    document.printErrors();
  }

Here is an example of using a converter that offers an option. The following code invokes SBMLStripPackageConverter to remove the SBML Level 3 Layout package from a model. It sets the name of the package to be removed by adding a value for the option named 'package' defined by that converter:

ConversionProperties config = new ConversionProperties();
if (config != None) {
  config.addOption('stripPackage');
  config.addOption('package', 'layout');
  status = document.convert(config);
  if (status != LIBSBML_OPERATION_SUCCESS) {
    // Handle error somehow.
    System.out.println('Error: unable to strip the Layout package');
    document.printErrors();
  }
} else {
  // Handle error somehow.
  System.out.println('Error: unable to create ConversionProperties object');
}

Available SBML converters in libSBML

LibSBML provides a number of built-in converters; by convention, their names end in Converter. The following are the built-in converters provided by libSBML 5.18.0:

• CobraToFbcConverter
• CompFlatteningConverter
• FbcToCobraConverter
• FbcV1ToV2Converter
• FbcV2ToV1Converter
• RenderLayoutConverter
• SBMLFunctionDefinitionConverter
• SBMLIdConverter
• SBMLInferUnitsConverter
• SBMLInitialAssignmentConverter
• SBMLLevel1Version1Converter
• SBMLLevelVersionConverter
• SBMLLocalParameterConverter
• SBMLRateOfConverter
• SBMLReactionConverter
• SBMLRuleConverter
• SBMLStripPackageConverter
• SBMLUnitsConverter

Constructor Summary

Constructors

Constructor and Description
SBMLLocalParameterConverter() Creates a new SBMLLocalParameterConverter object.
SBMLLocalParameterConverter(SBMLLocalParameterConverter obj) Copy constructor; creates a copy of an SBMLLocalParameterConverter object.

Method Summary

Modifier and Type	Method and Description
SBMLConverter	cloneObject() Creates and returns a deep copy of this SBMLLocalParameterConverter object.
int	convert() Perform the conversion.
void	delete() Explicitly deletes the underlying native object.
ConversionProperties	getDefaultProperties() Returns the default properties of this converter.
boolean	matchesProperties(ConversionProperties props) Returns true if this converter object's properties match the given properties.

Methods inherited from class org.sbml.libsbml.SBMLConverter

getDocument, getName, getProperties, getTargetNamespaces, setDocument, setProperties

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLLocalParameterConverter

public SBMLLocalParameterConverter()

Creates a new SBMLLocalParameterConverter object.

SBMLLocalParameterConverter

public SBMLLocalParameterConverter(SBMLLocalParameterConverter obj)

Copy constructor; creates a copy of an SBMLLocalParameterConverter object.

Parameters:

obj - the SBMLLocalParameterConverter object to copy.

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 SBMLLocalParameterConverter.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 SBMLLocalParameterConverter.delete() themselves.

Overrides:

delete in class SBMLConverter

cloneObject

public SBMLConverter cloneObject()

Creates and returns a deep copy of this SBMLLocalParameterConverter object.

Overrides:

cloneObject in class SBMLConverter

Returns:

a (deep) copy of this converter.

matchesProperties

public boolean matchesProperties(ConversionProperties props)

Returns true if this converter object's properties match the given properties.

A typical use of this method involves creating a ConversionProperties object, setting the options desired, and then calling this method on an SBMLLocalParameterConverter object to find out if the object's property values match the given ones. This method is also used by SBMLConverterRegistry.getConverterFor(ConversionProperties) to search across all registered converters for one matching particular properties.

Overrides:

matchesProperties in class SBMLConverter

Parameters:

props - the 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) and with the configuration options set by SBMLConverter.setProperties(ConversionProperties).

Overrides:

convert in class SBMLConverter

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_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.

Overrides:

getDefaultProperties in class SBMLConverter

Returns:

the ConversionProperties object describing the default properties for this converter.

See Also:

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