Inheritance diagram for libsbml.ConversionProperties:

Detailed Description

Set of configuration option values for a 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.

LibSBML provides a number of converters that can perform transformations on SBML documents. The properties of SBML converters are communicated using objects of class ConversionProperties, and within such objects, individual options are encapsulated using ConversionOption objects. The ConversionProperties class provides numerous methods for setting and getting options.

ConversionProperties objects are also used to determine the target SBML namespace when an SBML converter's behavior depends on the intended Level+Version combination of SBML. In addition, it is conceivable that conversions may be affected by SBML Level 3 packages being used by an SBML document; consequently, the packages in use are also communicated by the values of the SBML namespaces set on a ConversionProperties object.

General information about the use of SBML 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.

Example of invoking an SBML converter

The following code fragment illustrates an example using SBMLReactionConverter, which is invoked using the option string 'replaceReactions':

 config = ConversionProperties()
 if config != None:
   config.addOption('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:

 # Assume that the variable 'document' has been set to an SBMLDocument object.
 status = document.convert(config)
 if status != LIBSBML_OPERATION_SUCCESS:
   # Handle error somehow.
   print('Error: conversion failed due to the following:')
   document.printErrors()

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:

 def strip_layout_example(document):
   config = ConversionProperties()
   if config != None:
     config.addOption('stripPackage')
     config.addOption('package', 'layout')
     status = document.convert(config)
     if status != LIBSBML_OPERATION_SUCCESS:
       # Handle error somehow.
       print('Error: unable to strip the Layout package.')
       print('LibSBML returned error: ' + OperationReturnValue_toString(status).strip())
   else:
     # Handle error somehow.
     print('Error: unable to create ConversionProperties object')

Available SBML converters in libSBML

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:

See also: ConversionOption; SBMLNamespaces

Public Member Functions
def	__init__ (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

def	addOption (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

def	clone (self)
	Creates and returns a deep copy of this ConversionProperties object. More...

def	getBoolValue (self, key)
	Returns the value of the given option as a Boolean. More...

def	getDescription (self, key)
	Returns the description string for a given option in this properties object. More...

def	getDoubleValue (self, key)
	Returns the value of the given option as a `float`. More...

def	getFloatValue (self, key)
	Returns the value of the given option as a `float`. More...

def	getIntValue (self, key)
	Returns the value of the given option as an integer. More...

def	getNumOptions (self)
	Returns the number of options in this Conversion Properties object. More...

def	getOption (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

def	getTargetNamespaces (self)
	Returns the current target SBML namespace. More...

def	getType (self, key)
	Returns the type of a given option in this properties object. More...

def	getValue (self, key)
	Returns the value of the given option as a string. More...

def	hasOption (self, key)
	Returns `True` if this properties object contains an option with the given key. More...

def	hasTargetNamespaces (self)
	Returns `True` if the target SBML namespace has been set. More...

def	removeOption (self, key)
	Removes the option with the given key from this properties object. More...

def	setBoolValue (self, key, value)
	Sets the value of the given option to a Boolean. More...

def	setDoubleValue (self, key, value)
	Sets the value of the given option to a `float`. More...

def	setFloatValue (self, key, value)
	Sets the value of the given option to a `float`. More...

def	setIntValue (self, key, value)
	Sets the value of the given option to an integer. More...

def	setTargetNamespaces (self, targetNS)
	Sets the target namespace. More...

def	setValue (self, key, value)
	Sets the value of the given option to a string. More...

Constructor & Destructor Documentation

def libsbml.ConversionProperties.__init__	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

__init__(SBMLNamespaces targetNS)   ConversionProperties
__init__()   ConversionProperties
__init__(ConversionProperties orig)   ConversionProperties

Each variant is described separately below.

Method variant with the following signature:

ConversionProperties(ConversionProperties orig)

Copy constructor.

Parameters

orig	the object to copy.

Method variant with the following signature:

ConversionProperties(SBMLNamespaces targetNS)

Constructor that initializes the conversion properties with a specific SBML target namespace.

Parameters

targetNS the target namespace to convert to.

Member Function Documentation

def libsbml.ConversionProperties.addOption	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

addOption(ConversionOption option)
addOption(string key, string value, long type, string description)
addOption(string key, string value, long type)
addOption(string key, string value)
addOption(string key)
addOption(string key, long  value, string description)
addOption(string key, long  value)
addOption(string key, bool value, string description)
addOption(string key, bool value)
addOption(string key, float value, string description)
addOption(string key, float value)
addOption(string key, float value, string description)
addOption(string key, float value)
addOption(string key, int value, string description)
addOption(string key, int value)

Each variant is described separately below.

Method variant with the following signature:

addOption(ConversionOption option)

Adds a copy of the given option to this properties object.

Parameters

option the option to add.

Method variant with the following signature:

addOption(string key, float value, string description='')

Adds a new ConversionOption object with the given parameters.

Parameters

key	the key for the new option.
value	the float value of that option.
description	(optional) the description for the option.

Method variant with the following signature:

addOption(string key, string value='', long type, string description='')

Adds a new ConversionOption object with the given parameters.

Parameters

key	the key for the new option.
value	(optional) the value of that option.
type	(optional) the type of the option (see the documentation for ConversionOption for more information about the types).
description	(optional) the description for the option.

Method variant with the following signature:

addOption(string key, string value, string description='')

Adds a new ConversionOption object with the given parameters.

Parameters

key	the key for the new option.
value	the string value of that option.
description	(optional) the description for the option.

Method variant with the following signature:

addOption(string key, bool value, string description='')

Adds a new ConversionOption object with the given parameters.

Parameters

key	the key for the new option.
value	the boolean value of that option.
description	(optional) the description for the option.

Method variant with the following signature:

addOption(string key, float value, string description='')

Adds a new ConversionOption object with the given parameters.

Parameters

key	the key for the new option.
value	the float value of that option.
description	(optional) the description for the option.

Method variant with the following signature:

addOption(string key, int value, string description='')

Adds a new ConversionOption object with the given parameters.

Parameters

key	the key for the new option.
value	the integer value of that option.
description	(optional) the description for the option.

def libsbml.ConversionProperties.clone ( self )

Creates and returns a deep copy of this ConversionProperties object.

clone()   ConversionProperties

Returns: the (deep) copy of this ConversionProperties object.

def libsbml.ConversionProperties.getBoolValue	(	self,
		key
	)

Returns the value of the given option as a Boolean.

getBoolValue(string key)   bool

Parameters

key	the key for the option.

Returns: the boolean value of the option with the given key.

def libsbml.ConversionProperties.getDescription	(	self,
		key
	)

Returns the description string for a given option in this properties object.

getDescription(string key)   string

Parameters

key	the key for the option.

Returns: the description text of the option with the given key.

def libsbml.ConversionProperties.getDoubleValue	(	self,
		key
	)

Returns the value of the given option as a float.

getDoubleValue(string key)   float

Parameters

key	the key for the option.

Returns: the float value of the option with the given key.

def libsbml.ConversionProperties.getFloatValue	(	self,
		key
	)

Returns the value of the given option as a float.

getFloatValue(string key)   float

Parameters

key	the key for the option.

Returns: the float value of the option with the given key.

def libsbml.ConversionProperties.getIntValue	(	self,
		key
	)

Returns the value of the given option as an integer.

getIntValue(string key)   int

Parameters

key	the key for the option.

Returns: the int value of the option with the given key.

def libsbml.ConversionProperties.getNumOptions ( self )

Returns the number of options in this Conversion Properties object.

Returns: the number of options in this properties object.

getNumOptions()   int

def libsbml.ConversionProperties.getOption	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

getOption(string key)   ConversionOption
getOption(int index)   ConversionOption

Each variant is described separately below.

Method variant with the following signature:

getOption(int index)

Returns the ConversionOption object for the given index.

Parameters

index the index for the option.

Returns: the option with the given index.

Method variant with the following signature:

getOption(string key)

Returns the ConversionOption object for a given key.

Parameters

key	the key for the option.

Returns: the option with the given key.

def libsbml.ConversionProperties.getTargetNamespaces ( self )

Returns the current target SBML namespace.

getTargetNamespaces()   SBMLNamespaces

Returns: the SBMLNamepaces object expressing the target namespace.

def libsbml.ConversionProperties.getType	(	self,
		key
	)

Returns the type of a given option in this properties object.

getType(string key)   long

Parameters

key	the key for the option.

Returns: the type of the option with the given key.

def libsbml.ConversionProperties.getValue	(	self,
		key
	)

Returns the value of the given option as a string.

getValue(string key)   string

Parameters

key	the key for the option.

Returns: the string value of the option with the given key.

def libsbml.ConversionProperties.hasOption	(	self,
		key
	)

Returns True if this properties object contains an option with the given key.

hasOption(string key)   bool

Parameters

key	the key of the option to find.

Returns: True if an option with the given key exists in this properties object, False otherwise.

def libsbml.ConversionProperties.hasTargetNamespaces ( self )

Returns True if the target SBML namespace has been set.

hasTargetNamespaces()   bool

Returns: True if the target namespace has been set, False otherwise.

def libsbml.ConversionProperties.removeOption	(	self,
		key
	)

Removes the option with the given key from this properties object.

removeOption(string key)   ConversionOption

Parameters

key	the key for the new option to remove.

Returns: the removed option.

def libsbml.ConversionProperties.setBoolValue	(	self,
		key,
		value
	)

Sets the value of the given option to a Boolean.

setBoolValue(string key, bool value)

Parameters

key	the key for the option.
value	the new Boolean value.

def libsbml.ConversionProperties.setDoubleValue	(	self,
		key,
		value
	)

Sets the value of the given option to a float.

setDoubleValue(string key, float value)

Parameters

key	the key for the option.
value	the new float value.

def libsbml.ConversionProperties.setFloatValue	(	self,
		key,
		value
	)

Sets the value of the given option to a float.

setFloatValue(string key, float value)

Parameters

key	the key for the option.
value	the new float value.

def libsbml.ConversionProperties.setIntValue	(	self,
		key,
		value
	)

Sets the value of the given option to an integer.

setIntValue(string key, int value)

Parameters

key	the key for the option.
value	the new integer value.

def libsbml.ConversionProperties.setTargetNamespaces	(	self,
		targetNS
	)

Sets the target namespace.

setTargetNamespaces(SBMLNamespaces targetNS)

Parameters

targetNS the target namespace to use.

def libsbml.ConversionProperties.setValue	(	self,
		key,
		value
	)

Sets the value of the given option to a string.

setValue(string key, string value)

Parameters

key	the key for the option.
value	the new value.

Detailed Description

General information about the use of SBML converters

Example of invoking an SBML converter

Available SBML converters in libSBML

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation