libSBML Perl API
libSBML 5.17.2 Perl API
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{core}
Converter that removes SBML initial assignments.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 is an SBML converter for replacing InitialAssignment objects, when possible, by setting the initial value attributes on the model objects being assigned. In other words, for every object that is the target of an initial assignment in the model, the converter evaluates the mathematical expression of the assignment to get a numerical value, and then sets the corresponding attribute of the object to the value. The effects for different kinds of SBML components are as follows:
Component | Effect |
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Compartment | Sets the value of the size attribute. |
Species | Sets the value of either the initialAmount or the initialConcentration attributes, depending on the value of the Species object's hasOnlySubstanceUnits attribute. |
Parameter | Sets the value of the value attribute. |
SpeciesReference | Sets the value of the stoichiometry attribute in the Reaction object where the SpeciesReference object appears. |
SBMLInitialAssignmentConverter is enabled by creating a ConversionProperties object with the option "expandInitialAssignments"
, and passing this properties object to SBMLDocument::convert(). The converter offers no other options.
Public Member Functions | |
virtual SBMLInitialAssignmentConverter * | clone () const |
Creates and returns a deep copy of this SBMLInitialAssignmentConverter 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... | |
SBMLInitialAssignmentConverter () | |
Creates a new SBMLInitialAssignmentConverter object. More... | |
SBMLInitialAssignmentConverter (const SBMLInitialAssignmentConverter &obj) | |
Copy constructor; creates a copy of an SBMLInitialAssignmentConverter 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 | ~SBMLInitialAssignmentConverter () |
Destroy this SBMLInitialAssignmentConverter object. More... | |
SBMLInitialAssignmentConverter::SBMLInitialAssignmentConverter | ( | ) |
Creates a new SBMLInitialAssignmentConverter object.
SBMLInitialAssignmentConverter::SBMLInitialAssignmentConverter | ( | const SBMLInitialAssignmentConverter & | obj | ) |
Copy constructor; creates a copy of an SBMLInitialAssignmentConverter object.
obj | the SBMLInitialAssignmentConverter object to copy. |
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virtual |
Destroy this SBMLInitialAssignmentConverter object.
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virtual |
Creates and returns a deep copy of this SBMLInitialAssignmentConverter object.
Reimplemented from SBMLConverter.
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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().
Reimplemented from SBMLConverter.
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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.
Reimplemented from SBMLConverter.
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virtualinherited |
Returns the SBML document that is the subject of the conversions.
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virtualinherited |
Returns the SBML document that is the subject of the conversions.
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inherited |
Returns the name of this converter.
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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).
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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.
NULL
if none are set.
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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 SBMLInitialAssignmentConverter 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.
props | the properties to match. |
true
if this converter's properties match, false
otherwise. Reimplemented from SBMLConverter.
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virtualinherited |
Sets the SBML document to be converted.
doc | the document to use for this conversion. |
Reimplemented in SBMLReactionConverter, and SBMLRateOfConverter.
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virtualinherited |
Sets the SBML document to be converted.
doc | the document to use for this conversion. |
Reimplemented in SBMLReactionConverter, and SBMLRateOfConverter.
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virtualinherited |
Sets the configuration properties to be used by this converter.
props | the ConversionProperties object defining the properties to set. |