libSBML Perl API  libSBML 5.17.2 Perl API
CobraToFbcConverter Class Reference
Inheritance diagram for CobraToFbcConverter:
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Detailed Description

{fbc}

fbc COBRA to SBML Level 3 “fbc” 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 converter takes a model in COBRA format and converts it to the “fbc” Version 2 format.

CobraToFbcConverter is enabled by creating a ConversionProperties object with the option "convert cobra" (literally that full string, including the spaces), and passing this properties object to SBMLDocument::convert(). The converter offers two options:

  • "checkCompatibility": whether to check the SBML Level/Version compatibility
  • "removeUnits": whether to remove unit definitions

Public Member Functions

bool checkCompatibility () const
 Returns true if the option property to check Level and Version of the source document ("checkCompatibility") is true. More...
 
virtual CobraToFbcConverterclone () const
 Creates and returns a deep copy of this CobraToFbcConverter object. More...
 
 CobraToFbcConverter ()
 Creates a new CobraToFbcConverter object. More...
 
 CobraToFbcConverter (const CobraToFbcConverter &orig)
 Copy constructor; creates a copy of an CobraToFbcConverter 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...
 
const std::string & getName () const
 Returns the name of this converter. 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...
 
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 ~CobraToFbcConverter ()
 Destroy this CobraToFbcConverter object. More...
 

Constructor & Destructor Documentation

◆ CobraToFbcConverter() [1/2]

CobraToFbcConverter::CobraToFbcConverter ( )

Creates a new CobraToFbcConverter object.

◆ CobraToFbcConverter() [2/2]

CobraToFbcConverter::CobraToFbcConverter ( const CobraToFbcConverter orig)

Copy constructor; creates a copy of an CobraToFbcConverter object.

Parameters
origthe CobraToFbcConverter object to copy.

◆ ~CobraToFbcConverter()

CobraToFbcConverter::~CobraToFbcConverter ( )
virtual

Destroy this CobraToFbcConverter object.

Member Function Documentation

◆ checkCompatibility()

bool CobraToFbcConverter::checkCompatibility ( ) const

Returns true if the option property to check Level and Version of the source document ("checkCompatibility") is true.

Returns
true if the option "checkCompatibility" has been set to true, false otherwise.

◆ clone()

CobraToFbcConverter * CobraToFbcConverter::clone ( ) const
virtual

Creates and returns a deep copy of this CobraToFbcConverter object.

Returns
a (deep) copy of this CobraToFbcConverter.

Reimplemented from SBMLConverter.

◆ convert()

int CobraToFbcConverter::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().

Reimplemented from SBMLConverter.

◆ getDefaultProperties()

ConversionProperties CobraToFbcConverter::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 CobraToFbcConverter::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 CobraToFbcConverter 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.

◆ setDocument() [1/2]

int SBMLConverter::setDocument ( const SBMLDocument doc)
virtualinherited

Sets the SBML document to be converted.

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:

Reimplemented in SBMLReactionConverter, and SBMLRateOfConverter.

◆ setDocument() [2/2]

int SBMLConverter::setDocument ( SBMLDocument doc)
virtualinherited

Sets the SBML document to be converted.

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:

Reimplemented in SBMLReactionConverter, and SBMLRateOfConverter.

◆ setProperties()

int SBMLConverter::setProperties ( const ConversionProperties props)
virtualinherited

Sets the configuration properties to be used by 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: