libSBML C++ API
5.18.0
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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. Applications can also create their own converters by subclassing SBMLConverter and following the examples of the existing 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.
The following code fragment illustrates an example using SBMLReactionConverter, which is invoked using the option string "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:
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:
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:
Public Member Functions | |
virtual SBMLConverter * | clone () const |
Creates and returns a deep copy of this SBMLConverter 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 matches the given properties. More... | |
SBMLConverter & | operator= (const SBMLConverter &rhs) |
Assignment operator for SBMLConverter. More... | |
SBMLConverter () | |
Creates a new SBMLConverter object. More... | |
SBMLConverter (const std::string &name) | |
Creates a new SBMLConverter object with a given name. More... | |
SBMLConverter (const SBMLConverter &orig) | |
Copy constructor. 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 | ~SBMLConverter () |
Destroy this SBMLConverter object. More... | |
SBMLConverter::SBMLConverter | ( | ) |
Creates a new SBMLConverter object.
SBMLConverter::SBMLConverter | ( | const std::string & | name | ) |
Creates a new SBMLConverter object with a given name.
name | the name for the converter to create. |
SBMLConverter::SBMLConverter | ( | const SBMLConverter & | orig | ) |
Copy constructor.
This creates a copy of an SBMLConverter object.
orig | the SBMLConverter object to copy. |
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Destroy this SBMLConverter object.
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Creates and returns a deep copy of this SBMLConverter object.
Reimplemented in CompFlatteningConverter, SBMLLevelVersionConverter, SBMLLevel1Version1Converter, SBMLUnitsConverter, SBMLInitialAssignmentConverter, SBMLRuleConverter, SBMLStripPackageConverter, SBMLIdConverter, SBMLFunctionDefinitionConverter, SBMLInferUnitsConverter, SBMLReactionConverter, SBMLLocalParameterConverter, SBMLRateOfConverter, RenderLayoutConverter, CobraToFbcConverter, FbcToCobraConverter, FbcV1ToV2Converter, and FbcV2ToV1Converter.
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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 in CompFlatteningConverter, SBMLLevelVersionConverter, SBMLLevel1Version1Converter, SBMLInitialAssignmentConverter, SBMLRuleConverter, SBMLUnitsConverter, SBMLStripPackageConverter, SBMLIdConverter, SBMLFunctionDefinitionConverter, SBMLReactionConverter, SBMLInferUnitsConverter, SBMLRateOfConverter, SBMLLocalParameterConverter, CobraToFbcConverter, FbcToCobraConverter, FbcV1ToV2Converter, FbcV2ToV1Converter, and RenderLayoutConverter.
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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(const ConversionProperties *props).
Reimplemented in CompFlatteningConverter, SBMLLevelVersionConverter, SBMLLevel1Version1Converter, SBMLInitialAssignmentConverter, SBMLRuleConverter, SBMLUnitsConverter, SBMLStripPackageConverter, SBMLIdConverter, SBMLFunctionDefinitionConverter, SBMLReactionConverter, SBMLInferUnitsConverter, SBMLRateOfConverter, SBMLLocalParameterConverter, FbcV1ToV2Converter, CobraToFbcConverter, FbcToCobraConverter, FbcV2ToV1Converter, and RenderLayoutConverter.
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Returns the SBML document that is the subject of the conversions.
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Returns the SBML document that is the subject of the conversions.
const std::string & SBMLConverter::getName | ( | ) | const |
Returns the name of this converter.
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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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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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Returns true
if this converter matches the given properties.
Given a ConversionProperties object props
, this method checks that props
possesses an option value to enable this converter. If it does, this method returns true
.
props | the properties to match. |
true
if the properties props
would match the necessary properties for this type of converter, false
otherwise. Reimplemented in CompFlatteningConverter, SBMLLevelVersionConverter, SBMLLevel1Version1Converter, SBMLInitialAssignmentConverter, SBMLRuleConverter, SBMLUnitsConverter, SBMLStripPackageConverter, SBMLIdConverter, SBMLFunctionDefinitionConverter, SBMLReactionConverter, SBMLInferUnitsConverter, SBMLLocalParameterConverter, SBMLRateOfConverter, RenderLayoutConverter, CobraToFbcConverter, FbcToCobraConverter, FbcV1ToV2Converter, and FbcV2ToV1Converter.
SBMLConverter & SBMLConverter::operator= | ( | const SBMLConverter & | rhs | ) |
Assignment operator for SBMLConverter.
rhs | the object whose values are used as the basis of the assignment. |
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Sets the SBML document to be converted.
doc | the document to use for this conversion. |
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.
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Sets the SBML document to be converted.
doc | the document to use for this conversion. |
Reimplemented in SBMLReactionConverter, and SBMLRateOfConverter.
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Sets the configuration properties to be used by this converter.
props | the ConversionProperties object defining the properties to set. |