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

{fbc}

fbc SBML Level 3 “fbc” to COBRA 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 “fbc” Version 2 format and converts it to COBRA format.

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

  • "overwriteReactionNotes": should gene associations be written into the "notes" subelement attached to Reaction objects, even if a Reaction already has "notes" content?

Public Member Functions

virtual FbcToCobraConverterclone () const
 Creates and returns a deep copy of this FbcToCobraConverter object. More...
 
virtual int convert ()
 Perform the conversion. More...
 
 FbcToCobraConverter ()
 Creates a new FbcToCobraConverter object. More...
 
 FbcToCobraConverter (const FbcToCobraConverter &orig)
 Copy constructor; creates a copy of an FbcToCobraConverter object. 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 ~FbcToCobraConverter ()
 Destroy this FbcToCobraConverter object. More...
 

Constructor & Destructor Documentation

◆ FbcToCobraConverter() [1/2]

FbcToCobraConverter::FbcToCobraConverter ( )

Creates a new FbcToCobraConverter object.

◆ FbcToCobraConverter() [2/2]

FbcToCobraConverter::FbcToCobraConverter ( const FbcToCobraConverter orig)

Copy constructor; creates a copy of an FbcToCobraConverter object.

Parameters
origthe FbcToCobraConverter object to copy.

◆ ~FbcToCobraConverter()

FbcToCobraConverter::~FbcToCobraConverter ( )
virtual

Destroy this FbcToCobraConverter object.

Member Function Documentation

◆ clone()

FbcToCobraConverter * FbcToCobraConverter::clone ( ) const
virtual

Creates and returns a deep copy of this FbcToCobraConverter object.

Returns
a (deep) copy of this FbcToCobraConverter.

Reimplemented from SBMLConverter.

◆ convert()

int FbcToCobraConverter::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 FbcToCobraConverter::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 FbcToCobraConverter::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 FbcToCobraConverter 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: