SBMLLevel1Version1Converter Class Reference

Inheritance diagram for SBMLLevel1Version1Converter:

Detailed Description

Whole-document SBML Level/Version converter.

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 takes an SBML document having one SBML Level+Version combination, and attempts to convert it to an SBML document having a different Level+Version combination. This converter (SBMLLevel1Version1Converter) converts models to SBML Level 1 Version 1, to the extent possible by the limited features of that Level/Version combination of SBML.

Configuration and use of SBMLLevel1Version1Converter

SBMLLevel1Version1Converter is enabled by creating a ConversionProperties object with the option "convertToL1V1", and passing this properties object to SBMLDocument::convert(). The target SBML Level and Version combination are determined by the value of the SBML namespace set on the ConversionProperties object (using ConversionProperties::setTargetNamespaces(SBMLNamespaces *targetNS)).

In addition, this converter offers the following options:

• "changePow": Mathematical expressions for exponentiation of the form pow(s1, 2) will be converted to the expression s1^2.

• "inlineCompartmentSizes": Back in the days of SBML Level 1 Version 1, many software tools assumed that the "kinetic laws" of SBML were written in terms of units of concentration/time. These tools would not expect (and thus not handle) rate expressions such as CompartmentOfS1 * k * S1. When the option "inlineCompartmentSizes" is enabled, libSBML will replace the references to compartments (such as "CompartmentOfS1" in this example) with their initial sizes. This is not strictly correct in all cases; in particular, if the compartment volume varies during simulation, this conversion will not reflect the expected behavior. However, many models do not have time-varying compartment sizes, so this option makes it easy to get modern SBML rate expressions into a form that old software tools may better understand.

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() 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(). 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() 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;
props.addOption("replaceReactions");

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.
int status = document->convert(props);
if (status != LIBSBML_OPERATION_SUCCESS)
{
  cerr << "Unable to perform conversion due to the following:" << endl;
  document->printErrors(cerr);
}

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 props;
props.addOption("stripPackage");
props.addOption("package", "layout");
 
int status = document->convert(props);
if (status != LIBSBML_OPERATION_SUCCESS)
{
    cerr << "Unable to strip the Layout package from the model";
    cerr << "Error returned: " << status;
}

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 5.20.4 :

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

Public Member Functions
virtual SBMLLevel1Version1Converter *	clone () const
	Creates and returns a deep copy of this SBMLLevel1Version1Converter object. More...
virtual int	convert ()
	Perform the conversion. More...
virtual ConversionProperties	getDefaultProperties () const
	Returns the default properties of this converter. More...
virtual SBMLDocument *	getDocument ()
	Returns the SBML document that is the subject of the conversions. More...
virtual const SBMLDocument *	getDocument () const
	Returns the SBML document that is the subject of the conversions. More...
const std::string &	getName () const
	Returns the name of this converter. More...
virtual ConversionProperties *	getProperties () const
	Returns the current properties in effect for this converter. More...
virtual SBMLNamespaces *	getTargetNamespaces ()
	Returns the target SBML namespaces of the currently set properties. More...
virtual bool	matchesProperties (const ConversionProperties &props) const
	Returns true if this converter object's properties match the given properties. More...
SBMLLevel1Version1Converter &	operator= (const SBMLLevel1Version1Converter &rhs)
	Assignment operator for SBMLLevel1Version1Converter. More...
	SBMLLevel1Version1Converter ()
	Creates a new SBMLLevel1Version1Converter object. More...
	SBMLLevel1Version1Converter (const SBMLLevel1Version1Converter &obj)
	Copy constructor; creates a copy of an SBMLLevel1Version1Converter object. More...
virtual int	setDocument (const SBMLDocument *doc)
	Sets the SBML document to be converted. More...
virtual int	setDocument (SBMLDocument *doc)
	Sets the SBML document to be converted. More...
virtual int	setProperties (const ConversionProperties *props)
	Sets the configuration properties to be used by this converter. More...
virtual	~SBMLLevel1Version1Converter ()
	Destroys this object. More...

Constructor & Destructor Documentation

SBMLLevel1Version1Converter() [1/2]

SBMLLevel1Version1Converter::SBMLLevel1Version1Converter

(

)

Creates a new SBMLLevel1Version1Converter object.

SBMLLevel1Version1Converter() [2/2]

SBMLLevel1Version1Converter::SBMLLevel1Version1Converter

(

const SBMLLevel1Version1Converter &

obj

)

Copy constructor; creates a copy of an SBMLLevel1Version1Converter object.

Parameters

obj	the SBMLLevel1Version1Converter object to copy.

~SBMLLevel1Version1Converter()

SBMLLevel1Version1Converter::~SBMLLevel1Version1Converter ( )

virtual

Destroys this object.

Member Function Documentation

clone()

SBMLLevel1Version1Converter * SBMLLevel1Version1Converter::clone ( ) const

virtual

Creates and returns a deep copy of this SBMLLevel1Version1Converter object.

Returns

a (deep) copy of this converter.

Reimplemented from SBMLConverter.

convert()

int SBMLLevel1Version1Converter::convert ( )

virtual

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() and with the configuration options set by SBMLConverter::setProperties().

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_CONV_INVALID_TARGET_NAMESPACE
• LIBSBML_CONV_PKG_CONVERSION_NOT_AVAILABLE
• LIBSBML_CONV_INVALID_SRC_DOCUMENT

Reimplemented from SBMLConverter.

getDefaultProperties()

ConversionProperties SBMLLevel1Version1Converter::getDefaultProperties ( ) const

virtual

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.

Returns

the ConversionProperties object describing the default properties for this converter.

Reimplemented from SBMLConverter.

getDocument() [1/2]

SBMLDocument * SBMLConverter::getDocument ( )

virtualinherited

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

Returns

the current SBMLDocument object.

getDocument() [2/2]

const SBMLDocument * SBMLConverter::getDocument ( ) const

virtualinherited

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

Returns

the current SBMLDocument object.

getName()

const std::string & SBMLConverter::getName ( ) const

inherited

Returns the name of this converter.

Returns

a string, the name of this converter.

getProperties()

ConversionProperties * SBMLConverter::getProperties ( ) const

virtualinherited

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(const ConversionProperties *props).

Returns

the currently set configuration properties.

See also

setProperties()

matchesProperties()

getTargetNamespaces()

SBMLNamespaces * SBMLConverter::getTargetNamespaces ( )

virtualinherited

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, in SBMLLevelVersionConverter (the converter for converting SBML documents from one Level+Version combination to another), the actions are fundamentally dependent on the SBML namespaces targeted.

Returns

the SBMLNamespaces object that describes the SBML namespaces in effect, or NULL if none are set.

matchesProperties()

bool SBMLLevel1Version1Converter::matchesProperties ( const ConversionProperties &  props ) const

virtual

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 SBMLLevel1Version1Converter object to find out if the object's property values match the given ones. This method is also used by SBMLConverterRegistry::getConverterFor() to search across all registered converters for one matching particular properties.

Parameters

props

the properties to match.

Returns

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

Reimplemented from SBMLConverter.

operator=()

SBMLLevel1Version1Converter & SBMLLevel1Version1Converter::operator=

(

const SBMLLevel1Version1Converter &

rhs

)

Assignment operator for SBMLLevel1Version1Converter.

Parameters

rhs	the object whose values are used as the basis of the assignment.

setDocument() [1/2]

int SBMLConverter::setDocument ( const SBMLDocument *  doc )

virtualinherited

Sets the SBML document to be converted.

Parameters

doc	the document to use for this conversion.

Returns

integer value indicating the success/failure of the operation. The value is drawn from the enumeration OperationReturnValues_t. 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:

• LIBSBML_OPERATION_SUCCESS

Warning

Even though the argument doc is 'const', it is immediately cast to a non-const version, which is then usually changed by the converter upon a successful conversion. This variant of the setDocument() method is here solely to preserve backwards compatibility.

Reimplemented in SBMLReactionConverter, and SBMLRateOfConverter.

Examples

flattenModel.cpp.

setDocument() [2/2]

int SBMLConverter::setDocument ( SBMLDocument *  doc )

virtualinherited

Sets the SBML document to be converted.

Parameters

doc	the document to use for this conversion.

Returns

integer value indicating the success/failure of the operation. The value is drawn from the enumeration OperationReturnValues_t. 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:

• LIBSBML_OPERATION_SUCCESS

Reimplemented in SBMLReactionConverter, and SBMLRateOfConverter.

setProperties()

int SBMLConverter::setProperties ( const ConversionProperties *  props )

virtualinherited

Sets the configuration properties to be used by this converter.

Parameters

props

the ConversionProperties object defining the properties to set.

Returns

integer value indicating the success/failure of the operation. The value is drawn from the enumeration OperationReturnValues_t. 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

getProperties()

matchesProperties()