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SBMLRuleConverter Class Reference
Inheritance diagram for SBMLRuleConverter:
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Detailed Description

{core} SBML converter for reordering rules and assignments in a model.

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 reorders assignments in a model. Specifically, it sorts the list of assignment rules (i.e., the AssignmentRule objects contained in the ListOfAssignmentRules within the Model object) and the initial assignments (i.e., the InitialAssignment objects contained in the ListOfInitialAssignments) such that, within each set, assignments that depend on prior values are placed after the values are set. For example, if there is an assignment rule stating a = b + 1, and another rule stating b = 3, the list of rules is sorted and the rules are arranged so that the rule for b = 3 appears before the rule for a = b + 1. Similarly, if dependencies of this sort exist in the list of initial assignments in the model, the initial assignments are sorted as well.

Beginning with SBML Level 2, assignment rules have no ordering required—the order in which the rules appear in an SBML file has no significance. Software tools, however, may need to reorder assignments for purposes of evaluating them. For example, for simulators that use time integration methods, it would be a good idea to reorder assignment rules such as the following,

b = a + 10 seconds
a = time

so that the evaluation of the rules is independent of integrator step sizes. (This is due to the fact that, in this case, the order in which the rules are evaluated changes the result.) This converter can be used to reorder the SBML objects regardless of whether the input file contained them in the desired order. Here is a code fragment to illustrate how to do that:

ConversionProperties props;
props.addOption("sortRules", true, "sort rules");

SBMLConverter converter;
converter.setProperties(&props);
converter.setDocument(&doc);
converter.convert(); 
Note
The two sets of assignments (list of assignment rules on the one hand, and list of initial assignments on the other hand) are handled independently. In an SBML model, these entities are treated differently and no amount of sorting can deal with inter-dependencies between assignments of the two kinds.
See also
SBMLFunctionDefinitionConverter
SBMLInitialAssignmentConverter
SBMLLevelVersionConverter
SBMLStripPackageConverter
SBMLUnitsConverter

Public Member Functions

virtual SBMLConverterclone () const
 Creates and returns a deep copy of this SBMLLevelVersionConverter object. More...
 
virtual int convert ()
 Perform the conversion. More...
 
virtual ConversionProperties getDefaultProperties () const
 Returns the default properties of this converter. More...
 
virtual SBMLDocumentgetDocument ()
 Returns the SBML document that is the subject of the conversions. More...
 
virtual const SBMLDocumentgetDocument () const
 Returns the SBML document that is the subject of the conversions. More...
 
virtual ConversionPropertiesgetProperties () const
 Returns the current properties in effect for this converter. More...
 
virtual SBMLNamespacesgetTargetNamespaces ()
 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...
 
 SBMLRuleConverter ()
 Creates a new SBMLLevelVersionConverter object. More...
 
 SBMLRuleConverter (const SBMLRuleConverter &obj)
 Copy constructor; creates a copy of an SBMLLevelVersionConverter object. More...
 
virtual int setDocument (const SBMLDocument *doc)
 Sets the current SBML document to the given SBMLDocument object. More...
 
virtual int setDocument (SBMLDocument *doc)
 Sets the current SBML document to the given SBMLDocument object. More...
 
virtual int setProperties (const ConversionProperties *props)
 Sets the configuration properties to be used by this converter. More...
 
virtual ~SBMLRuleConverter ()
 Destroy this SBMLRuleConverter object. More...
 

Constructor & Destructor Documentation

SBMLRuleConverter::SBMLRuleConverter ( )

Creates a new SBMLLevelVersionConverter object.

SBMLRuleConverter::SBMLRuleConverter ( const SBMLRuleConverter obj)

Copy constructor; creates a copy of an SBMLLevelVersionConverter object.

Parameters
objthe SBMLLevelVersionConverter object to copy.
SBMLRuleConverter::~SBMLRuleConverter ( )
virtual

Destroy this SBMLRuleConverter object.

Member Function Documentation

SBMLConverter * SBMLRuleConverter::clone ( ) const
virtual

Creates and returns a deep copy of this SBMLLevelVersionConverter object.

Returns
a (deep) copy of this converter.

Reimplemented from SBMLConverter.

int SBMLRuleConverter::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 the success/failure of the operation. The possible values are:

Reimplemented from SBMLConverter.

ConversionProperties SBMLRuleConverter::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.

SBMLDocument * SBMLConverter::getDocument ( )
virtualinherited

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

Returns
the current SBMLDocument object.
const SBMLDocument * SBMLConverter::getDocument ( ) const
virtualinherited

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

Returns
the current SBMLDocument object, as a const reference.
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()
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, 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.
bool SBMLRuleConverter::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 SBMLLevelVersionConverter 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
propsthe properties to match.
Returns
true if this converter's properties match, false otherwise.

Reimplemented from SBMLConverter.

int SBMLConverter::setDocument ( const SBMLDocument doc)
virtualinherited

Sets the current SBML document to the given SBMLDocument object.

Parameters
docthe document to use for this conversion.
Warning
Even though the 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 function is here solely to preserve backwards compatibility.
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:

Reimplemented in SBMLReactionConverter.

int SBMLConverter::setDocument ( SBMLDocument doc)
virtualinherited

Sets the current SBML document to the given SBMLDocument object.

Parameters
docthe 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:

Reimplemented in SBMLReactionConverter.

int SBMLConverter::setProperties ( const ConversionProperties props)
virtualinherited

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
propsthe 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:
See also
getProperties()
matchesProperties()